#include <msh_vtkreader.hh>

Inheritance diagram for VtkMeshReader:

Collaboration diagram for VtkMeshReader:

Public Types
enum	DataSections { points, cells, cell_data }
	Possible data sections in UnstructuredGrid - Piece node. More...

enum	DataFormat { ascii, binary_uncompressed, binary_zlib }
	Type of data formats - ascii, binary or compressed with zLib. More...

Public Member Functions
	TYPEDEF_ERR_INFO (EI_VTKFile, std::string)

	TYPEDEF_ERR_INFO (EI_ExpectedFormat, std::string)

	TYPEDEF_ERR_INFO (EI_ErrMessage, std::string)

	TYPEDEF_ERR_INFO (EI_SectionTypeName, std::string)

	TYPEDEF_ERR_INFO (EI_TagType, std::string)

	TYPEDEF_ERR_INFO (EI_TagName, std::string)

	DECLARE_EXCEPTION (ExcInvalidFormat,<< "Invalid format of DataArray "<< EI_FieldName::val<< ", expected "<< EI_ExpectedFormat::val<< "\n"<< "in the input file: "<< EI_VTKFile::qval)

	DECLARE_EXCEPTION (ExcUnknownFormat,<< "Unsupported or missing format of DataArray "<< EI_FieldName::val<< "\n"<< "in the input file: "<< EI_VTKFile::qval)

	DECLARE_EXCEPTION (ExcWrongType,<< EI_ErrMessage::val<< " data type of "<< EI_SectionTypeName::val<< "\n"<< "in the input file: "<< EI_VTKFile::qval)

	DECLARE_EXCEPTION (ExcIncompatibleMesh,<< "Incompatible meshes, "<< EI_ErrMessage::val<< "\n"<< "for VTK input file: "<< EI_VTKFile::qval)

	DECLARE_EXCEPTION (ExcMissingTag,<< "Missing "<< EI_TagType::val<< " "<< EI_TagName::val<< "\n"<< " in the input file: "<< EI_VTKFile::qval)

	DECLARE_EXCEPTION (ExcInvalidDofHandler,<< "Invalid DOF handler hash for field: "<< EI_FieldName::qval<< " in the input file: "<< EI_VTKFile::qval<< ".\n")

	VtkMeshReader (const FilePath &file_name)

virtual	~VtkMeshReader ()
	Destructor. More...

void	read_physical_names (Mesh *mesh) override

void	check_compatible_mesh (Mesh &mesh) override

MeshDataHeader &	find_header (HeaderQuery &header_query) override

Public Member Functions inherited from BaseMeshReader
	TYPEDEF_ERR_INFO (EI_FieldName, std::string)

	TYPEDEF_ERR_INFO (EI_Time, double)

	TYPEDEF_ERR_INFO (EI_MeshFile, std::string)

	TYPEDEF_ERR_INFO (EI_Type, std::string)

	TYPEDEF_ERR_INFO (EI_TokenizerMsg, std::string)

	TYPEDEF_ERR_INFO (EI_FileExtension, std::string)

	DECLARE_INPUT_EXCEPTION (ExcFieldNameNotFound,<< "No data for field: "<< EI_FieldName::qval<< " and time: "<< EI_Time::val<< " in the input file: "<< EI_MeshFile::qval)

	DECLARE_INPUT_EXCEPTION (ExcMissingFieldDiscretization,<< "Missing data type specification for field: "<< EI_FieldName::qval<< " and time: "<< EI_Time::val<< " in the input file: "<< EI_MeshFile::qval<< "\nPlease, add value of key 'input_discretization'.")

	DECLARE_EXCEPTION (ExcWrongFormat,<< "Wrong format of "<< EI_Type::val<< ", "<< EI_TokenizerMsg::val<< "\n"<< "in the input file: "<< EI_MeshFile::qval)

	DECLARE_EXCEPTION (ExcWrongExtension,<< "Unsupported extension "<< EI_FileExtension::qval<< " of the input file: "<< EI_MeshFile::qval)

	BaseMeshReader (const FilePath &file_name)
	Constructor. More...

void	read_raw_mesh (Mesh *mesh)

template<typename T >
ElementDataCache< T >::ComponentDataPtr	get_element_data (unsigned int n_entities, unsigned int n_components, bool boundary_domain, unsigned int component_idx)

std::vector< int > const &	get_element_vector (bool boundary_domain)

CheckResult	scale_and_check_limits (string field_name, double coef, double default_val, double lower_bound=-std::numeric_limits< double >::max(), double upper_bound=std::numeric_limits< double >::max())

Protected Types
typedef std::multimap< std::string, MeshDataHeader >	HeaderTable

Protected Types inherited from BaseMeshReader
typedef std::shared_ptr< ElementDataCacheBase >	ElementDataPtr

typedef std::map< string, ElementDataPtr >	ElementDataFieldMap

Protected Member Functions
	VtkMeshReader (const FilePath &file_name, std::shared_ptr< ElementDataFieldMap > element_data_values, double time_step)

void	read_nodes (Mesh *mesh)

void	read_elements (Mesh *mesh)

void	create_node_element_caches ()

void	make_header_table () override
	Reads table of DataArray headers through pugixml interface. More...

MeshDataHeader	create_header (pugi::xml_node node, unsigned int n_entities, Tokenizer::Position pos, OutputTime::DiscreteSpace disc)
	Helper method that create DataArray header of given xml node (used from `make_header_table`) More...

DataType	get_data_type (std::string type_str)
	Get DataType by value of string. More...

unsigned int	type_value_size (DataType data_type)
	Return size of value of data_type. More...

void	parse_ascii_data (ElementDataCacheBase &data_cache, unsigned int n_components, unsigned int n_entities, Tokenizer::Position pos, bool boundary_domain)
	Parse ascii data to data cache. More...

void	parse_binary_data (ElementDataCacheBase &data_cache, unsigned int n_components, unsigned int n_entities, Tokenizer::Position pos, bool boundary_domain, DataType value_type)
	Parse binary data to data cache. More...

void	parse_compressed_data (ElementDataCacheBase &data_cache, unsigned int n_components, unsigned int n_entities, Tokenizer::Position pos, bool boundary_domain, DataType value_type)
	Uncompress and parse binary compressed data to data cache. More...

void	read_base_vtk_attributes (pugi::xml_node vtk_node, unsigned int &n_nodes, unsigned int &n_elements)
	Set base attributes of VTK and get count of nodes and elements. More...

Tokenizer::Position	get_appended_position ()
	Get position of AppendedData tag in VTK file. More...

void	read_element_data (ElementDataCacheBase &data_cache, MeshDataHeader actual_header, unsigned int n_components, bool boundary_domain) override

bool	compare_points (const arma::vec3 &p1, const arma::vec3 &p2)

Protected Member Functions inherited from BaseMeshReader
	BaseMeshReader (const FilePath &file_name, std::shared_ptr< ElementDataFieldMap > element_data_values)
	Constructor. More...

Protected Attributes
DataType	header_type_
	header type of VTK file (only for appended data) More...

DataFormat	data_format_
	variants of data format (ascii, appended, compressed appended) More...

HeaderTable	header_table_
	Table with data of DataArray headers. More...

std::istream *	data_stream_
	input stream allow read appended data, used only if this tag exists More...

unsigned int	n_read_
	store count of read entities More...

double	time_step_
	time of VTK file (getting only during initialization from PVD reader) More...

Protected Attributes inherited from BaseMeshReader
bool	has_compatible_mesh_

std::string	data_section_name_
	Store name of field data section specify for type of mesh file. More...

std::shared_ptr< ElementDataFieldMap >	element_data_values_
	Cache with last read element data. More...

Tokenizer	tok_
	Tokenizer used for reading ASCII file format. More...

vector< LongIdx >	bulk_elements_id_

vector< LongIdx >	boundary_elements_id_

MeshDataHeader	actual_header_
	Header of actual loaded data. More...

Static Protected Attributes
static const double	point_tolerance = 1E-10
	Tolerance during comparison point data with GMSH nodes. More...

Friends
class	PvdMeshReader

Additional Inherited Members
Static Public Member Functions inherited from BaseMeshReader
static std::shared_ptr< BaseMeshReader >	reader_factory (const FilePath &file_name)

static Mesh *	mesh_factory (const Input::Record &input_mesh_rec)

Detailed Description

Definition at line 40 of file msh_vtkreader.hh.

Member Typedef Documentation

typedef std::multimap< std::string, MeshDataHeader > VtkMeshReader::HeaderTable

protected

Map of DataArray sections in VTK file.

For each field_name contains MeshDataHeader.

Definition at line 114 of file msh_vtkreader.hh.

Member Enumeration Documentation

enum VtkMeshReader::DataFormat

Type of data formats - ascii, binary or compressed with zLib.

Enumerator
ascii
binary_uncompressed
binary_zlib

Definition at line 70 of file msh_vtkreader.hh.

enum VtkMeshReader::DataSections

Possible data sections in UnstructuredGrid - Piece node.

Enumerator
points
cells
cell_data

Definition at line 65 of file msh_vtkreader.hh.

Constructor & Destructor Documentation

VtkMeshReader::VtkMeshReader ( const FilePath & file_name )

Construct the VTK format reader from given FilePath. This opens the file for reading.

Definition at line 68 of file msh_vtkreader.cc.

VtkMeshReader::~VtkMeshReader ( )

virtual

Destructor.

Definition at line 90 of file msh_vtkreader.cc.

VtkMeshReader::VtkMeshReader	(	const FilePath &	file_name,
		std::shared_ptr< ElementDataFieldMap >	element_data_values,
		double	time_step
	)

protected

Special constructor of VTK files defined in PVD file. Constructor is called from PVD mesh reader.

Construct the VTK format reader from given FilePath and set shared map of element data values. This opens the file for reading.

Definition at line 79 of file msh_vtkreader.cc.

Member Function Documentation

void VtkMeshReader::check_compatible_mesh ( Mesh & mesh )

overridevirtual

Check if nodes and elements of VTK mesh is compatible with mesh.

to all nodes of VTK mesh must exists one and only one nodes in second mesh
the same must occur for elements
method fill vector bulk_elements_id_
it is necessary to call this method before calling get_element_data

OBSOLETE method - will be replace with Mesh::check_compatible_mesh after merge fields!

Implements BaseMeshReader.

Definition at line 462 of file msh_vtkreader.cc.

bool VtkMeshReader::compare_points	(	const arma::vec3 &	p1,
		const arma::vec3 &	p2
	)

protected

Compare two points representing by armadillo vector.

used in check_compatible_mesh method
calculate with point_tolerance parameter

Definition at line 560 of file msh_vtkreader.cc.

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BaseMeshReader::MeshDataHeader VtkMeshReader::create_header	(	pugi::xml_node	node,
		unsigned int	n_entities,
		Tokenizer::Position	pos,
		OutputTime::DiscreteSpace	disc
	)

protected

Helper method that create DataArray header of given xml node (used from make_header_table)

Definition at line 158 of file msh_vtkreader.cc.

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void VtkMeshReader::create_node_element_caches ( )

protected

create data caches of node and elements DataArray tags

Definition at line 627 of file msh_vtkreader.cc.

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VtkMeshReader::DECLARE_EXCEPTION	(	ExcInvalidFormat	,
		<< "Invalid format of DataArray "<< EI_FieldName::val<< "	,
		expected"<< EI_ExpectedFormat::val<< "\n"<< "in the input file:"<< EI_VTKFile::qval
	)

VtkMeshReader::DECLARE_EXCEPTION	(	ExcUnknownFormat	,
		<< "Unsupported or missing format of DataArray "<< EI_FieldName::val<< "\n"<< "in the input file: "<< EI_VTKFile::qval
	)

VtkMeshReader::DECLARE_EXCEPTION	(	ExcWrongType	,
		<< EI_ErrMessage::val<< " data type of "<< EI_SectionTypeName::val<< "\n"<< "in the input file: "<< EI_VTKFile::qval
	)

VtkMeshReader::DECLARE_EXCEPTION	(	ExcIncompatibleMesh	,
		<< "Incompatible	meshes,
		"<< EI_ErrMessage::val<< "\n"<< "for VTK input file:"<< EI_VTKFile::qval
	)

VtkMeshReader::DECLARE_EXCEPTION	(	ExcMissingTag	,
		<< "Missing "<< EI_TagType::val<< " "<< EI_TagName::val<< "\n"<< " in the input file: "<< EI_VTKFile::qval
	)

VtkMeshReader::DECLARE_EXCEPTION	(	ExcInvalidDofHandler	,
		<< "Invalid DOF handler hash for field: "<< EI_FieldName::qval<< " in the input file: "<< EI_VTKFile::qval<< ".\n"
	)

BaseMeshReader::MeshDataHeader & VtkMeshReader::find_header ( BaseMeshReader::HeaderQuery & header_query )

overridevirtual

Find header of DataArray section of VTK file by field name given by header_query.

Implements BaseMeshReader.

Definition at line 262 of file msh_vtkreader.cc.

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Tokenizer::Position VtkMeshReader::get_appended_position ( )

protected

Get position of AppendedData tag in VTK file.

Definition at line 128 of file msh_vtkreader.cc.

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DataType VtkMeshReader::get_data_type ( std::string type_str )

protected

Get DataType by value of string.

Definition at line 303 of file msh_vtkreader.cc.

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void VtkMeshReader::make_header_table ( )

overrideprotectedvirtual

Reads table of DataArray headers through pugixml interface.

Implements BaseMeshReader.

Definition at line 205 of file msh_vtkreader.cc.

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void VtkMeshReader::parse_ascii_data	(	ElementDataCacheBase &	data_cache,
		unsigned int	n_components,
		unsigned int	n_entities,
		Tokenizer::Position	pos,
		bool	boundary_domain
	)

protected

Parse ascii data to data cache.

Definition at line 373 of file msh_vtkreader.cc.

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void VtkMeshReader::parse_binary_data	(	ElementDataCacheBase &	data_cache,
		unsigned int	n_components,
		unsigned int	n_entities,
		Tokenizer::Position	pos,
		bool	boundary_domain,
		DataType	value_type
	)

protected

Parse binary data to data cache.

Definition at line 392 of file msh_vtkreader.cc.

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void VtkMeshReader::parse_compressed_data	(	ElementDataCacheBase &	data_cache,
		unsigned int	n_components,
		unsigned int	n_entities,
		Tokenizer::Position	pos,
		bool	boundary_domain,
		DataType	value_type
	)

protected

Uncompress and parse binary compressed data to data cache.

Definition at line 407 of file msh_vtkreader.cc.

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void VtkMeshReader::read_base_vtk_attributes	(	pugi::xml_node	vtk_node,
		unsigned int &	n_nodes,
		unsigned int &	n_elements
	)

protected

Set base attributes of VTK and get count of nodes and elements.

Definition at line 97 of file msh_vtkreader.cc.

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void VtkMeshReader::read_element_data	(	ElementDataCacheBase &	data_cache,
		MeshDataHeader	actual_header,
		unsigned int	n_components,
		bool	boundary_domain
	)

overrideprotectedvirtual

Implements BaseMeshReader::read_element_data.

Implements BaseMeshReader.

Definition at line 340 of file msh_vtkreader.cc.

void VtkMeshReader::read_elements ( Mesh * mesh )

protectedvirtual

Method for reading of elements. Input of the mesh allows changing regions within the input file.

Implements BaseMeshReader.

Definition at line 594 of file msh_vtkreader.cc.

void VtkMeshReader::read_nodes ( Mesh * mesh )

protectedvirtual

private method for reading of nodes

Implements BaseMeshReader.

Definition at line 572 of file msh_vtkreader.cc.

void VtkMeshReader::read_physical_names ( Mesh * mesh )

overridevirtual

Read regions from the VTK file and save the physical sections as regions in the RegionDB.

Region Labels starting with '!' are treated as boundary regions. Elements of these regions are used just to assign regions to the boundary and are not used in actual FEM computations.

Implements BaseMeshReader.

Definition at line 567 of file msh_vtkreader.cc.

unsigned int VtkMeshReader::type_value_size ( DataType data_type )

protected

Return size of value of data_type.

Definition at line 331 of file msh_vtkreader.cc.

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VtkMeshReader::TYPEDEF_ERR_INFO	(	EI_VTKFile	,
		std::string
	)

VtkMeshReader::TYPEDEF_ERR_INFO	(	EI_ExpectedFormat	,
		std::string
	)

VtkMeshReader::TYPEDEF_ERR_INFO	(	EI_ErrMessage	,
		std::string
	)

VtkMeshReader::TYPEDEF_ERR_INFO	(	EI_SectionTypeName	,
		std::string
	)

VtkMeshReader::TYPEDEF_ERR_INFO	(	EI_TagType	,
		std::string
	)

VtkMeshReader::TYPEDEF_ERR_INFO	(	EI_TagName	,
		std::string
	)

Friends And Related Function Documentation

friend class PvdMeshReader

friend

Definition at line 41 of file msh_vtkreader.hh.

Member Data Documentation

DataFormat VtkMeshReader::data_format_

protected

variants of data format (ascii, appended, compressed appended)

Definition at line 191 of file msh_vtkreader.hh.

std::istream* VtkMeshReader::data_stream_

protected

input stream allow read appended data, used only if this tag exists

Definition at line 197 of file msh_vtkreader.hh.

HeaderTable VtkMeshReader::header_table_

protected

Table with data of DataArray headers.

Definition at line 194 of file msh_vtkreader.hh.

DataType VtkMeshReader::header_type_

protected

header type of VTK file (only for appended data)

Definition at line 188 of file msh_vtkreader.hh.

unsigned int VtkMeshReader::n_read_

protected

store count of read entities

Definition at line 200 of file msh_vtkreader.hh.

const double VtkMeshReader::point_tolerance = 1E-10

staticprotected

Tolerance during comparison point data with GMSH nodes.

Definition at line 185 of file msh_vtkreader.hh.

double VtkMeshReader::time_step_

protected

time of VTK file (getting only during initialization from PVD reader)

Definition at line 203 of file msh_vtkreader.hh.

The documentation for this class was generated from the following files:

/opt/flow123d/flow123d/src/io/msh_vtkreader.hh
/opt/flow123d/flow123d/src/io/msh_vtkreader.cc

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation