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 fileName;
    std::string varName;
    DataBlocks dataBlocks;
    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 Constructor.
    ESCRIPTEXPORT_DLL_API
    EscriptDataset();

    /// \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.
    ESCRIPTEXPORT_DLL_API
    bool loadNetCDF(const std::string meshFile, 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 loadVariablesFromNetCDF();
    void convertMeshVariables();
    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 fileName;
37	std::string varName;
38	DataBlocks dataBlocks;
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 Constructor.
63	ESCRIPTEXPORT_DLL_API
64	EscriptDataset();
65
66	/// \brief Destructor.
67	ESCRIPTEXPORT_DLL_API
68	~EscriptDataset();
69
70	/// \brief Initialises with instances of escript domain and data.
71	ESCRIPTEXPORT_DLL_API
72	bool initFromEscript(escript::const_Domain_ptr mesh,
73	DataVec& escriptVars, const StringVec& varNames);
74
75	/// \brief Loads mesh and variables from escript NetCDF files.
76	ESCRIPTEXPORT_DLL_API
77	bool loadNetCDF(const std::string meshFile, const StringVec& varFiles,
78	const StringVec& varNames, int nBlocks);
79
80	/// \brief Loads only variables from escript NetCDF files using given mesh.
81	ESCRIPTEXPORT_DLL_API
82	bool loadNetCDF(const MeshBlocks& mesh, const StringVec& varFiles,
83	const StringVec& varNames);
84
85	/// \brief Sets the cycle number and time value for this dataset.
86	ESCRIPTEXPORT_DLL_API
87	void setCycleAndTime(int c, double t) { cycle=c; time=t; }
88
89	/// \brief Saves the dataset in the Silo file format.
90	ESCRIPTEXPORT_DLL_API
91	bool saveSilo(const std::string fileName, bool useMultiMesh=true);
92
93	/// \brief Saves the dataset in the VTK XML file format.
94	/// \note NOT IMPLEMENTED.
95	ESCRIPTEXPORT_DLL_API
96	bool saveVTK(const std::string fileName);
97
98	/// \brief Returns the dataset's mesh.
99	///
100	/// \note The caller is responsible for freeing the memory of the returned
101	/// mesh.
102	ESCRIPTEXPORT_DLL_API
103	MeshBlocks extractMesh() { keepMesh = true; return meshBlocks; }
104
105	/// \brief Returns the dataset's mesh.
106	ESCRIPTEXPORT_DLL_API
107	const MeshBlocks& getMesh() const { return meshBlocks; }
108
109	/// \brief Returns a vector with the dataset's variables.
110	ESCRIPTEXPORT_DLL_API
111	const VarVector& getVariables() const { return variables; }
112
113	/// \brief Returns a vector with the mesh variables.
114	ESCRIPTEXPORT_DLL_API
115	const VarVector& getMeshVariables() const { return meshVariables; }
116
117	private:
118	bool loadMeshFromNetCDF();
119	bool loadVariablesFromNetCDF();
120	void convertMeshVariables();
121	void putSiloMultiMesh(DBfile* dbfile, const std::string& meshName);
122	void putSiloMultiTensor(DBfile* dbfile, const VarInfo& vi);
123	void putSiloMultiVar(DBfile* dbfile, const VarInfo& vi,
124	bool useMeshFile = false);
125
126	int numParts;
127	int cycle;
128	double time;
129	bool keepMesh, externalMesh;
130	std::string meshFmt;
131	MeshBlocks meshBlocks;
132	VarVector variables, meshVariables;
133	int mpiRank, mpiSize;
134	#if HAVE_MPI
135	MPI_Comm mpiComm;
136	#else
137	void* mpiComm;
138	#endif
139	};
140
141	} // namespace escriptexport
142
143	#endif // __ESCRIPTDATASET_H__
144