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/*****************************************************************************/
/* Xdmf */
/* eXtensible Data Model and Format */
/* */
/* Id : XdmfHDF5Controller.cpp */
/* */
/* Author: */
/* Kenneth Leiter */
/* kenneth.leiter@arl.army.mil */
/* US Army Research Laboratory */
/* Aberdeen Proving Ground, MD */
/* */
/* Copyright @ 2011 US Army Research Laboratory */
/* All Rights Reserved */
/* See Copyright.txt for details */
/* */
/* This software is distributed WITHOUT ANY WARRANTY; without */
/* even the implied warranty of MERCHANTABILITY or FITNESS */
/* FOR A PARTICULAR PURPOSE. See the above copyright notice */
/* for more information. */
/* */
/*****************************************************************************/
#include <H5public.h>
#include <hdf5.h>
#include <numeric>
#include <sstream>
#include "string.h"
#include "XdmfArray.hpp"
#include "XdmfArrayType.hpp"
#include "XdmfError.hpp"
#include "XdmfHDF5Controller.hpp"
#include "XdmfSystemUtils.hpp"
unsigned int XdmfHDF5Controller::mMaxOpenedFiles = 0;
static std::map<std::string, hid_t> mOpenFiles;
std::map<std::string, unsigned int> XdmfHDF5Controller::mOpenFileUsage;
shared_ptr<XdmfHDF5Controller>
XdmfHDF5Controller::New(const std::string & hdf5FilePath,
const std::string & dataSetPath,
const shared_ptr<const XdmfArrayType> & type,
const std::vector<unsigned int> & start,
const std::vector<unsigned int> & stride,
const std::vector<unsigned int> & dimensions,
const std::vector<unsigned int> & dataspaceDimensions)
{
shared_ptr<XdmfHDF5Controller>
p(new XdmfHDF5Controller(hdf5FilePath,
dataSetPath,
type,
start,
stride,
dimensions,
dataspaceDimensions));
return p;
}
XdmfHDF5Controller::XdmfHDF5Controller(const std::string & hdf5FilePath,
const std::string & dataSetPath,
const shared_ptr<const XdmfArrayType> & type,
const std::vector<unsigned int> & start,
const std::vector<unsigned int> & stride,
const std::vector<unsigned int> & dimensions,
const std::vector<unsigned int> & dataspaceDimensions) :
XdmfHeavyDataController(hdf5FilePath,
type,
start,
stride,
dimensions,
dataspaceDimensions),
mDataSetPath(dataSetPath),
mDataSetPrefix(""),
mDataSetId(-1)
{
unsigned int i = 0;
for (; i < mDataSetPath.size(); ++i) {
if (mDataSetPath[(mDataSetPath.size() - 1) - i] != '0' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '1' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '2' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '3' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '4' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '5' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '6' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '7' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '8' &&
mDataSetPath[(mDataSetPath.size() - 1) - i] != '9') {
break;
}
}
unsigned int endOfPrefix = (mDataSetPath.size()) - i;
mDataSetPrefix = mDataSetPath.substr(0, endOfPrefix);
if (mDataSetPrefix.compare(mDataSetPath) != 0) {
mDataSetId = atoi(mDataSetPath.substr(endOfPrefix).c_str());
}
}
XdmfHDF5Controller::XdmfHDF5Controller(const XdmfHDF5Controller& refController):
XdmfHeavyDataController(refController),
mDataSetPath(refController.getDataSetPath()),
mDataSetPrefix(refController.mDataSetPrefix),
mDataSetId(refController.mDataSetId)
{
}
XdmfHDF5Controller::~XdmfHDF5Controller()
{
}
void
XdmfHDF5Controller::closeFiles()
{
for (std::map<std::string, hid_t>::iterator closeIter = mOpenFiles.begin();
closeIter != mOpenFiles.end();
++closeIter) {
H5Fclose(closeIter->second);
}
mOpenFiles.clear();
mOpenFileUsage.clear();
}
std::string
XdmfHDF5Controller::getDataSetPath() const
{
return mDataSetPath;
}
const std::string
XdmfHDF5Controller::getDataSetPrefix() const
{
return mDataSetPrefix;
}
int
XdmfHDF5Controller::getDataSetId() const
{
return mDataSetId;
}
std::string
XdmfHDF5Controller::getDescriptor() const
{
return ":" + mDataSetPath;
}
std::string
XdmfHDF5Controller::getName() const
{
return "HDF";
}
unsigned int
XdmfHDF5Controller::getMaxOpenedFiles()
{
return XdmfHDF5Controller::mMaxOpenedFiles;
}
void
XdmfHDF5Controller::getProperties(std::map<std::string, std::string> & collectedProperties) const
{
collectedProperties["Format"] = this->getName();
}
void
XdmfHDF5Controller::read(XdmfArray * const array)
{
this->read(array, H5P_DEFAULT);
}
void
XdmfHDF5Controller::read(XdmfArray * const array, const int fapl)
{
herr_t status;
hid_t hdf5Handle;
if (XdmfHDF5Controller::mMaxOpenedFiles == 0) {
hdf5Handle = H5Fopen(mFilePath.c_str(), H5F_ACC_RDONLY, fapl);
}
else {
std::map<std::string, hid_t>::iterator checkOpen = mOpenFiles.find(mFilePath);
if (checkOpen == mOpenFiles.end()) {
// If the number of open files would become larger than allowed
if (mOpenFiles.size() + 1 > mMaxOpenedFiles) {
// Close least used one
std::map<std::string, unsigned int>::iterator walker = mOpenFileUsage.begin();
std::string oldestFile = walker->first;
while (walker != mOpenFileUsage.end()) {
// We want the file with the fewest accesses
// If two are tied, we use the older one
if (mOpenFileUsage[oldestFile] > walker->second) {
oldestFile = walker->first;
}
++walker;
}
status = H5Fclose(mOpenFiles[oldestFile]);
mOpenFiles.erase(oldestFile);
mOpenFileUsage.erase(oldestFile);
}
hdf5Handle = H5Fopen(mFilePath.c_str(), H5F_ACC_RDONLY, fapl);
mOpenFiles[mFilePath] = hdf5Handle;
mOpenFileUsage[mFilePath] = 1;
}
else {
hdf5Handle = checkOpen->second;
mOpenFileUsage[mFilePath]++;
}
}
const hid_t dataset = H5Dopen(hdf5Handle, mDataSetPath.c_str(), H5P_DEFAULT);
const hid_t dataspace = H5Dget_space(dataset);
const unsigned int dataspaceDims = H5Sget_simple_extent_ndims(dataspace);
const std::vector<hsize_t> count(mDimensions.begin(), mDimensions.end());
if(dataspaceDims != mDimensions.size()) {
// special case where the number of dimensions of the hdf5 dataset
// does not equal the number of dimensions in the light data
// description - in this case we cannot properly take a hyperslab
// selection, so we assume we are reading the entire dataset and
// check whether that is ok to do
const int numberValuesHDF5 = H5Sget_select_npoints(dataspace);
const int numberValuesXdmf =
std::accumulate(mDimensions.begin(),
mDimensions.end(),
1,
std::multiplies<unsigned int>());
if(numberValuesHDF5 != numberValuesXdmf) {
XdmfError::message(XdmfError::FATAL,
"Number of dimensions in light data description in "
"Xdmf does not match number of dimensions in hdf5 "
"file.");
}
}
else {
const std::vector<hsize_t> start(mStart.begin(), mStart.end());
const std::vector<hsize_t> stride(mStride.begin(), mStride.end());
status = H5Sselect_hyperslab(dataspace,
H5S_SELECT_SET,
&start[0],
&stride[0],
&count[0],
NULL);
}
const hssize_t numVals = H5Sget_select_npoints(dataspace);
hid_t memspace = H5Screate_simple(mDimensions.size(),
&count[0],
NULL);
/* status = H5Sselect_hyperslab(memspace,
H5S_SELECT_SET,
&memStart[0],
&memStride[0],
&memCount[0],
NULL);*/
hid_t datatype = H5T_NO_CLASS;
bool closeDatatype = false;
if(mType == XdmfArrayType::Int8()) {
datatype = H5T_NATIVE_CHAR;
}
else if(mType == XdmfArrayType::Int16()) {
datatype = H5T_NATIVE_SHORT;
}
else if(mType == XdmfArrayType::Int32()) {
datatype = H5T_NATIVE_INT;
}
else if(mType == XdmfArrayType::Int64()) {
datatype = H5T_NATIVE_LONG;
}
else if(mType == XdmfArrayType::Float32()) {
datatype = H5T_NATIVE_FLOAT;
}
else if(mType == XdmfArrayType::Float64()) {
datatype = H5T_NATIVE_DOUBLE;
}
else if(mType == XdmfArrayType::UInt8()) {
datatype = H5T_NATIVE_UCHAR;
}
else if(mType == XdmfArrayType::UInt16()) {
datatype = H5T_NATIVE_USHORT;
}
else if(mType == XdmfArrayType::UInt32()) {
datatype = H5T_NATIVE_UINT;
}
else if(mType == XdmfArrayType::String()) {
datatype = H5Tcopy(H5T_C_S1);
H5Tset_size(datatype, H5T_VARIABLE);
closeDatatype = true;
}
else {
XdmfError::message(XdmfError::FATAL,
"Unknown XdmfArrayType encountered in hdf5 "
"controller.");
}
array->initialize(mType, mDimensions);
if(numVals != array->getSize()) {
std::stringstream errOut;
errOut << "Number of values in hdf5 dataset (" << numVals;
errOut << ")\ndoes not match allocated size in XdmfArray (" << array->getSize() << ").";
XdmfError::message(XdmfError::FATAL,
errOut.str());
}
if(closeDatatype) {
char ** data = new char*[numVals];
status = H5Dread(dataset,
datatype,
memspace,
dataspace,
H5P_DEFAULT,
data);
for(hssize_t i=0; i<numVals; ++i) {
array->insert<std::string>(i, data[i]);
}
status = H5Dvlen_reclaim(datatype,
dataspace,
H5P_DEFAULT,
data);
delete [] data;
}
else {
status = H5Dread(dataset,
datatype,
memspace,
dataspace,
H5P_DEFAULT,
array->getValuesInternal());
}
status = H5Sclose(dataspace);
status = H5Sclose(memspace);
status = H5Dclose(dataset);
if(closeDatatype) {
status = H5Tclose(datatype);
}
if (XdmfHDF5Controller::mMaxOpenedFiles == 0) {
status = H5Fclose(hdf5Handle);
}
}
void
XdmfHDF5Controller::setMaxOpenedFiles(unsigned int newMax)
{
XdmfHDF5Controller::mMaxOpenedFiles = newMax;
}
// C Wrappers
XDMFHDF5CONTROLLER * XdmfHDF5ControllerNew(char * hdf5FilePath,
char * dataSetPath,
int type,
unsigned int * start,
unsigned int * stride,
unsigned int * dimensions,
unsigned int * dataspaceDimensions,
unsigned int numDims,
int * status)
{
XDMF_ERROR_WRAP_START(status)
try
{
std::vector<unsigned int> startVector(start, start + numDims);
std::vector<unsigned int> strideVector(stride, stride + numDims);
std::vector<unsigned int> dimVector(dimensions, dimensions + numDims);
std::vector<unsigned int> dataspaceVector(dataspaceDimensions, dataspaceDimensions + numDims);
shared_ptr<const XdmfArrayType> buildType = shared_ptr<XdmfArrayType>();
switch (type) {
case XDMF_ARRAY_TYPE_UINT8:
buildType = XdmfArrayType::UInt8();
break;
case XDMF_ARRAY_TYPE_UINT16:
buildType = XdmfArrayType::UInt16();
break;
case XDMF_ARRAY_TYPE_UINT32:
buildType = XdmfArrayType::UInt32();
break;
case XDMF_ARRAY_TYPE_INT8:
buildType = XdmfArrayType::Int8();
break;
case XDMF_ARRAY_TYPE_INT16:
buildType = XdmfArrayType::Int16();
break;
case XDMF_ARRAY_TYPE_INT32:
buildType = XdmfArrayType::Int32();
break;
case XDMF_ARRAY_TYPE_INT64:
buildType = XdmfArrayType::Int64();
break;
case XDMF_ARRAY_TYPE_FLOAT32:
buildType = XdmfArrayType::Float32();
break;
case XDMF_ARRAY_TYPE_FLOAT64:
buildType = XdmfArrayType::Float64();
break;
default:
XdmfError::message(XdmfError::FATAL,
"Error: Invalid ArrayType.");
break;
}
shared_ptr<XdmfHDF5Controller> generatedController = XdmfHDF5Controller::New(std::string(hdf5FilePath), std::string(dataSetPath), buildType, startVector, strideVector, dimVector, dataspaceVector);
return (XDMFHDF5CONTROLLER *)((void *)(new XdmfHDF5Controller(*generatedController.get())));
}
catch (...)
{
std::vector<unsigned int> startVector(start, start + numDims);
std::vector<unsigned int> strideVector(stride, stride + numDims);
std::vector<unsigned int> dimVector(dimensions, dimensions + numDims);
std::vector<unsigned int> dataspaceVector(dataspaceDimensions, dataspaceDimensions + numDims);
shared_ptr<const XdmfArrayType> buildType = shared_ptr<XdmfArrayType>();
switch (type) {
case XDMF_ARRAY_TYPE_UINT8:
buildType = XdmfArrayType::UInt8();
break;
case XDMF_ARRAY_TYPE_UINT16:
buildType = XdmfArrayType::UInt16();
break;
case XDMF_ARRAY_TYPE_UINT32:
buildType = XdmfArrayType::UInt32();
break;
case XDMF_ARRAY_TYPE_INT8:
buildType = XdmfArrayType::Int8();
break;
case XDMF_ARRAY_TYPE_INT16:
buildType = XdmfArrayType::Int16();
break;
case XDMF_ARRAY_TYPE_INT32:
buildType = XdmfArrayType::Int32();
break;
case XDMF_ARRAY_TYPE_INT64:
buildType = XdmfArrayType::Int64();
break;
case XDMF_ARRAY_TYPE_FLOAT32:
buildType = XdmfArrayType::Float32();
break;
case XDMF_ARRAY_TYPE_FLOAT64:
buildType = XdmfArrayType::Float64();
break;
default:
XdmfError::message(XdmfError::FATAL,
"Error: Invalid ArrayType.");
break;
}
shared_ptr<XdmfHDF5Controller> generatedController = XdmfHDF5Controller::New(std::string(hdf5FilePath), std::string(dataSetPath), buildType, startVector, strideVector, dimVector, dataspaceVector);
return (XDMFHDF5CONTROLLER *)((void *)(new XdmfHDF5Controller(*generatedController.get())));
}
XDMF_ERROR_WRAP_END(status)
return NULL;
}
char * XdmfHDF5ControllerGetDataSetPath(XDMFHDF5CONTROLLER * controller)
{
char * returnPointer = strdup(((XdmfHDF5Controller *)(controller))->getDataSetPath().c_str());
return returnPointer;
}
// C Wrappers for parent classes are generated by macros
XDMF_HEAVYCONTROLLER_C_CHILD_WRAPPER(XdmfHDF5Controller, XDMFHDF5CONTROLLER)
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