msh_basereader.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_basereader.hh
 * @brief
 * @author  dalibor
 */
 
#ifndef MSH_BASE_READER_HH
#define MSH_BASE_READER_HH
 
 
 
#include <map>                       // for map, map<>::value_compare
#include <memory>                    // for shared_ptr
#include <string>                    // for string
#include <vector>                    // for vector
#include "input/accessors.hh"        // for Record
#include "input/input_exception.hh"  // for DECLARE_INPUT_EXCEPTION, Exception
#include "io/element_data_cache.hh"  // for ElementDataCache
#include "io/output_time.hh"
#include "mesh/partitioning.hh"
#include "system/index_types.hh"
#include "system/exceptions.hh"      // for ExcStream, operator<<, EI, TYPED...
#include "system/file_path.hh"       // for FilePath
#include "system/tokenizer.hh"       // for Tokenizer, Tokenizer::Position
 
class ElementDataCacheBase;
class Mesh;
class ReaderCache;
 
 
 
/// Types of VTK data (value 'undefined' for empty value)
enum DataType {
    int8, uint8, int16, uint16, int32, uint32, int64, uint64, float32, float64, undefined
};
 
 
 
/**
 * Abstract parent of mesh readers.
 *
 * Supported are:
 *  - GMSH reader (class GmshMeshReader)
 *  - VTK reader (class VtkMeshReader)
 */
class BaseMeshReader {
public:
    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);
  DECLARE_EXCEPTION(ExcWrongComponentsCount,
            << "Wrong number of components of field " << EI_FieldName::qval
      << " at time " << EI_Time::val
      << " in the input file: " << EI_MeshFile::qval);
 
 
    /***********************************
     * Structure to store the information from a header of \\$ElementData (GMSH file) or DataArray (VTK file) section.
     *
     * Format of GMSH ASCII data sections
     *
       number-of-string-tags (== 2)
         field_name
         interpolation_scheme_name
       number-of-real-tags (==1)
         time_of_dataset
       number-of-integer-tags
         time_step_index (starting from zero)
         number_of_field_components (1, 3, or 9 - i.e. 3d scalar, vector or tensor data)
         number_of entities (nodes or elements)
         partition_index (0 == no partition, not clear if GMSH support reading different partition from different files)
       elm-number value ...
    *
    */
    struct MeshDataHeader {
        /// Set field_name value to empty string, that signs invalid header (using after reading data)
        void reset() { field_name = ""; }
        /// Name of field
        std::string field_name;
        /// Currently d'ont used
        std::string interpolation_scheme;
        /// Time of field data (used only for GMSH reader)
        double time;
        /// Currently d'ont used
        unsigned int time_index;
        /// Number of values on one row
        unsigned int n_components;
        /// Number of rows
        unsigned int n_entities;
        /// Currently d'ont used
        unsigned int partition_index;
        /// Position of data in mesh file
        Tokenizer::Position position;
        /// Type of data (used only for VTK reader)
        DataType type;
        /// Flag marks input discretization of data of VTK file
        OutputTime::DiscreteSpace discretization;
        /// Hash of DOF handler object (only for native data of VTK file)
        std::size_t dof_handler_hash;
    };
 
    /**
     * Store base data that allows search mesh data header.
     *
     * Data members discretization and dof_handler_hash are specific for VTK files.
     */
    struct HeaderQuery {
        /// Constructor
        HeaderQuery(std::string name, double t, OutputTime::DiscreteSpace disc, std::size_t hash=0)
        : field_name(name), time(t), discretization(disc), dof_handler_hash(hash) {};
 
        std::string field_name;                   ///< Name of field
        double time;                              ///< Time of field data (used only for GMSH and PVD reader)
        OutputTime::DiscreteSpace discretization; ///< Flag determinate type of discrete of Field (typically is used for native data of VTK)
        std::size_t dof_handler_hash;             ///< Hash of DOF handler object
    };
 
    /// Constructor
    BaseMeshReader(const FilePath &file_name);
 
    /**
     * This static method gets file path object of reader,
     * dispatch to correct constructor and initialize appropriate function object from the input.
     * Returns shared pointer to BaseMeshReader.
     */
    static std::shared_ptr< BaseMeshReader > reader_factory(const FilePath &file_name);
 
    /**
     * This static method gets accessor to record with function input,
     * dispatch to correct constructor and initialize appropriate function object from the input.
     * Allow to make optimization of elements and nodes order if flag optimize_mesh is set
     * Returns pointer to Mesh.
     */
    static Mesh * mesh_factory(const Input::Record &input_mesh_rec);
 
    /**
     * Reads @p raw data of mesh (only nodes and elements) from the GMSH or VTKfile.
     * Input of the mesh allows changing regions within the input file.
     *
     */
    void read_raw_mesh(Mesh * mesh);
 
    /**
     * Read regions from the mesh file and save the physical sections as regions in the RegionDB.
     */
    virtual void read_physical_names(Mesh * mesh)=0;
 
    /**
     *  Reads ElementData sections of opened mesh file. Method must be call after \p set_data_header method. If such section
     *  has not been yet read, we read the data section into raw buffer @p data. The buffer must have size at least
     *  @p n_components * @p n_entities. Indexes in the map must be smaller then @p n_entities.
     *
     *  Possible optimizations:
     *  If the map ID lookup seem slow, we may assume that IDs are in increasing order, use simple array of IDs instead of map
     *  and just check that they comes in in correct order.
     *
     *  @param n_entities count of entities (elements)
     *  @param n_components count of components (size of returned data is given by n_entities*n_components)
     *  @param boundary_domain flag determines that data is read for boundary or bulk elements
     *  @param component_idx component index of MultiField; 0 for single component fields.
     */
    template<typename T>
    typename ElementDataCache<T>::CacheData get_element_data(
            MeshDataHeader header, unsigned int expected_n_entities,
            unsigned int expected_n_components, bool boundary_domain);
 
    /**
     * Set ID vectors from a different mesh.
     * Must be set in order to determine for which IDs the GMSH reader should read the data.
     * Could possibly read just a subset.
     */
    void set_element_ids(const Mesh &mesh);
 
    /**
     * Returns vector of boundary or bulk element IDs to read.
     * Used by GMSH reader only.
     */
    std::vector<int> const & get_element_ids(bool boundary_domain);
 
    /**
     * Find data header for time and field given by header_query.
     */
    virtual MeshDataHeader & find_header(HeaderQuery &header_query)=0;
 
    /**
     * Scale and check data stored in ElementDataCache of given field.
     */
    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:
    typedef std::shared_ptr<ElementDataCacheBase> ElementDataPtr;
    typedef std::map< string, ElementDataPtr > ElementDataFieldMap;
 
    /// Constructor
    BaseMeshReader(const FilePath &file_name, std::shared_ptr<ElementDataFieldMap> element_data_values);
 
 
    /**
     * private method for reading of nodes
     */
    virtual void read_nodes(Mesh * mesh)=0;
 
    /**
     * Method for reading of elements.
     */
    virtual void read_elements(Mesh * mesh)=0;
 
    /**
     * Reads table of data headers specific for each descendants.
     */
    virtual void make_header_table()=0;
 
    /**
     * Read element data to data cache
     */
    virtual void read_element_data(ElementDataCacheBase &data_cache, MeshDataHeader header,
            bool boundary_domain)=0;
 
    /**
     * Flag stores that check of compatible mesh was performed.
     *
     * This flag has effect only for VTK reader.
     */
    bool has_compatible_mesh_;
 
    /// Store name of field data section specify for type of mesh file.
    std::string data_section_name_;
 
    /// Cache with last read element data
    std::shared_ptr<ElementDataFieldMap> element_data_values_;
 
    /// Tokenizer used for reading ASCII file format.
    Tokenizer tok_;
 
    /// Vector of both bulk and boundary IDs. Bulk elements come first, then boundary elements, but only the portion that appears
    /// in input mesh file and has ID assigned.
    /// If set through set_element_ids, the GMSH reader only reads given IDs and check that all IDs are read.
    vector<LongIdx> bulk_elements_id_, boundary_elements_id_;
 
    friend class ReaderCache;
};
 
#endif  /* MSH_BASE_READER_HH */