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Field3DFileHDF5.cpp
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1671 lines (1360 loc) · 48.5 KB
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//----------------------------------------------------------------------------//
/*
* Copyright (c) 2009 Sony Pictures Imageworks Inc
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the
* distribution. Neither the name of Sony Pictures Imageworks nor the
* names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written
* permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
* FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
* COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
* INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
* STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
* OF THE POSSIBILITY OF SUCH DAMAGE.
*/
//----------------------------------------------------------------------------//
/*! \file Field3DFileHDF5.cpp
\brief Contains implementations of Field3DFileHDF5-related member functions
\ingroup field
*/
//----------------------------------------------------------------------------//
#include <sys/stat.h>
#ifndef WIN32
#include <unistd.h>
#endif
#include <hdf5.h>
#include <H5Epublic.h>
#include <boost/tokenizer.hpp>
#include <boost/utility.hpp>
#include "Field3DFileHDF5.h"
#include "Field.h"
#include "ClassFactory.h"
//----------------------------------------------------------------------------//
using namespace std;
//----------------------------------------------------------------------------//
FIELD3D_NAMESPACE_OPEN
//----------------------------------------------------------------------------//
// Field3D namespaces
//----------------------------------------------------------------------------//
using namespace Exc;
using namespace Hdf5Util;
using namespace FileHDF5;
//----------------------------------------------------------------------------//
// Local namespace
//----------------------------------------------------------------------------//
namespace {
// Strings used only in this file --------------------------------------------
const std::string k_mappingStr("mapping");
const std::string k_partitionName("partition");
const std::string k_versionAttrName("version_number");
const std::string k_classNameAttrName("class_name");
const std::string k_mappingTypeAttrName("mapping_type");
//! This version is stored in every file to determine which library version
//! produced it.
int k_currentFileVersion[3] =
{ FIELD3D_MAJOR_VER, FIELD3D_MINOR_VER, FIELD3D_MICRO_VER };
int k_minFileVersion[2] = { 0, 0 };
// Function objects used only in this file -----------------------------------
std::vector<std::string> makeUnique(std::vector<std::string> vec)
{
std::vector<string> ret;
std::sort(vec.begin(), vec.end());
std::vector<std::string>::iterator newEnd =
std::unique(vec.begin(), vec.end());
ret.resize(std::distance(vec.begin(), newEnd));
std::copy(vec.begin(), newEnd, ret.begin());
return ret;
}
//----------------------------------------------------------------------------//
//! Functor used with for_each to print a container
template <class T>
class print : std::unary_function<T, void>
{
public:
print(int indentAmt)
: indent(indentAmt)
{ }
void operator()(const T& x) const
{
for (int i = 0; i < indent; i++)
std::cout << " ";
std::cout << x << std::endl;
}
int indent;
};
//----------------------------------------------------------------------------//
/*! \brief checks to see if a file/directory exists or not
\param[in] filename the file/directory to check
\retval true if it exists
\retval false if it does not exist
*/
bool fileExists(const std::string &filename)
{
#ifdef WIN32
struct __stat64 statbuf;
return (_stat64(filename.c_str(), &statbuf) != -1);
#else
struct stat statbuf;
return (stat(filename.c_str(), &statbuf) != -1);
#endif
}
/*! \brief wrapper around fileExists. Throws instead if the file
does not exist.
\throw NoSuchFileException if the file or directory does not exist
\param[in] filename the file/directory to check
*/
void checkFile(const std::string &filename)
{
if (!fileExists(filename))
{
throw NoSuchFileException(filename);
}
}
//----------------------------------------------------------------------------//
bool isSupportedFileVersion(const int fileVersion[3],
const int minVersion[2])
{
stringstream currentVersionStr;
currentVersionStr << k_currentFileVersion[0] << "."
<< k_currentFileVersion[1] << "."
<< k_currentFileVersion[2];
stringstream fileVersionStr;
fileVersionStr << fileVersion[0] << "."
<< fileVersion[1] << "."
<< fileVersion[2];
stringstream minVersionStr;
minVersionStr << minVersion[0] << "."
<< minVersion[1];
if (fileVersion[0] > k_currentFileVersion[0] ||
(fileVersion[0] == k_currentFileVersion[0] &&
fileVersion[1] > k_currentFileVersion[1])) {
Msg::print(Msg::SevWarning, "File version " + fileVersionStr.str() +
" is higher than the current version " +
currentVersionStr.str());
return true;
}
if (fileVersion[0] < minVersion[0] ||
(fileVersion[0] == minVersion[0] &&
fileVersion[1] < minVersion[1])) {
Msg::print(Msg::SevWarning, "File version " + fileVersionStr.str() +
" is lower than the minimum supported version " +
minVersionStr.str());
return false;
}
return true;
}
//----------------------------------------------------------------------------//
static herr_t localPrintError( hid_t estack_id, void *stream )
{
printf("H5E message -----------------------\n");
return H5Eprint2(estack_id, static_cast<FILE*>(stream));
}
//----------------------------------------------------------------------------//
} // end of local namespace
//----------------------------------------------------------------------------//
// Partition implementations
//----------------------------------------------------------------------------//
std::string Partition::className() const
{
return k_partitionName;
}
//----------------------------------------------------------------------------//
void
Partition::addScalarLayer(const Layer &layer)
{
m_scalarLayers.push_back(layer);
}
//----------------------------------------------------------------------------//
void
Partition::addVectorLayer(const Layer &layer)
{
m_vectorLayers.push_back(layer);
}
//----------------------------------------------------------------------------//
const Layer*
Partition::scalarLayer(const std::string &name) const
{
for (ScalarLayerList::const_iterator i = m_scalarLayers.begin();
i != m_scalarLayers.end(); ++i) {
if (i->name == name)
return &(*i);
}
return NULL;
}
//----------------------------------------------------------------------------//
const Layer*
Partition::vectorLayer(const std::string &name) const
{
for (VectorLayerList::const_iterator i = m_vectorLayers.begin();
i != m_vectorLayers.end(); ++i) {
if (i->name == name)
return &(*i);
}
return NULL;
}
//----------------------------------------------------------------------------//
void
Partition::getScalarLayerNames(std::vector<std::string> &names) const
{
// We don't want to do names.clear() here, since this gets called
// inside some loops that want to accumulate names.
for (ScalarLayerList::const_iterator i = m_scalarLayers.begin();
i != m_scalarLayers.end(); ++i) {
names.push_back(i->name);
}
}
//----------------------------------------------------------------------------//
void
Partition::getVectorLayerNames(std::vector<std::string> &names) const
{
// We don't want to do names.clear() here, since this gets called
// inside some loops that want to accumulate names.
for (VectorLayerList::const_iterator i = m_vectorLayers.begin();
i != m_vectorLayers.end(); ++i) {
names.push_back(i->name);
}
}
//----------------------------------------------------------------------------//
// Field3DFileHDF5Base implementations
//----------------------------------------------------------------------------//
Field3DFileHDF5Base::Field3DFileHDF5Base()
: m_file(-1), m_metadata(this)
{
GlobalLock lock(g_hdf5Mutex);
// Suppressing HDF error messages
// Explanation about the function for the error stack is here:
// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5E.html#Error-SetAuto2
if (getenv("DEBUG_HDF")) {
cerr << "Field3DFileHDF5 -- HDF5 messages are on" << endl;
H5Eset_auto(H5E_DEFAULT, localPrintError, NULL);
} else {
H5Eset_auto(H5E_DEFAULT, NULL, NULL);
}
}
//----------------------------------------------------------------------------//
Field3DFileHDF5Base::~Field3DFileHDF5Base()
{
close();
}
//----------------------------------------------------------------------------//
std::string
Field3DFileHDF5Base::intPartitionName(const std::string &partitionName,
const std::string & /* layerName */,
FieldRes::Ptr field)
{
// Loop over existing partitions and see if there's a matching mapping
for (PartitionList::const_iterator i = m_partitions.begin();
i != m_partitions.end(); ++i) {
if (removeUniqueId((**i).name) == partitionName) {
if ((**i).mapping->isIdentical(field->mapping())) {
return (**i).name;
}
}
}
// If there was no previously matching name, then make a new one
int nextIdx = -1;
if (m_partitionCount.find(partitionName) != m_partitionCount.end()) {
nextIdx = ++m_partitionCount[partitionName];
} else {
nextIdx = 0;
m_partitionCount[partitionName] = 0;
}
return makeIntPartitionName(partitionName, nextIdx);
}
//----------------------------------------------------------------------------//
Partition::Ptr Field3DFileHDF5Base::partition(const string &partitionName)
{
for (PartitionList::iterator i = m_partitions.begin();
i != m_partitions.end(); ++i) {
if ((**i).name == partitionName)
return *i;
}
return Partition::Ptr();
}
//----------------------------------------------------------------------------//
Partition::Ptr
Field3DFileHDF5Base::partition(const string &partitionName) const
{
for (PartitionList::const_iterator i = m_partitions.begin();
i != m_partitions.end(); ++i) {
if ((**i).name == partitionName)
return *i;
}
return Partition::Ptr();
}
//----------------------------------------------------------------------------//
std::string
Field3DFileHDF5Base::removeUniqueId(const std::string &partitionName) const
{
size_t pos = partitionName.rfind(".");
if (pos == partitionName.npos) {
return partitionName;
} else {
return partitionName.substr(0, pos);
}
}
//----------------------------------------------------------------------------//
void
Field3DFileHDF5Base::getPartitionNames(vector<string> &names) const
{
names.clear();
vector<string> tempNames;
for (PartitionList::const_iterator i = m_partitions.begin();
i != m_partitions.end(); ++i) {
tempNames.push_back(removeUniqueId((**i).name));
}
names = makeUnique(tempNames);
}
//----------------------------------------------------------------------------//
void
Field3DFileHDF5Base::getScalarLayerNames(vector<string> &names,
const string &partitionName) const
{
names.clear();
for (int i = 0; i < numIntPartitions(partitionName); i++) {
string internalName = makeIntPartitionName(partitionName, i);
Partition::Ptr part = partition(internalName);
if (part)
part->getScalarLayerNames(names);
}
names = makeUnique(names);
}
//----------------------------------------------------------------------------//
void
Field3DFileHDF5Base::getVectorLayerNames(vector<string> &names,
const string &partitionName) const
{
names.clear();
for (int i = 0; i < numIntPartitions(partitionName); i++) {
string internalName = makeIntPartitionName(partitionName, i);
Partition::Ptr part = partition(internalName);
if (part)
part->getVectorLayerNames(names);
}
names = makeUnique(names);
}
//----------------------------------------------------------------------------//
void
Field3DFileHDF5Base::getIntPartitionNames(vector<string> &names) const
{
names.clear();
for (PartitionList::const_iterator i = m_partitions.begin();
i != m_partitions.end(); ++i) {
names.push_back((**i).name);
}
}
//----------------------------------------------------------------------------//
void
Field3DFileHDF5Base::getIntScalarLayerNames(vector<string> &names,
const string &intPartitionName) const
{
names.clear();
Partition::Ptr part = partition(intPartitionName);
if (!part) {
Msg::print("getIntScalarLayerNames no partition: " + intPartitionName);
return;
}
part->getScalarLayerNames(names);
}
//----------------------------------------------------------------------------//
void
Field3DFileHDF5Base::getIntVectorLayerNames(vector<string> &names,
const string &intPartitionName) const
{
names.clear();
Partition::Ptr part = partition(intPartitionName);
if (!part) {
Msg::print("getIntVectorLayerNames no partition: " + intPartitionName);
return;
}
part->getVectorLayerNames(names);
}
//----------------------------------------------------------------------------//
void Field3DFileHDF5Base::clear()
{
closeInternal();
m_partitions.clear();
m_groupMembership.clear();
}
//----------------------------------------------------------------------------//
bool Field3DFileHDF5Base::close()
{
closeInternal();
return true;
}
//----------------------------------------------------------------------------//
void Field3DFileHDF5Base::closeInternal()
{
GlobalLock lock(g_hdf5Mutex);
if (m_file != -1) {
if (H5Fclose(m_file) < 0) {
Msg::print(Msg::SevWarning, "Failed to close hdf5 file handle");
return;
}
m_file = -1;
}
}
//----------------------------------------------------------------------------//
int
Field3DFileHDF5Base::numIntPartitions(const std::string &partitionName) const
{
int count = 0;
for (PartitionList::const_iterator i = m_partitions.begin();
i != m_partitions.end(); ++i) {
string name = (**i).name;
size_t pos = name.rfind(".");
if (pos != name.npos) {
if (name.substr(0, pos) == partitionName) {
count++;
}
}
}
return count;
}
//----------------------------------------------------------------------------//
string
Field3DFileHDF5Base::makeIntPartitionName(const std::string &partitionName,
int i) const
{
return partitionName + "." + boost::lexical_cast<std::string>(i);
}
//----------------------------------------------------------------------------//
void
Field3DFileHDF5Base::addGroupMembership(const GroupMembershipMap& groupMembers)
{
GroupMembershipMap::const_iterator i= groupMembers.begin();
GroupMembershipMap::const_iterator end= groupMembers.end();
for (; i != end; ++i) {
GroupMembershipMap::iterator foundGroupIter =
m_groupMembership.find(i->first);
if (foundGroupIter != m_groupMembership.end()){
std::string value = m_groupMembership[i->first] + i->second;
m_groupMembership[i->first] = value;
} else {
m_groupMembership[i->first] = i->second;
}
}
}
//----------------------------------------------------------------------------//
// Field3DInputFileHDF5 implementations
//----------------------------------------------------------------------------//
Field3DInputFileHDF5::Field3DInputFileHDF5()
{
// Empty
}
//----------------------------------------------------------------------------//
Field3DInputFileHDF5::~Field3DInputFileHDF5()
{
clear();
}
//----------------------------------------------------------------------------//
bool Field3DInputFileHDF5::open(const string &filename)
{
GlobalLock lock(g_hdf5Mutex);
clear();
bool success = true;
// Record filename
m_filename = filename;
try {
string version;
// Throws exceptions if the file doesn't exist.
// This was added because H5Fopen prints out a lot of junk
// to the terminal.
checkFile(filename);
m_file = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if (m_file < 0)
throw NoSuchFileException(filename);
int fileVersion[3];
try {
if (!readAttribute(m_file, k_versionAttrName, 3, fileVersion[0])) {
//Msg::print(Msg::SevWarning, "Missing version_number attribute");
} else {
if (!isSupportedFileVersion(fileVersion, k_minFileVersion)) {
stringstream versionStr;
versionStr << fileVersion[0] << "."
<< fileVersion[1] << "."
<< fileVersion[2];
throw UnsupportedVersionException(versionStr.str());
}
}
}
catch (MissingAttributeException &) {
//Msg::print(Msg::SevWarning, "Missing version_number attribute");
}
try {
if (H5Lexists(m_file, "field3d_global_metadata", H5P_DEFAULT)) {
// read the metadata
H5ScopedGopen metadataGroup(m_file, "field3d_global_metadata");
if (metadataGroup.id() > 0) {
readMetadata(metadataGroup.id());
}
}
}
catch (...) {
Msg::print(Msg::SevWarning,
"Unknown error when reading file metadata ");
//throw BadFileHierarchyException(filename);
}
try {
if (!readPartitionAndLayerInfo()) {
success = false;
}
}
catch (MissingGroupException &e) {
Msg::print(Msg::SevWarning, "Missing group: " + string(e.what()));
throw BadFileHierarchyException(filename);
}
catch (ReadMappingException &e) {
Msg::print(Msg::SevWarning, "Couldn't read mapping for partition: "
+ string(e.what()));
throw BadFileHierarchyException(filename);
}
catch (Exception &e) {
Msg::print(Msg::SevWarning, "Unknown error when reading file hierarchy: "
+ string(e.what()));
throw BadFileHierarchyException(filename);
}
catch (...) {
Msg::print(Msg::SevWarning,
"Unknown error when reading file hierarchy. ");
throw BadFileHierarchyException(filename);
}
}
catch (NoSuchFileException &e) {
Msg::print(Msg::SevWarning, "Couldn't open file: "
+ string(e.what()) );
success = false;
}
catch (MissingAttributeException &e) {
Msg::print(Msg::SevWarning,
"In file: " + filename + " - "
+ string(e.what()) );
success = false;
}
catch (UnsupportedVersionException &e) {
Msg::print(Msg::SevWarning,
"In file: " + filename + " - File version can not be read: "
+ string(e.what()));
success = false;
}
catch (BadFileHierarchyException &) {
Msg::print(Msg::SevWarning,
"In file: " + filename + " - Bad file hierarchy. ");
success = false;
}
catch (...) {
Msg::print(Msg::SevWarning,
"In file: " + filename + " Unknown exception ");
success = false;
}
if (!success)
close();
return success;
}
//----------------------------------------------------------------------------//
bool Field3DInputFileHDF5::readPartitionAndLayerInfo()
{
using namespace InputFileHDF5;
GlobalLock lock(g_hdf5Mutex);
// First, find the partitions ---
herr_t status;
status = H5Literate(m_file, H5_INDEX_NAME, H5_ITER_NATIVE, NULL,
&parsePartitions, this);
// Get the partition names to store
m_partitions.clear();
for (size_t i=0; i < m_partitionNames.size(); i++) {
Partition::Ptr part(new Partition);
part->name = m_partitionNames[i];
m_partitions.push_back(part);
}
// For each partition, find its mapping ---
for (PartitionList::iterator i = m_partitions.begin();
i != m_partitions.end(); ++i) {
// Open the partition
H5ScopedGopen partitionGroup(m_file, (**i).name);
string mappingPath = "/" + (**i).name + "/" + k_mappingStr;
// Open up the mapping group
H5ScopedGopen mappingGroup(m_file, mappingPath);
if (mappingGroup.id() < 0)
throw MissingGroupException((**i).name + "/" + k_mappingStr);
// Try to build a mapping from it
FieldMapping::Ptr mapping;
mapping = readFieldMapping(mappingGroup.id());
if (!mapping) {
Msg::print(Msg::SevWarning, "Got a null pointer when reading mapping");
throw ReadMappingException((**i).name);
}
// Attach the mapping to the partition
(**i).mapping = mapping;
}
// ... And then find its layers ---
for (PartitionList::const_iterator i = m_partitions.begin();
i != m_partitions.end(); ++i) {
// Open the partition
H5ScopedGopen partitionGroup(m_file, (**i).name);
// Set up the info struct for the callback
ParseLayersInfo info;
info.file = this;
info.partitionName = (**i).name;
m_layerInfo.clear();
status = H5Literate(partitionGroup.id(), H5_INDEX_NAME, H5_ITER_NATIVE,
NULL, &parseLayers, &info);
//set the layer information on the partitions here
for (std::vector<LayerInfo>::iterator i = m_layerInfo.begin();
i != m_layerInfo.end(); i++) {
std::string parent = i->parentName;
Partition::Ptr part = partition(parent);
Layer layer;
layer.name = i->name;
layer.parent = i->parentName;
if (i->components == 1) {
part->addScalarLayer(layer);
} else if (i->components == 3) {
part->addVectorLayer(layer);
}
}
}
return true;
}
//----------------------------------------------------------------------------//
herr_t Field3DInputFileHDF5::parsePartition(hid_t /* loc_id */,
const std::string itemName)
{
// Add the partition ---
m_partitionNames.push_back(string(itemName));
return 0;
}
//----------------------------------------------------------------------------//
//! \note Don't throw exceptions into the hdf5 lib.
//! \todo Set some sort of flag if we fail during this call. We can't
//! throw exceptions inside hdf5.
herr_t Field3DInputFileHDF5::parseLayer(hid_t layerGroup,
const std::string &partitionName,
const std::string &layerName)
{
int components;
if (!readAttribute(layerGroup, string("components"), 1, components)) {
Msg::print(Msg::SevWarning, "Couldn't read components attribute for layer "
+ partitionName + "/" + layerName);
return 0;
}
LayerInfo linfo(partitionName,layerName,components);
m_layerInfo.push_back(linfo);
return 0;
}
//----------------------------------------------------------------------------//
//! \todo Replace char* with std::string
bool
Field3DInputFileHDF5::
readMetadata(hid_t metadata_id, FieldBase::Ptr field) const
{
GlobalLock lock(g_hdf5Mutex);
hsize_t num_attrs = H5Aget_num_attrs(metadata_id);
if (num_attrs > 0) {
for (hsize_t idx=0; idx < num_attrs ; ++idx) {
H5ScopedAopenIdx attrIdx(metadata_id, idx);
size_t len = H5Aget_name(attrIdx.id(), 0, NULL);
if (len > 0) {
char *name = new char[len+1];
if (H5Aget_name(attrIdx.id(), len+1, name) > 0) {
H5ScopedAopen attr(metadata_id, name, H5P_DEFAULT);
H5ScopedAget_space attrSpace(attr);
H5ScopedAget_type attrType(attr);
H5T_class_t typeClass = H5Tget_class(attrType);
if (typeClass == H5T_STRING) {
string value;
if (!readAttribute(metadata_id, name, value)) {
Msg::print(Msg::SevWarning,
"Failed to read metadata " + string(name));
if (name) {
delete[] name;
}
continue;
}
field->metadata().setStrMetadata(name, value);
}
else {
if (H5Sget_simple_extent_ndims(attrSpace) != 1) {
Msg::print(Msg::SevWarning, "Bad attribute rank for attribute "
+ string(name));
if (name) {
delete[] name;
}
continue;
}
hsize_t dims[1];
H5Sget_simple_extent_dims(attrSpace, dims, NULL);
if (typeClass == H5T_INTEGER) {
if (dims[0] == 1){
int value;
if (!readAttribute(metadata_id, name, dims[0], value))
Msg::print(Msg::SevWarning, "Failed to read metadata "
+ string(name));
field->metadata().setIntMetadata(name, value);
}
else if (dims[0] == 3){
V3i value;
if (!readAttribute(metadata_id, name, dims[0], value.x))
Msg::print(Msg::SevWarning, "Failed to read metadata " +
string(name) );
field->metadata().setVecIntMetadata(name, value);
}
else {
Msg::print(Msg::SevWarning,
"Attribute of size " +
boost::lexical_cast<std::string>(dims[0])
+ " is not valid for metadata");
}
}
else if (typeClass == H5T_FLOAT) {
if (dims[0] == 1){
float value;
if (!readAttribute(metadata_id, name, dims[0], value))
Msg::print(Msg::SevWarning, "Failed to read metadata " +
string(name) );
field->metadata().setFloatMetadata(name, value);
}
else if (dims[0] == 3){
V3f value;
if (!readAttribute(metadata_id, name, dims[0], value.x))
Msg::print(Msg::SevWarning, "Failed to read metadata "+
string(name) );
field->metadata().setVecFloatMetadata(name, value);
}
else {
Msg::print(Msg::SevWarning, "Attribute of size " +
boost::lexical_cast<std::string>(dims[0]) +
" is not valid for metadata");
}
}
else {
Msg::print(Msg::SevWarning, "Attribute '" + string(name) +
+ "' has unsupported data type for metadata");
}
}
}
if (name) {
delete[] name;
}
}
}
}
return true;
}
//----------------------------------------------------------------------------//
//! \todo Replace char* with std::string
bool
Field3DInputFileHDF5::readMetadata(hid_t metadata_id)
{
GlobalLock lock(g_hdf5Mutex);
hsize_t num_attrs = H5Aget_num_attrs(metadata_id);
if (num_attrs > 0) {
for (hsize_t idx=0; idx < num_attrs ; ++idx) {
H5ScopedAopenIdx attrIdx(metadata_id, idx);
size_t len = H5Aget_name(attrIdx.id(), 0, NULL);
if (len > 0) {
char *name = new char[len+1];
if (H5Aget_name(attrIdx.id(), len+1, name) > 0) {
H5ScopedAopen attr(metadata_id, name, H5P_DEFAULT);
H5ScopedAget_space attrSpace(attr);
H5ScopedAget_type attrType(attr);
H5T_class_t typeClass = H5Tget_class(attrType);
if (typeClass == H5T_STRING) {
string value;
if (!readAttribute(metadata_id, name, value)) {
Msg::print(Msg::SevWarning,
"Failed to read metadata " + string(name));
if (name) {
delete[] name;
}
continue;
}
metadata().setStrMetadata(name, value);
}
else {
if (H5Sget_simple_extent_ndims(attrSpace) != 1) {
Msg::print(Msg::SevWarning, "Bad attribute rank for attribute "
+ string(name));
if (name) {
delete[] name;
}
continue;
}
hsize_t dims[1];
H5Sget_simple_extent_dims(attrSpace, dims, NULL);
if (typeClass == H5T_INTEGER) {
if (dims[0] == 1){
int value;
if (!readAttribute(metadata_id, name, dims[0], value))
Msg::print(Msg::SevWarning, "Failed to read metadata "
+ string(name));
metadata().setIntMetadata(name, value);
}
else if (dims[0] == 3){