Template for implementing new file readers in MOAB This class is a template for writing new file readers in MOAB. This shows how to efficiently create vertices and elements using the ReadUtilIface class, and to translate indices in connectivity lists into vertex handles created during the read. More...

#include <ReadTemplate.hpp>

Inheritance diagram for moab::ReadTemplate:

Collaboration diagram for moab::ReadTemplate:

Public Member Functions
ErrorCode	load_file (const char file_name, const EntityHandle file_set, const FileOptions &opts, const SubsetList subset_list=0, const Tag file_id_tag=0)
	Load mesh from a file.
ErrorCode	read_tag_values (const char file_name, const char tag_name, const FileOptions &opts, std::vector< int > &tag_values_out, const SubsetList *subset_list=0)
	Read tag values from a file.
	ReadTemplate (Interface *impl=NULL)
	Constructor.
virtual	~ReadTemplate ()
	Destructor.
Static Public Member Functions
static ReaderIface *	factory (Interface *)
	factory method
Private Member Functions
ErrorCode	read_vertices (int num_verts, EntityHandle &start_vertex, Range &read_ents)
	Read vertex data and create vertices in MOAB database.
ErrorCode	read_elements (int num_elems, EntityHandle start_vertex, EntityHandle &start_elem, Range &read_ents)
	Read element data and create elements in MOAB database.
ErrorCode	create_sets (int num_sets, EntityHandle start_vertex, int num_verts, EntityHandle start_elem, int num_elems, Range &read_ents)
	Read entity set data and create/populate sets in MOAB database.
ErrorCode	process_options (const FileOptions &opts)
	Process options passed into the reader.
Private Attributes
ReadUtilIface *	readMeshIface
Interface *	mbImpl
	interface instance
const char *	fileName

Detailed Description

Template for implementing new file readers in MOAB This class is a template for writing new file readers in MOAB. This shows how to efficiently create vertices and elements using the ReadUtilIface class, and to translate indices in connectivity lists into vertex handles created during the read.

After writing the new reader class, you should also modify src/ReaderWriterSet.cpp, to register the new reader along with the file extensions that it reads. This will turn on automatic creating of this reader based on file extension, which is done in Core::serial_load_file.

Definition at line 23 of file ReadTemplate.hpp.

Constructor & Destructor Documentation

ReadTemplate::ReadTemplate ( Interface * impl = NULL )

Constructor.

Definition at line 24 of file ReadTemplate.cpp.

References mbImpl, moab::Interface::query_interface(), and readMeshIface.

Referenced by factory().

                                            : mbImpl( impl ), fileName( NULL )
{
    mbImpl->query_interface( readMeshIface );
}

ReadTemplate::~ReadTemplate ( ) [virtual]

Destructor.

Definition at line 29 of file ReadTemplate.cpp.

References mbImpl, readMeshIface, and moab::Interface::release_interface().

{
    if( readMeshIface )
    {
        mbImpl->release_interface( readMeshIface );
        readMeshIface = 0;
    }
}

Member Function Documentation

ErrorCode ReadTemplate::create_sets	(	int	num_sets,
		EntityHandle	start_vertex,
		int	num_verts,
		EntityHandle	start_elem,
		int	num_elems,
		Range &	read_ents
	)		`[private]`

Read entity set data and create/populate sets in MOAB database.

Read/create sets.

Parameters:

num_sets	Number of sets to be read
start_vertex	Starting vertex handle
num_verts	Total number of vertices read from file
start_elem	Starting element handle
num_elems	Total number of elements read from file
read_ents	Range storing all entities read from this file

Definition at line 208 of file ReadTemplate.cpp.

References moab::Interface::add_entities(), moab::Interface::create_meshset(), ErrorCode, fileName, moab::Range::insert(), MB_CHK_SET_ERR, MB_SUCCESS, mbImpl, and MESHSET_SET.

Referenced by load_file().

{
    ErrorCode result = MB_SUCCESS;
    EntityHandle this_set;

    for( int i = 0; i < num_sets; i++ )
    {
        // Create set
        result = mbImpl->create_meshset( MESHSET_SET, this_set );MB_CHK_SET_ERR( result, fileName << ": Trouble creating set" );

        Range set_ents;
        // Read/compute what's in this set; REMEMBER TO CONVERT THESE TO MOAB HANDLES

        // Add them to the set
        result = mbImpl->add_entities( this_set, set_ents );MB_CHK_SET_ERR( result, fileName << ": Trouble putting entities in set" );

        // Add the new set to read_ents
        read_ents.insert( this_set );
    }

    return MB_SUCCESS;
}

ReaderIface * ReadTemplate::factory ( Interface * iface ) [static]

factory method

Definition at line 19 of file ReadTemplate.cpp.

References ReadTemplate().

Referenced by moab::ReaderWriterSet::ReaderWriterSet().

{
    return new ReadTemplate( iface );
}

ErrorCode ReadTemplate::load_file	(	const char *	file_name,
		const EntityHandle *	file_set,
		const FileOptions &	opts,
		const SubsetList *	subset_list = `0`,
		const Tag *	file_id_tag = `0`
	)		`[virtual]`

Load mesh from a file.

Method all readers must provide to import a mesh.

Parameters:

file_name	The file to read.
file_set	Optional pointer to entity set representing file. If this is not NULL, reader may optionally tag the pointed-to set with format-specific meta-data.
subset_list	An optional struct pointer specifying the tags identifying entity sets to be read.
file_id_tag	If specified, reader should store for each entity it reads, a unique integer ID for this tag.

Author:: Jason Kraftcheck

Implements moab::ReaderIface.

Definition at line 47 of file ReadTemplate.cpp.

References moab::Interface::add_entities(), create_sets(), ErrorCode, filename, fileName, MB_CHK_SET_ERR, MB_FILE_DOES_NOT_EXIST, MB_SET_ERR, MB_SUCCESS, mbImpl, process_options(), read_elements(), and read_vertices().

{
    if( subset_list )
    {
        // See src/moab/ReaderIface.hpp, definition of SubsetList struct; this basically specifies
        // an integer tag and tag values for sets to read on this proc, or a part number and total #
        // parts for reading a trivial partition of entities
    }

    // Save filename to member variable so we don't need to pass as an argument
    // to called functions
    fileName = filename;

    // Process options; see src/FileOptions.hpp for API for FileOptions class, and
    // doc/metadata_info.doc for a description of various options used by some of the readers in
    // MOAB
    ErrorCode result = process_options( opts );MB_CHK_SET_ERR( result, fileName << ": problem reading options" );

    // Open file; filePtr is member of ReadTemplate, change to whatever mechanism is used to
    // identify file
    FILE* filePtr = fopen( fileName, "r" );
    if( !filePtr )
    {
        MB_SET_ERR( MB_FILE_DOES_NOT_EXIST, fileName << ": fopen returned error" );
    }

    // Read number of verts, elements, sets
    long num_verts = 0, num_elems = 0, num_sets = 0;

    // read_ents keeps a running set of entities read from this file, including vertices, elements,
    // and sets; these will get added to file_set (if input) at the end of the read
    Range read_ents;

    // start_vertex is passed back so we know how to convert indices from the file into vertex
    // handles; most of the time this is done by adding start_vertex to the (0-based) index; if the
    // index is 1-based, you also need to subtract one; see read_elements for details
    EntityHandle start_vertex;
    result = read_vertices( num_verts, start_vertex, read_ents );
    if( MB_SUCCESS != result )
    {
        fclose( filePtr );
        return result;
    }

    // Create/read elements; this template assumes that all elements are the same type, so can be
    // read in a single call to read_elements, and kept track of with a single start_elem handle. If
    // there are more entity types, might have to keep these start handles in an array/vector.
    // start_elem is only really needed if you're reading sets later, and need to convert some
    // file-based index to an entity handle
    EntityHandle start_elem;
    result = read_elements( num_elems, start_vertex, start_elem, read_ents );
    if( MB_SUCCESS != result )
    {
        fclose( filePtr );
        return result;
    }

    // Read/create entity sets; typically these sets have some tag identifying what they're for, see
    // doc/metadata_info.doc for examples of different kinds of sets and how they're marked
    result = create_sets( num_sets, start_vertex, num_verts, start_elem, num_elems, read_ents );
    if( MB_SUCCESS != result )
    {
        fclose( filePtr );
        return result;
    }

    // Finally, add all read_ents into the file set, if one was input
    if( file_set && *file_set )
    {
        result = mbImpl->add_entities( *file_set, read_ents );
        if( MB_SUCCESS != result )
        {
            fclose( filePtr );
            return result;
        }
    }

    fclose( filePtr );

    return result;
}

ErrorCode ReadTemplate::process_options ( const FileOptions & opts ) [private]

Process options passed into the reader.

Parameters:

opts	Options passed into this read

Definition at line 236 of file ReadTemplate.cpp.

References moab::FileOptions::mark_all_seen(), and MB_SUCCESS.

Referenced by load_file().

{
    // Mark all options seen, to avoid compile warning on unused variable
    opts.mark_all_seen();
    return MB_SUCCESS;
}

ErrorCode ReadTemplate::read_elements	(	int	num_elems,
		EntityHandle	start_vertex,
		EntityHandle &	start_elem,
		Range &	read_ents
	)		`[private]`

Read element data and create elements in MOAB database.

Read/create elements.

Parameters:

num_elems	Number of elements to be read
start_vertex	Starting vertex handle; used to offset connectivity indices
start_elem	Starting element handle; may be used later to offset set entities
read_ents	Range storing all entities read from this file

Definition at line 157 of file ReadTemplate.cpp.

References ErrorCode, fileName, moab::ReadUtilIface::get_element_connect(), moab::Range::insert(), MB_CHK_SET_ERR, MB_SUCCESS, MBHEX, OFFSET, moab::Range::rbegin(), readMeshIface, and moab::ReadUtilIface::update_adjacencies().

Referenced by load_file().

{
    // Get the entity type being read
    EntityType ent_type = MBHEX;

    // Get the number of vertices per entity
    int verts_per_elem = 8;

    // Create the element sequence; passes back a pointer to the internal storage for connectivity
    // and the starting entity handle
    EntityHandle* conn_array;
    ErrorCode result =
        readMeshIface->get_element_connect( num_elems, verts_per_elem, ent_type, 1, start_elem, conn_array );MB_CHK_SET_ERR( result, fileName << ": Trouble reading elements" );

    // Read connectivity into conn_array directly
    for( long i = 0; i < num_elems; i++ )
    {
        // Read connectivity
    }

    // Convert file-based connectivity indices to vertex handles in-place; be careful, if indices
    // are smaller than handles, need to do from the end of the list so we don't overwrite data
    //
    // Here, we assume indices are smaller than handles, just for demonstration; create an
    // integer-type pointer to connectivity initialized to same start of connectivity array
    int* ind_array = reinterpret_cast< int* >( conn_array );
    // OFFSET is value of first vertex index in file; most files are 1-based, but some might be
    // 0-based
    int OFFSET = 1;
    for( long i = num_elems * verts_per_elem - 1; i >= 0; i-- )
    {
        conn_array[i] = ind_array[i] + start_vertex + OFFSET;

        // This assert assumes last handle in read_ents is highest vertex handle in this file
        assert( conn_array[i] >= start_vertex && conn_array[i] <= *read_ents.rbegin() );
    }

    // Notify MOAB of the new elements
    result = readMeshIface->update_adjacencies( start_elem, num_elems, verts_per_elem, conn_array );
    if( MB_SUCCESS != result ) return result;

    // Add elements to read_ents
    if( num_elems ) read_ents.insert( start_elem, start_elem + num_elems - 1 );

    return MB_SUCCESS;
}

ErrorCode ReadTemplate::read_tag_values	(	const char *	file_name,
		const char *	tag_name,
		const FileOptions &	opts,
		std::vector< int > &	tag_values_out,
		const SubsetList *	subset_list = `0`
	)		`[virtual]`

Read tag values from a file.

Read the list if all integer tag values from the file for a tag that is a single integer value per entity.

Parameters:

file_name	The file to read.
tag_name	The tag for which to read values
tag_values_out	Output: The list of tag values.
subset_list	An array of tag name and value sets specifying the subset of the file to read. If multiple tags are specified, the sets that match all tags (intersection) should be read.
subset_list_length	The length of the 'subset_list' array.

Implements moab::ReaderIface.

Definition at line 38 of file ReadTemplate.cpp.

References MB_NOT_IMPLEMENTED.

{
    return MB_NOT_IMPLEMENTED;
}

ErrorCode ReadTemplate::read_vertices	(	int	num_verts,
		EntityHandle &	start_vertex,
		Range &	read_ents
	)		`[private]`

Read vertex data and create vertices in MOAB database.

Parameters:

num_verts	Number of vertices to be read
start_vertex	Starting vertex handle; used later to offset connectivity indices
read_ents	Range storing all entities read from this file

Definition at line 133 of file ReadTemplate.cpp.

References ErrorCode, fileName, moab::ReadUtilIface::get_node_coords(), moab::Range::insert(), MB_CHK_SET_ERR, and readMeshIface.

Referenced by load_file().

{
    // Allocate nodes; these are allocated in one shot, get contiguous handles starting with
    // start_handle, and the reader is passed back double*'s pointing to MOAB's native storage for
    // vertex coordinates for those verts
    std::vector< double* > coord_arrays;
    ErrorCode result = readMeshIface->get_node_coords( 3, num_verts, 1, start_vertex, coord_arrays );MB_CHK_SET_ERR( result, fileName << ": Trouble reading vertices" );

    // Fill in vertex coordinate arrays
    double *x = coord_arrays[0], *y = coord_arrays[1], *z = coord_arrays[2];
    for( long i = 0; i < num_verts; ++i )
    {
        // Read x/y/z; do something with them for now to avoid warning
        if( x || y || z )
        {
        }
    }

    if( num_verts ) read_ents.insert( start_vertex, start_vertex + num_verts - 1 );

    return result;
}