/usr/include/XdmfHDF5Writer.hpp is in libxdmf-dev 3.0+git20160803-4.
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/* XDMF */
/* eXtensible Data Model and Format */
/* */
/* Id : XdmfHDF5Writer.hpp */
/* */
/* 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. */
/* */
/*****************************************************************************/
#ifndef XDMFHDF5WRITER_HPP_
#define XDMFHDF5WRITER_HPP_
// C Compatible includes
#include "XdmfCore.hpp"
#include "XdmfHeavyDataWriter.hpp"
#include "XdmfHeavyDataController.hpp"
// So that hdf5 does not need to be included in the header files
// It would add a dependancy to programs that use Xdmf
#ifndef _H5Ipublic_H
#ifndef XDMF_HID_T
#define XDMF_HID_T
typedef int hid_t;
#endif
#endif
#ifdef __cplusplus
// Forward Declarations
class XdmfArray;
class XdmfArrayType;
class XdmfHDF5Controller;
// Includes
#include <list>
#include <set>
/**
* @brief Traverse the Xdmf graph and write heavy data stored in
* XdmfArrays to HDF5 on disk.
*
* XdmfHDF5Writer traverses an Xdmf graph structure and writes data
* stored in XdmfArrays to HDF5. Writing begins by calling the
* accept() operation on any XdmfItem and supplying this writer as the
* parameter. The writer will write all XdmfArrays under the XdmfItem
* to an hdf5 file on disk. It will also attach an XdmfHDF5Controller
* to all XdmfArrays that it writes to disk.
*
* This writer supports all heavy data writing modes listed in
* XdmfHeavyDataWriter.
*/
class XDMFCORE_EXPORT XdmfHDF5Writer : public XdmfHeavyDataWriter {
public:
/**
* Construct XdmfHDF5Writer.
*
* Example of use:
*
* C++
*
* @dontinclude ExampleXdmfHDF5Writer.cpp
* @skipline //#initialization
* @until //#initialization
*
* Python
*
* @dontinclude XdmfExampleHDF5Writer.py
* @skipline #//initialization
* @until #//initialization
*
* @param filePath The location of the hdf5 file to output to on disk.
* @param clobberFile Whether to overwrite the previous file if it exists.
*
* @return New XdmfHDF5Writer.
*/
static shared_ptr<XdmfHDF5Writer> New(const std::string & filePath,
const bool clobberFile = false);
virtual ~XdmfHDF5Writer();
virtual void closeFile();
/**
* Get the chunk size used to output datasets to hdf5.
*
* C++
*
* @dontinclude ExampleXdmfHDF5Writer.cpp
* @skipline //#initialization
* @until //#initialization
* @skipline //#getChunkSize
* @until //#getChunkSize
*
* Python
*
* @dontinclude XdmfExampleHDF5Writer.py
* @skipline #//initialization
* @until #//initialization
* @skipline #//getChunkSize
* @until #//getChunkSize
*
* @return Chunk size used to output datasets to hdf5.
*/
unsigned int getChunkSize() const;
virtual int getDataSetSize(const std::string & fileName,
const std::string & dataSetName);
/**
* Gets the factor that Deflate uses to compress data.
*
* Example of use:
*
* C++
*
* @dontinclude ExampleXdmfHDF5Writer.cpp
* @skipline //#initialization
* @until //#initialization
* @skipline //#getDeflateFactor
* @until //#getDeflateFactor
*
* Python
*
* @dontinclude XdmfExampleHDF5Writer.py
* @skipline #//initialization
* @until #//initialization
* @skipline #//getDeflateFactor
* @until #//getDeflateFactor
*
* @return The factor Deflate uses.
*/
int getDeflateFactor() const;
/**
* Gets whether Deflate is enabled.
*
* Example of use:
*
* C++
*
* @dontinclude ExampleXdmfHDF5Writer.cpp
* @skipline //#initialization
* @until //#initialization
* @skipline //#getUseDeflate
* @until //#getUseDeflate
*
* Python
*
* @dontinclude XdmfExampleHDF5Writer.py
* @skipline #//initialization
* @until #//initialization
* @skipline #//getUseDeflate
* @until #//getUseDeflate
*
* @return Whether Deflate is in use.
*/
bool getUseDeflate() const;
virtual void openFile();
/**
* Set the chunk size used to output datasets to hdf5. For
* multidimensional datasets the chunk size is the total number of
* elements in the chunk.
*
* C++
*
* @dontinclude ExampleXdmfHDF5Writer.cpp
* @skipline //#initialization
* @until //#initialization
* @skipline //#setChunkSize
* @until //#setChunkSize
*
* Python
*
* @dontinclude XdmfExampleHDF5Writer.py
* @skipline #//initialization
* @until #//initialization
* @skipline #//setChunkSize
* @until #//setChunkSize
*
* @param chunkSize The number of elements per chunk.
*/
void setChunkSize(const unsigned int chunkSize);
/**
* Sets the factor that Deflate will use to compress data.
*
* Example of use:
*
* C++
*
* @dontinclude ExampleXdmfHDF5Writer.cpp
* @skipline //#initialization
* @until //#initialization
* @skipline //#setDeflateFactor
* @until //#setDeflateFactor
*
* Python
*
* @dontinclude XdmfExampleHDF5Writer.py
* @skipline #//initialization
* @until #//initialization
* @skipline #//setDeflateFactor
* @until #//setDeflateFactor
*
* @param factor The factor Deflate will use.
*/
void setDeflateFactor(int factor);
/**
* Sets whether HDF5 will use Deflate compression
*
* Example of use:
*
* C++
*
* @dontinclude ExampleXdmfHDF5Writer.cpp
* @skipline //#initialization
* @until //#initialization
* @skipline //#setUseDeflate
* @until //#setUseDeflate
*
* Python
*
* @dontinclude XdmfExampleHDF5Writer.py
* @skipline #//initialization
* @until #//initialization
* @skipline #//setUseDeflate
* @until #//setUseDeflate
*
* @param status Whether Deflate will be used.
*/
void setUseDeflate(bool status);
using XdmfHeavyDataWriter::visit;
virtual void visit(XdmfArray & array,
const shared_ptr<XdmfBaseVisitor> visitor);
virtual void visit(XdmfItem & item,
const shared_ptr<XdmfBaseVisitor> visitor);
XdmfHDF5Writer(const XdmfHDF5Writer &);
protected:
XdmfHDF5Writer(const std::string & filePath);
/**
* Create a new HDF5 Controller that is able to read in after being
* written by this writer.
*
* @param hdf5FilePath the location of the hdf5 file the data set resides in.
* @param dataSetPath the location of the dataset within the hdf5 file.
* @param type the data type of the dataset to read.
* @param start the offset of the starting element in each dimension in
* the hdf5 data set.
* @param stride the number of elements to move in each dimension from the
* hdf5 data set.
* @param dimensions the number of elements to select in each
* dimension from the hdf5 data set. (size in each dimension)
* @param dataspaceDimensions the number of elements in the entire
* hdf5 data set (may be larger that dimensions if using
* hyperslabs).
*
* @return new HDF5 Controller.
*/
virtual shared_ptr<XdmfHeavyDataController>
createController(const std::string & hdf5FilePath,
const std::string & descriptor,
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);
virtual int getDataSetSize(shared_ptr<XdmfHeavyDataController> descriptionController);
/**
* Write the XdmfArray to a hdf5 file.
*
* @param array An XdmfArray to write to hdf5.
*/
virtual void write(XdmfArray & array);
/**
* PIMPL
*/
class XdmfHDF5WriterImpl
{
public:
XdmfHDF5WriterImpl();
virtual ~XdmfHDF5WriterImpl();
virtual void
closeFile();
virtual int
openFile(const std::string & filePath,
const int mDataSetId);
hid_t mHDF5Handle;
int mFapl;
unsigned int mChunkSize;
std::string mOpenFile;
int mDepth;
std::set<const XdmfItem *> mWrittenItems;
};
XdmfHDF5WriterImpl * mImpl;
bool mUseDeflate;
int mDeflateFactor;
private:
void operator=(const XdmfHDF5Writer &); // Not implemented.
virtual void controllerSplitting(XdmfArray & array,
int & controllerIndexOffset,
shared_ptr<XdmfHeavyDataController> heavyDataController,
const std::string & checkFileName,
const std::string & checkFileExt,
const std::string & dataSetPath,
int dataSetId,
const std::vector<unsigned int> & dimensions,
const std::vector<unsigned int> & dataspaceDimensions,
const std::vector<unsigned int> & start,
const std::vector<unsigned int> & stride,
std::list<std::string> & filesWritten,
std::list<std::string> & datasetsWritten,
std::list<int> & datasetIdsWritten,
std::list<void *> & arraysWritten,
std::list<std::vector<unsigned int> > & startsWritten,
std::list<std::vector<unsigned int> > & stridesWritten,
std::list<std::vector<unsigned int> > & dimensionsWritten,
std::list<std::vector<unsigned int> > & dataSizesWritten,
std::list<unsigned int> & arrayOffsetsWritten);
};
#endif
#ifdef __cplusplus
extern "C" {
#endif
// C wrappers go here
struct XDMFHDF5WRITER; // Simply as a typedef to ensure correct typing
typedef struct XDMFHDF5WRITER XDMFHDF5WRITER;
XDMFCORE_EXPORT XDMFHDF5WRITER * XdmfHDF5WriterNew(char * fileName, int clobberFile);
XDMFCORE_EXPORT void XdmfHDF5WriterCloseFile(XDMFHDF5WRITER * writer, int * status);
XDMFCORE_EXPORT unsigned int XdmfHDF5WriterGetChunkSize(XDMFHDF5WRITER * writer, int * status);
XDMFCORE_EXPORT void XdmfHDF5WriterOpenFile(XDMFHDF5WRITER * writer, int * status);
XDMFCORE_EXPORT void XdmfHDF5WriterSetChunkSize(XDMFHDF5WRITER * writer, unsigned int chunkSize, int * status);
#define XDMF_HDF5WRITER_C_CHILD_DECLARE(ClassName, CClassName, Level) \
\
Level##_EXPORT void ClassName##CloseFile( CClassName * writer, int * status); \
Level##_EXPORT unsigned int ClassName##GetChunkSize( CClassName * writer, int * status); \
Level##_EXPORT void ClassName##OpenFile( CClassName * writer, int * status); \
Level##_EXPORT void ClassName##SetChunkSize( CClassName * writer, unsigned int chunkSize, int * status);
#define XDMF_HDF5WRITER_C_CHILD_WRAPPER(ClassName, CClassName) \
\
void ClassName##CloseFile( CClassName * writer, int * status) \
{ \
XdmfHDF5WriterCloseFile((XDMFHDF5WRITER *)((void *)writer), status); \
} \
\
unsigned int ClassName##GetChunkSize( CClassName * writer, int * status) \
{ \
return XdmfHDF5WriterGetChunkSize((XDMFHDF5WRITER *)((void *)writer), status); \
} \
\
void ClassName##OpenFile( CClassName * writer, int * status) \
{ \
XdmfHDF5WriterOpenFile((XDMFHDF5WRITER *)((void *)writer), status); \
} \
\
void ClassName##SetChunkSize( CClassName * writer, unsigned int chunkSize, int * status) \
{ \
XdmfHDF5WriterSetChunkSize((XDMFHDF5WRITER *)((void *)writer), chunkSize, status); \
}
// C Wrappers for parent classes are generated by macros
XDMF_HEAVYWRITER_C_CHILD_DECLARE(XdmfHDF5Writer, XDMFHDF5WRITER, XDMFCORE)
#ifdef __cplusplus
}
#endif
#endif /* XDMFHDF5WRITER_HPP_ */
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