Flow123d  release_3.0.0-955-g4db4b48
Public Types | Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Static Protected Attributes | Friends | List of all members
VtkMeshReader Class Reference

#include <msh_vtkreader.hh>

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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
 
MeshDataHeaderfind_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, MeshDataHeaderHeaderTable
 
- Protected Types inherited from BaseMeshReader
typedef std::shared_ptr< ElementDataCacheBaseElementDataPtr
 
typedef std::map< string, ElementDataPtrElementDataFieldMap
 

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< ElementDataFieldMapelement_data_values_
 Cache with last read element data. More...
 
Tokenizer tok_
 Tokenizer used for reading ASCII file format. More...
 
vector< LongIdxbulk_elements_id_
 
vector< LongIdxboundary_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< BaseMeshReaderreader_factory (const FilePath &file_name)
 
static Meshmesh_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

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.

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: