msh_vtkreader.hh

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/*!
 *
 * Copyright (C) 2015 Technical University of Liberec.  All rights reserved.
 *
 * This program is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License version 3 as published by the
 * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
 *
 * This program is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 *
 *
 * @file    msh_vtkreader.hh
 * @brief
 * @author  dalibor
 */

#ifndef MSH_VTK_READER_HH
#define MSH_VTK_READER_HH

#include <string>
#include <istream>
#include <pugixml.hpp>

#include "io/msh_basereader.hh"
#include "system/file_path.hh"


class PvdMeshReader;


class VtkMeshReader : public BaseMeshReader {
    friend class PvdMeshReader;

public:
    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");

    /// Possible data sections in UnstructuredGrid - Piece node.
    enum DataSections {
        points, cells, cell_data
    };

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

    /**
     * Construct the VTK format reader from given FilePath.
     * This opens the file for reading.
     */
    VtkMeshReader(const FilePath &file_name);

    /// Destructor
    virtual ~VtkMeshReader();

    /**
     * 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.
     */
    void read_physical_names(Mesh * mesh) override;

    /**
     * Check if nodes and elements of VTK mesh is compatible with \p 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 \p bulk_elements_id_
     *  - it is necessary to call this method before calling \p get_element_data
     */
    void check_compatible_mesh(Mesh &mesh) override;

    /**
     * Find header of DataArray section of VTK file by field name given by header_query.
     */
    MeshDataHeader & find_header(HeaderQuery &header_query) override;

protected:
    /**
     * Map of DataArray sections in VTK file.
     *
     * For each field_name contains MeshDataHeader.
     */
    typedef typename std::multimap< std::string, MeshDataHeader > HeaderTable;

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

    /**
     * private method for reading of nodes
     */
    void read_nodes(Mesh * mesh);

    /**
     * Method for reading of elements.
     * Input of the mesh allows changing regions within the input file.
     */
    void read_elements(Mesh * mesh);

    /**
     * create data caches of node and elements DataArray tags
     */
    void create_node_element_caches();

    /// Reads table of DataArray headers through pugixml interface
    void make_header_table() override;

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

    /// Get DataType by value of string
    DataType get_data_type(std::string type_str);

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

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

    /// Parse binary data to data cache
    void parse_binary_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
    void parse_compressed_data(ElementDataCacheBase &data_cache, unsigned int n_components, unsigned int n_entities,
            Tokenizer::Position pos, bool boundary_domain, DataType value_type);

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

    /// Get position of AppendedData tag in VTK file
    Tokenizer::Position get_appended_position();

    /**
     * Implements @p BaseMeshReader::read_element_data.
     */
    void read_element_data(ElementDataCacheBase &data_cache, MeshDataHeader actual_header, unsigned int n_components,
            bool boundary_domain) override;

    /**
     * Compare two points representing by armadillo vector.
     *
     *  - used in \p check_compatible_mesh method
     *  - calculate with \p point_tolerance parameter
     */
    bool compare_points(arma::vec3 &p1, arma::vec3 &p2);

    /// Tolerance during comparison point data with GMSH nodes.
    static const double point_tolerance;

    /// header type of VTK file (only for appended data)
    DataType header_type_;

    /// variants of data format (ascii, appended, compressed appended)
    DataFormat data_format_;

    /// Table with data of DataArray headers
    HeaderTable header_table_;

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

    /// store count of read entities
    unsigned int n_read_;

    /// time of VTK file (getting only during initialization from PVD reader)
    double time_step_;
};

#endif  /* MSH_VTK_READER_HH */