dataexporter/src/EscriptDataset.h


/*******************************************************
*
* Copyright (c) 2003-2009 by University of Queensland
* Earth Systems Science Computational Center (ESSCC)
* http://www.uq.edu.au/esscc
*
* Primary Business: Queensland, Australia
* Licensed under the Open Software License version 3.0
* http://www.opensource.org/licenses/osl-3.0.php
*
*******************************************************/

#ifndef __ESCRIPTDATASET_H__
#define __ESCRIPTDATASET_H__

#include <escriptexport/escriptexport.h>
#include <escript/AbstractDomain.h>

class DBfile;

namespace escript {

class Data;

}


namespace escriptexport {

typedef std::vector<escript::Data>  DataVec;
typedef std::vector<DataVar_ptr>    DataBlocks;
typedef std::vector<FinleyMesh_ptr> MeshBlocks;

struct VarInfo {
    std::string varName;
    DataBlocks dataBlocks;
    IntVec sampleDistribution;
    bool valid;
};

typedef std::vector<VarInfo> VarVector;


/// \brief Represents an escript dataset including domain and variables for
/// one timestep.
//
/// This class represents an escript/finley dataset complete with domain and
/// variable data. It can read the dataset from NetCDF files generated by the
/// dump() methods within escript or through an escript domain instance plus
/// a number of escript::Data instances. Subsequently, the dataset can be
/// saved in the Silo file format or accessed through a number of accessor
/// methods.
///
/// If the data is distributed via MPI then all ranks should create an instance
/// of this class and call the respective methods. NetCDF files that stem from
/// a parallel run can be read on one processor or on the same number of MPI
/// processes as they were created with.
class EscriptDataset
{
public:
    /// \brief Default constructor.
    ESCRIPTEXPORT_DLL_API
    EscriptDataset();

#if HAVE_MPI
    /// \brief Constructor with communicator.
    ESCRIPTEXPORT_DLL_API
    EscriptDataset(MPI_Comm comm);
#endif

    /// \brief Destructor.
    ESCRIPTEXPORT_DLL_API
    ~EscriptDataset();

    /// \brief Initialises with instances of escript domain and data.
    ESCRIPTEXPORT_DLL_API
    bool initFromEscript(escript::const_Domain_ptr mesh,
                         DataVec& escriptVars, const StringVec& varNames);
                         
    /// \brief Loads mesh and variables from escript NetCDF files.
    ///
    /// \param meshFilePattern a printf-style pattern for the mesh file names
    ///                        (e.g. "mesh.%02d.nc")
    /// \param varFiles a vector of file name patterns for variables
    /// \param varNames a vector of variable names
    /// \param nBlocks number of blocks/chunks to load
    ///
    /// \note If MPI is enabled nBlocks must be equal to the size of the
    ///       communicator or this method fails.
    ESCRIPTEXPORT_DLL_API
    bool loadNetCDF(const std::string meshFilePattern,
                    const StringVec& varFiles, const StringVec& varNames,
                    int nBlocks);

    /// \brief Loads only variables from escript NetCDF files using given mesh.
    ESCRIPTEXPORT_DLL_API
    bool loadNetCDF(const MeshBlocks& mesh, const StringVec& varFiles,
                    const StringVec& varNames);

    /// \brief Sets the cycle number and time value for this dataset.
    ESCRIPTEXPORT_DLL_API
    void setCycleAndTime(int c, double t) { cycle=c; time=t; }

    /// \brief Saves the dataset in the Silo file format.
    ESCRIPTEXPORT_DLL_API
    bool saveSilo(const std::string fileName, bool useMultiMesh=true);

    /// \brief Saves the dataset in the VTK XML file format.
    /// \note NOT IMPLEMENTED.
    ESCRIPTEXPORT_DLL_API
    bool saveVTK(const std::string fileName);

    /// \brief Returns the dataset's mesh.
    ///
    /// \note The caller is responsible for freeing the memory of the returned
    /// mesh.
    ESCRIPTEXPORT_DLL_API
    MeshBlocks extractMesh() { keepMesh = true; return meshBlocks; }

    /// \brief Returns the dataset's mesh.
    ESCRIPTEXPORT_DLL_API
    const MeshBlocks& getMesh() const { return meshBlocks; }

    /// \brief Returns a vector with the dataset's variables.
    ESCRIPTEXPORT_DLL_API
    const VarVector& getVariables() const { return variables; }

    /// \brief Returns a vector with the mesh variables.
    ESCRIPTEXPORT_DLL_API
    const VarVector& getMeshVariables() const { return meshVariables; }

private:
    bool loadMeshFromNetCDF();
    bool loadVarFromNetCDF(const std::string& fileName,
                           const std::string& varName);
    void convertMeshVariables();
    void updateSampleDistribution(VarInfo& vi);
    void putSiloMultiMesh(DBfile* dbfile, const std::string& meshName);
    void putSiloMultiTensor(DBfile* dbfile, const VarInfo& vi);
    void putSiloMultiVar(DBfile* dbfile, const VarInfo& vi,
                         bool useMeshFile = false);

    int numParts;
    int cycle;
    double time;
    bool keepMesh, externalMesh;
    std::string meshFmt;
    MeshBlocks meshBlocks;
    VarVector variables, meshVariables;
    int mpiRank, mpiSize;
#if HAVE_MPI
    MPI_Comm mpiComm;
#else
    void* mpiComm;
#endif
};

} // namespace escriptexport

#endif // __ESCRIPTDATASET_H__

1
2	/*******************************************************
3	*
4	* Copyright (c) 2003-2009 by University of Queensland
5	* Earth Systems Science Computational Center (ESSCC)
6	* http://www.uq.edu.au/esscc
7	*
8	* Primary Business: Queensland, Australia
9	* Licensed under the Open Software License version 3.0
10	* http://www.opensource.org/licenses/osl-3.0.php
11	*
12	*******************************************************/
13
14	#ifndef __ESCRIPTDATASET_H__
15	#define __ESCRIPTDATASET_H__
16
17	#include <escriptexport/escriptexport.h>
18	#include <escript/AbstractDomain.h>
19
20	class DBfile;
21
22	namespace escript {
23
24	class Data;
25
26	}
27
28
29	namespace escriptexport {
30
31	typedef std::vector<escript::Data> DataVec;
32	typedef std::vector<DataVar_ptr> DataBlocks;
33	typedef std::vector<FinleyMesh_ptr> MeshBlocks;
34
35	struct VarInfo {
36	std::string varName;
37	DataBlocks dataBlocks;
38	IntVec sampleDistribution;
39	bool valid;
40	};
41
42	typedef std::vector<VarInfo> VarVector;
43
44
45	/// \brief Represents an escript dataset including domain and variables for
46	/// one timestep.
47	//
48	/// This class represents an escript/finley dataset complete with domain and
49	/// variable data. It can read the dataset from NetCDF files generated by the
50	/// dump() methods within escript or through an escript domain instance plus
51	/// a number of escript::Data instances. Subsequently, the dataset can be
52	/// saved in the Silo file format or accessed through a number of accessor
53	/// methods.
54	///
55	/// If the data is distributed via MPI then all ranks should create an instance
56	/// of this class and call the respective methods. NetCDF files that stem from
57	/// a parallel run can be read on one processor or on the same number of MPI
58	/// processes as they were created with.
59	class EscriptDataset
60	{
61	public:
62	/// \brief Default constructor.
63	ESCRIPTEXPORT_DLL_API
64	EscriptDataset();
65
66	#if HAVE_MPI
67	/// \brief Constructor with communicator.
68	ESCRIPTEXPORT_DLL_API
69	EscriptDataset(MPI_Comm comm);
70	#endif
71
72	/// \brief Destructor.
73	ESCRIPTEXPORT_DLL_API
74	~EscriptDataset();
75
76	/// \brief Initialises with instances of escript domain and data.
77	ESCRIPTEXPORT_DLL_API
78	bool initFromEscript(escript::const_Domain_ptr mesh,
79	DataVec& escriptVars, const StringVec& varNames);
80
81	/// \brief Loads mesh and variables from escript NetCDF files.
82	///
83	/// \param meshFilePattern a printf-style pattern for the mesh file names
84	/// (e.g. "mesh.%02d.nc")
85	/// \param varFiles a vector of file name patterns for variables
86	/// \param varNames a vector of variable names
87	/// \param nBlocks number of blocks/chunks to load
88	///
89	/// \note If MPI is enabled nBlocks must be equal to the size of the
90	/// communicator or this method fails.
91	ESCRIPTEXPORT_DLL_API
92	bool loadNetCDF(const std::string meshFilePattern,
93	const StringVec& varFiles, const StringVec& varNames,
94	int nBlocks);
95
96	/// \brief Loads only variables from escript NetCDF files using given mesh.
97	ESCRIPTEXPORT_DLL_API
98	bool loadNetCDF(const MeshBlocks& mesh, const StringVec& varFiles,
99	const StringVec& varNames);
100
101	/// \brief Sets the cycle number and time value for this dataset.
102	ESCRIPTEXPORT_DLL_API
103	void setCycleAndTime(int c, double t) { cycle=c; time=t; }
104
105	/// \brief Saves the dataset in the Silo file format.
106	ESCRIPTEXPORT_DLL_API
107	bool saveSilo(const std::string fileName, bool useMultiMesh=true);
108
109	/// \brief Saves the dataset in the VTK XML file format.
110	/// \note NOT IMPLEMENTED.
111	ESCRIPTEXPORT_DLL_API
112	bool saveVTK(const std::string fileName);
113
114	/// \brief Returns the dataset's mesh.
115	///
116	/// \note The caller is responsible for freeing the memory of the returned
117	/// mesh.
118	ESCRIPTEXPORT_DLL_API
119	MeshBlocks extractMesh() { keepMesh = true; return meshBlocks; }
120
121	/// \brief Returns the dataset's mesh.
122	ESCRIPTEXPORT_DLL_API
123	const MeshBlocks& getMesh() const { return meshBlocks; }
124
125	/// \brief Returns a vector with the dataset's variables.
126	ESCRIPTEXPORT_DLL_API
127	const VarVector& getVariables() const { return variables; }
128
129	/// \brief Returns a vector with the mesh variables.
130	ESCRIPTEXPORT_DLL_API
131	const VarVector& getMeshVariables() const { return meshVariables; }
132
133	private:
134	bool loadMeshFromNetCDF();
135	bool loadVarFromNetCDF(const std::string& fileName,
136	const std::string& varName);
137	void convertMeshVariables();
138	void updateSampleDistribution(VarInfo& vi);
139	void putSiloMultiMesh(DBfile* dbfile, const std::string& meshName);
140	void putSiloMultiTensor(DBfile* dbfile, const VarInfo& vi);
141	void putSiloMultiVar(DBfile* dbfile, const VarInfo& vi,
142	bool useMeshFile = false);
143
144	int numParts;
145	int cycle;
146	double time;
147	bool keepMesh, externalMesh;
148	std::string meshFmt;
149	MeshBlocks meshBlocks;
150	VarVector variables, meshVariables;
151	int mpiRank, mpiSize;
152	#if HAVE_MPI
153	MPI_Comm mpiComm;
154	#else
155	void* mpiComm;
156	#endif
157	};
158
159	} // namespace escriptexport
160
161	#endif // __ESCRIPTDATASET_H__
162