Branch data Line data Source code
1 : : /** \file ReadHDF5VarLen.hpp
2 : : * \author Jason Kraftcheck
3 : : * \date 2010-09-04
4 : : */
5 : :
6 : : #ifndef moab_READ_HDF5_VAR_LEN_HPP
7 : : #define moab_READ_HDF5_VAR_LEN_HPP
8 : :
9 : : #include "moab/MOABConfig.h"
10 : : #ifdef MOAB_HAVE_MPI
11 : : #include "moab_mpi.h"
12 : : #endif
13 : : #include "DebugOutput.hpp"
14 : : #include "moab/Range.hpp"
15 : : #include "H5Ipublic.h"
16 : :
17 : : namespace moab
18 : : {
19 : :
20 : : class ReadHDF5Dataset;
21 : :
22 : : /**\brief Read variable-length data from 1-D array dataset
23 : : *
24 : : * Utility class for reading variable-length data from an HDF5 dataset.
25 : : * Used for reading set contents, set parents, set children,
26 : : * polygon and polyhedron connectivity, and variable-length tag
27 : : * data.
28 : : *
29 : : * This is an abstract class. The pure virtual \c store_data method
30 : : * must be implemented to create a concrete instance.
31 : : */
32 : : class ReadHDF5VarLen
33 : : {
34 : : protected:
35 : : DebugOutput& dbgOut;
36 : :
37 : : private:
38 : : void* const dataBuffer;
39 : : const size_t bufferSize;
40 : :
41 : : /**\brief Test if passed file_id is value pointed to by ranged_iter,
42 : : * and if so, incremenet ranged_iter
43 : : */
44 : : static bool is_ranged( EntityHandle file_id, Range::const_iterator& ranged_iter, Range::const_iterator ranged_end );
45 : :
46 : : protected:
47 : : /**\brief Store data list for a single entity
48 : : *
49 : : * The is the pure virtual method that must be provided.
50 : : * It is responsible for storing the data read for a single
51 : : * entity.
52 : : *
53 : : * This function will always be called in the order of the
54 : : * file_ids in the range passed to the \c read method.
55 : : *
56 : : *\param file_id The file ID for the entity
57 : : *\param data A pointer to the data for the entity
58 : : *\param num_data Number of values for the entity
59 : : *\param ranged For set contents, true if in ranged format.
60 : : */
61 : : virtual ErrorCode store_data( EntityHandle file_id, void* data, long num_data, bool ranged ) = 0;
62 : :
63 : : public:
64 : : /**\brief Constructor
65 : : *\param buffer A temporary buffer to use during read
66 : : *\param buffer_size Size of \c buffer, in bytes.
67 : : */
68 : 73 : ReadHDF5VarLen( DebugOutput& debug_output, void* buffer, size_t buffer_size )
69 : 73 : : dbgOut( debug_output ), dataBuffer( buffer ), bufferSize( buffer_size )
70 : : {
71 : 73 : }
72 : :
73 [ - + ]: 146 : virtual ~ReadHDF5VarLen() {}
74 : :
75 : : /**\brief Do actual read of data set
76 : : *\param data_set The data set to read.
77 : : *\param file_ids The file ids of the entities to read.
78 : : *\param start_file_id The file id corresponding to the first row of the dataset
79 : : *\param data_type The desired, in-memory data type for values
80 : : *\param vals_per_ent The number of values for each entity
81 : : *\param ranged_file_ids Those file ids for which the 'ranged'
82 : : * argument to \c storedata should be passed
83 : : * as \c true.
84 : : */
85 : : ErrorCode read_data( ReadHDF5Dataset& data_set, const Range& offsets, EntityHandle start_offset, hid_t data_type,
86 : : const Range& file_ids, const std::vector< unsigned >& vals_per_ent,
87 : : const Range& ranged_file_ids );
88 : :
89 : : /**\brief Read set description table or offset vector for
90 : : * var-len tags or old-format poly(gon|hedra) connectivity.
91 : : *\param data_set The data set to read.
92 : : *\param file_ids The file ids of the entities to read.
93 : : *\param start_file_id The file id corresponding to the first row of the dataset
94 : : *\param num_columns The number of columns of offsets in the dataset
95 : : *\param indices Array of length \c num_columns contaning the
96 : : * indices of the columns to read.
97 : : *\param nudge Amount by which to offset values in
98 : : * \c offset_out to avoid putting zeros in
99 : : * Range. Must be greater than 0. Probably 1.
100 : : *\param offsets_out An array of length \c num_columns which will
101 : : * be populated with the resulting list of offsets
102 : : * into the contents list calculated from reading
103 : : * the offsets from the passed data set.
104 : : *\param counts_out An array of length \c num_columns of std::vectors,
105 : : * where each vector will be filled with one value
106 : : * per file ID indicating the length of the data for
107 : : * the corresponding file ID.
108 : : *\param ranged_file_ids If non-null, the last column of the table will
109 : : * be read and tested for the ranged bit. For
110 : : * all file_ids for which the range bit is set,
111 : : * the file ID will be added to this list.
112 : : */
113 : : /*
114 : : ErrorCode read_offsets( ReadHDF5Dataset& data_set,
115 : : const Range& file_ids,
116 : : EntityHandle start_file_id,
117 : : unsigned num_columns,
118 : : const unsigned indices[],
119 : : EntityHandle nudge,
120 : : Range offsets_out[],
121 : : std::vector<unsigned> counts_out[],
122 : : Range* ranged_file_ids = 0 );
123 : : */
124 : : ErrorCode read_offsets( ReadHDF5Dataset& data_set, const Range& file_ids, EntityHandle start_file_id,
125 : : EntityHandle nudge, Range& offsets_out, std::vector< unsigned >& counts_out );
126 : :
127 : 0 : ErrorCode read( ReadHDF5Dataset& offset_data, ReadHDF5Dataset& value_data, const Range& file_ids,
128 : : EntityHandle start_file_id, hid_t data_type, const Range* ranged = 0 )
129 : : {
130 : : ErrorCode rval;
131 : 0 : const EntityHandle nudge = 1;
132 [ # # ]: 0 : Range offsets;
133 [ # # ]: 0 : std::vector< unsigned > counts;
134 [ # # ]: 0 : rval = read_offsets( offset_data, file_ids, start_file_id, nudge, offsets, counts );
135 [ # # ]: 0 : if( MB_SUCCESS != rval ) return rval;
136 [ # # ]: 0 : Range empty;
137 [ # # ][ # # ]: 0 : rval = read_data( value_data, offsets, nudge, data_type, file_ids, counts, ranged ? *ranged : empty );
138 : 0 : return rval;
139 : : }
140 : : };
141 : :
142 : : } // namespace moab
143 : :
144 : : #endif // moab_READ_HDF5_VAR_LEN_HPP
|
