dataexporter/src/DataVar.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 __DATAVAR_H__
#define __DATAVAR_H__

#include <escriptexport/escriptexport.h>

class DBfile;
class NcFile;

namespace escript {
    class Data;
}

namespace escriptexport {

class FinleyMesh;

/// \brief A class that provides functionality to read an escript data object
/// from NetCDF file or an escript::Data instance and write that data in Silo
/// or VTK XML formats.
class DataVar
{
public:
    /// \brief Constructor with variable name
    ESCRIPTEXPORT_DLL_API
    DataVar(const std::string& name);

    /// \brief Copy constructor. Performs a deep copy of the data values.
    ESCRIPTEXPORT_DLL_API
    DataVar(const DataVar& d);

    /// \brief Destructor
    ESCRIPTEXPORT_DLL_API
    ~DataVar();

    /// \brief Initialises values and IDs from an escript::Data instance.
    ///
    /// \return true if a valid instance of expanded data was supplied,
    ///         false if the initialisation was unsuccessful.
    ESCRIPTEXPORT_DLL_API
    bool initFromEscript(escript::Data& escriptData, FinleyMesh_ptr mesh);

    /// \brief Initialises with integral mesh data like IDs or tags.
    ///
    /// The data is retrieved from the mesh using the variable name.
    ESCRIPTEXPORT_DLL_API
    bool initFromMesh(FinleyMesh_ptr mesh);

    /// \brief Reads values and IDs for this variable from escript NetCDF file.
    ///
    /// \return true if the file was found and contains valid escript data
    ///         with at least one sample, false otherwise.
    /// \note Only expanded data with rank <=2 is supported at the moment.
    ESCRIPTEXPORT_DLL_API
    bool initFromNetCDF(const std::string& filename, FinleyMesh_ptr mesh);

    /// \brief Writes the data into given directory in given Silo file.
    ///
    /// If Silo was not available at compile time or the mesh was not set
    /// beforehand using setMesh() or if a Silo function fails this method
    /// returns false.
    ESCRIPTEXPORT_DLL_API
    bool writeToSilo(DBfile* dbfile, const std::string& siloPath);

    /// \brief Returns the rank of the data.
    ESCRIPTEXPORT_DLL_API
    int getRank() const { return rank; }

    /// \brief Returns true if the variable data is node centered, false if
    ///        zone centered.
    ESCRIPTEXPORT_DLL_API
    bool isNodeCentered() const;

    /// \brief Returns the name of the associated mesh.
    ///
    /// The returned name is one of the sub-meshes of the mesh set with
    /// setMesh() determined on the basis of the function space type and
    /// whether reduced elements are used or not.
    ESCRIPTEXPORT_DLL_API
    std::string getMeshName() const { return meshName; }

    /// \brief Returns the shape vector of the data.
    ///
    /// The shape vector has as many elements as the rank of this variable.
    ESCRIPTEXPORT_DLL_API
    const IntVec& getShape() const { return shape; }

    /// \brief Returns the variable name.
    ESCRIPTEXPORT_DLL_API
    std::string getName() const { return varName; }

    /// \brief Returns the Silo tensor definition for this tensor.
    ///
    /// If the data is tensor data then the components of the tensor are stored
    /// separately in the Silo file. This method then returns a string that
    /// contains the proper Silo expression to put the tensor together again.
    /// For non-tensor data this method returns an empty string.
    ESCRIPTEXPORT_DLL_API
    std::string getTensorDef() const;

    /// \brief Returns the number of data values.
    ESCRIPTEXPORT_DLL_API
    int getNumberOfSamples() const { return numSamples; }

    /// \brief Returns the array of data values where array[i] is the i-th
    ///        component of the data.
    ESCRIPTEXPORT_DLL_API
    const CoordArray& getData() const { return dataArray; }

private:
    void cleanup();

    /// \brief Averages and filters data.
    ///
    /// If a sample consists of more than one data point then this method
    /// averages over the data points and returns the resulting array.
    /// In any case, the data is filtered according to the stride value.
    float* averageData(const float* src, size_t stride);

    /// \brief Prepares a sample ID -> index mapping which is used to reorder
    ///        data.
    IndexMap buildIndexMap();

    /// \brief Reorders the samples according to the corresponding node IDs.
    ///
    /// \return true if the function space is supported and the number of
    ///         elements or nodes corresponds to the number of data samples.
    bool filterSamples(const FinleyMesh_ptr mesh);

    bool initialized;
    std::string varName;
    int numSamples, rank, ptsPerSample, centering, funcSpace;
    IntVec shape;
    IntVec sampleID;
    CoordArray dataArray;
    std::string meshName, siloMeshName;
};

inline IndexMap DataVar::buildIndexMap()
{
    IndexMap sampleID2idx;
    int idx = 0;
    IntVec::const_iterator idIt;
    for (idIt = sampleID.begin(); idIt != sampleID.end(); idIt++, idx++)
        sampleID2idx[*idIt] = idx;

    return sampleID2idx;
}

} // namespace escriptexport

#endif // __DATAVAR_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 __DATAVAR_H__
15	#define __DATAVAR_H__
16
17	#include <escriptexport/escriptexport.h>
18
19	class DBfile;
20	class NcFile;
21
22	namespace escript {
23	class Data;
24	}
25
26	namespace escriptexport {
27
28	class FinleyMesh;
29
30	/// \brief A class that provides functionality to read an escript data object
31	/// from NetCDF file or an escript::Data instance and write that data in Silo
32	/// or VTK XML formats.
33	class DataVar
34	{
35	public:
36	/// \brief Constructor with variable name
37	ESCRIPTEXPORT_DLL_API
38	DataVar(const std::string& name);
39
40	/// \brief Copy constructor. Performs a deep copy of the data values.
41	ESCRIPTEXPORT_DLL_API
42	DataVar(const DataVar& d);
43
44	/// \brief Destructor
45	ESCRIPTEXPORT_DLL_API
46	~DataVar();
47
48	/// \brief Initialises values and IDs from an escript::Data instance.
49	///
50	/// \return true if a valid instance of expanded data was supplied,
51	/// false if the initialisation was unsuccessful.
52	ESCRIPTEXPORT_DLL_API
53	bool initFromEscript(escript::Data& escriptData, FinleyMesh_ptr mesh);
54
55	/// \brief Initialises with integral mesh data like IDs or tags.
56	///
57	/// The data is retrieved from the mesh using the variable name.
58	ESCRIPTEXPORT_DLL_API
59	bool initFromMesh(FinleyMesh_ptr mesh);
60
61	/// \brief Reads values and IDs for this variable from escript NetCDF file.
62	///
63	/// \return true if the file was found and contains valid escript data
64	/// with at least one sample, false otherwise.
65	/// \note Only expanded data with rank <=2 is supported at the moment.
66	ESCRIPTEXPORT_DLL_API
67	bool initFromNetCDF(const std::string& filename, FinleyMesh_ptr mesh);
68
69	/// \brief Writes the data into given directory in given Silo file.
70	///
71	/// If Silo was not available at compile time or the mesh was not set
72	/// beforehand using setMesh() or if a Silo function fails this method
73	/// returns false.
74	ESCRIPTEXPORT_DLL_API
75	bool writeToSilo(DBfile* dbfile, const std::string& siloPath);
76
77	/// \brief Returns the rank of the data.
78	ESCRIPTEXPORT_DLL_API
79	int getRank() const { return rank; }
80
81	/// \brief Returns true if the variable data is node centered, false if
82	/// zone centered.
83	ESCRIPTEXPORT_DLL_API
84	bool isNodeCentered() const;
85
86	/// \brief Returns the name of the associated mesh.
87	///
88	/// The returned name is one of the sub-meshes of the mesh set with
89	/// setMesh() determined on the basis of the function space type and
90	/// whether reduced elements are used or not.
91	ESCRIPTEXPORT_DLL_API
92	std::string getMeshName() const { return meshName; }
93
94	/// \brief Returns the shape vector of the data.
95	///
96	/// The shape vector has as many elements as the rank of this variable.
97	ESCRIPTEXPORT_DLL_API
98	const IntVec& getShape() const { return shape; }
99
100	/// \brief Returns the variable name.
101	ESCRIPTEXPORT_DLL_API
102	std::string getName() const { return varName; }
103
104	/// \brief Returns the Silo tensor definition for this tensor.
105	///
106	/// If the data is tensor data then the components of the tensor are stored
107	/// separately in the Silo file. This method then returns a string that
108	/// contains the proper Silo expression to put the tensor together again.
109	/// For non-tensor data this method returns an empty string.
110	ESCRIPTEXPORT_DLL_API
111	std::string getTensorDef() const;
112
113	/// \brief Returns the number of data values.
114	ESCRIPTEXPORT_DLL_API
115	int getNumberOfSamples() const { return numSamples; }
116
117	/// \brief Returns the array of data values where array[i] is the i-th
118	/// component of the data.
119	ESCRIPTEXPORT_DLL_API
120	const CoordArray& getData() const { return dataArray; }
121
122	private:
123	void cleanup();
124
125	/// \brief Averages and filters data.
126	///
127	/// If a sample consists of more than one data point then this method
128	/// averages over the data points and returns the resulting array.
129	/// In any case, the data is filtered according to the stride value.
130	float* averageData(const float* src, size_t stride);
131
132	/// \brief Prepares a sample ID -> index mapping which is used to reorder
133	/// data.
134	IndexMap buildIndexMap();
135
136	/// \brief Reorders the samples according to the corresponding node IDs.
137	///
138	/// \return true if the function space is supported and the number of
139	/// elements or nodes corresponds to the number of data samples.
140	bool filterSamples(const FinleyMesh_ptr mesh);
141
142	bool initialized;
143	std::string varName;
144	int numSamples, rank, ptsPerSample, centering, funcSpace;
145	IntVec shape;
146	IntVec sampleID;
147	CoordArray dataArray;
148	std::string meshName, siloMeshName;
149	};
150
151	inline IndexMap DataVar::buildIndexMap()
152	{
153	IndexMap sampleID2idx;
154	int idx = 0;
155	IntVec::const_iterator idIt;
156	for (idIt = sampleID.begin(); idIt != sampleID.end(); idIt++, idx++)
157	sampleID2idx[*idIt] = idx;
158
159	return sampleID2idx;
160	}
161
162	} // namespace escriptexport
163
164	#endif // __DATAVAR_H__
165