output_vtk.cc

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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    output_vtk.cc
 * @brief   The functions for outputs to VTK files.
 */
 
#include "output_vtk.hh"
#include "element_data_cache_base.hh"
#include "element_data_cache.hh"
#include "output_mesh.hh"
#include "mesh/mesh.h"
 
#include <limits.h>
#include "input/factory.hh"
#include "input/accessors_forward.hh"
#include "system/file_path.hh"
#include "tools/time_governor.hh"
#include "la/distribution.hh"
 
#include "config.h"
 
FLOW123D_FORCE_LINK_IN_CHILD(vtk)
 
 
using namespace Input::Type;
 
const Record & OutputVTK::get_input_type() {
    return Record("vtk", "Parameters of vtk output format.")
        // It is derived from abstract class
        .derive_from(OutputTime::get_input_format_type())
        .declare_key("variant", OutputVTK::get_input_type_variant(), Default("\"ascii\""),
            "Variant of output stream file format.")
        // The parallel or serial variant
        .declare_key("parallel", Bool(), Default("false"),
            "Parallel or serial version of file format.")
        .close();
}
 
 
const Selection & OutputVTK::get_input_type_variant() {
    return Selection("VTK variant (ascii or binary)")
        .add_value(OutputVTK::VARIANT_ASCII, "ascii",
            "ASCII variant of VTK file format")
        .add_value(OutputVTK::VARIANT_BINARY_UNCOMPRESSED, "binary",
            "Uncompressed appended binary XML VTK format without usage of base64 encoding of appended data.")
#ifdef FLOW123D_HAVE_ZLIB
        .add_value(OutputVTK::VARIANT_BINARY_ZLIB, "binary_zlib",
            "Appended binary XML VTK format without usage of base64 encoding of appended data. Compressed with ZLib.")
#endif // FLOW123D_HAVE_ZLIB
        .close();
}
 
 
const int OutputVTK::registrar = Input::register_class< OutputVTK >("vtk") +
        OutputVTK::get_input_type().size();
 
 
const std::vector<std::string> OutputVTK::formats = { "ascii", "appended", "appended" };
 
 
 
OutputVTK::OutputVTK()
{
    this->enable_refinement_ = true;
}
 
 
 
OutputVTK::~OutputVTK()
{
    // Perform output of last time step
    this->write_time_frame();
 
    this->write_tail();
}
 
 
 
void OutputVTK::init_from_input(const std::string &equation_name,
                                const Input::Record &in_rec,
                                const std::shared_ptr<TimeUnitConversion>& time_unit_conv)
{
    OutputTime::init_from_input(equation_name, in_rec, time_unit_conv);
 
    auto format_rec = (Input::Record)(input_record_.val<Input::AbstractRecord>("format"));
    variant_type_ = format_rec.val<VTKVariant>("variant");
    this->parallel_ = format_rec.val<bool>("parallel");
    this->fix_main_file_extension(".pvd");
 
    if(this->rank_ == 0) {
        try {
            this->_base_filename.open_stream( this->_base_file );
            this->set_stream_precision(this->_base_file);
        } INPUT_CATCH(FilePath::ExcFileOpen, FilePath::EI_Address_String, input_record_)
 
        LogOut() << "Writing flow output file: " << this->_base_filename << " ... ";
    }
 
    this->make_subdirectory();
    this->write_head();
 
}
 
string OutputVTK::form_vtu_filename_(string basename, int i_step, int rank) {
    ostringstream ss;
    if (this->parallel_) {
        // parallel file
        ss << basename << "/" << basename << "-"
           << std::setw(6) << std::setfill('0') << i_step << "." << rank << ".vtu";
    } else {
        // serial file
        ss << basename << "/" << basename << "-"
           << std::setw(6) << std::setfill('0') << i_step << ".vtu";
    }
    return ss.str();
}
 
string pvd_dataset_line(double step, int rank, string file) {
    ostringstream ss;
    ss
        << "<DataSet timestep=\"" << step
        << "\" group=\"\" part=\"" << rank
        << "\" file=\"" << file
        << "\"/>\n";
    return ss.str();
}
 
int OutputVTK::write_data(void)
{
    ASSERT_PTR(this->nodes_).error();
 
    /* Output of serial format is implemented only in the first process */
    if ( (this->rank_ != 0) && (!parallel_) ) {
        return 0;
    }
 
    /**
     * TODO:
     * - common creation of the VTU filename
     * - names of parallel file: <base name>_<frame>.<rank>.vtu
     * - for serial case use rank=0
     */
 
    /* Write DataSets to the PVD file only in the first process */
    if (this->rank_ == 0) {
        ASSERT(this->_base_file.is_open())(this->_base_filename).error();
 
        /* Set floating point precision to max */
        //this->_base_file.precision(std::numeric_limits<double>::digits10);
        //int current_step = this->get_parallel_current_step();
 
        /* Write dataset lines to the PVD file. */
        double corrected_time = (isfinite(this->registered_time_)?this->registered_time_:0);
        corrected_time /= this->time_unit_converter->get_coef();
        if (parallel_) {
            for (int i_rank=0; i_rank<n_proc_; ++i_rank) {
                string file = this->form_vtu_filename_(main_output_basename_, current_step, i_rank);
                this->_base_file << pvd_dataset_line(corrected_time, i_rank, file);
            }
        } else {
            string file = this->form_vtu_filename_(main_output_basename_, current_step, -1);
            this->_base_file << pvd_dataset_line(corrected_time, 0, file);
        }
    }
 
    /* write VTU file */
    {
        /* Open VTU file */
        std::string frame_file_name = this->form_vtu_filename_(main_output_basename_, current_step, this->rank_);
        FilePath frame_file_path({main_output_dir_, frame_file_name}, FilePath::output_file);
        try {
            frame_file_path.open_stream(_data_file);
            this->set_stream_precision(_data_file);
        } INPUT_CATCH(FilePath::ExcFileOpen, FilePath::EI_Address_String, input_record_)
 
        LogOut() << __func__ << ": Writing output (frame: " << this->current_step
                 << ", rank: " << this->rank_
                 << ") file: " << frame_file_name << " ... ";
 
        this->write_vtk_vtu();
 
        /* Close stream for file of current frame */
        _data_file.close();
        //delete data_file;
        //this->_data_file = NULL;
 
        LogOut() << "O.K.";
 
    }
 
    return 1;
}
 
 
 
 
void OutputVTK::make_subdirectory()
{
    ASSERT_EQ(this->_base_filename.extension(), ".pvd").error();
    main_output_dir_ = this->_base_filename.parent_path();
    main_output_basename_ = this->_base_filename.stem();
 
    if(this->rank_ == 0) {
        vector<string> sub_path = { main_output_dir_, main_output_basename_, "__tmp__" };
        FilePath fp(sub_path, FilePath::output_file);
        fp.create_output_dir();
    }
}
 
 
 
 
void OutputVTK::write_vtk_vtu_head(void)
{
    ofstream &file = this->_data_file;
 
    file << "<?xml version=\"1.0\"?>" << endl;
    // TODO: test endianess of platform (this would be important, when raw
    // data will be saved to the VTK file)
    file << "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\"";
    if ( this->variant_type_ != VTKVariant::VARIANT_ASCII ) {
        file << " header_type=\"UInt64\"";
    }
    if ( this->variant_type_ == VTKVariant::VARIANT_BINARY_ZLIB ) {
        file << " compressor=\"vtkZLibDataCompressor\"";
    }
    file << ">" << endl;
    file << "<UnstructuredGrid>" << endl;
}
 
 
 
std::shared_ptr<ElementDataCache<unsigned int>> OutputVTK::fill_element_types_data()
{    
    auto &offsets = *( this->offsets_->get_component_data(0).get() );
    unsigned int n_elements = offsets.size()-1;
    
    auto types = std::make_shared<ElementDataCache<unsigned int>>("types", (unsigned int)ElementDataCacheBase::N_SCALAR, n_elements);
    std::vector< unsigned int >& data = *( types->get_component_data(0).get() );
    int n_nodes;
    
    for(unsigned int i=0; i < n_elements; i++)
    {
        n_nodes = offsets[i+1]-offsets[i];
        switch(n_nodes) {
        case 2:
            data[i] = (unsigned int)VTK_LINE;
            break;
        case 3:
            data[i] = (unsigned int)VTK_TRIANGLE;
            break;
        case 4:
            data[i] = (unsigned int)VTK_TETRA;
            break;
        }
    }
 
    return types;
}
 
 
 
void OutputVTK::write_vtk_data(OutputTime::OutputDataPtr output_data, unsigned int start)
{
    // names of types in DataArray section
    static const std::vector<std::string> types = {
        "Int8", "UInt8", "Int16", "UInt16", "Int32", "UInt32", "Float32", "Float64" };
 
    ofstream &file = this->_data_file;
 
    file    << "<DataArray type=\"" << types[output_data->vtk_type()] << "\" ";
    // possibly write name
    if( ! output_data->field_input_name().empty())
        file << "Name=\"" << output_data->field_input_name() <<"\" ";
    // write number of components
    if (output_data->n_comp() > 1)
    {
        file
            << "NumberOfComponents=\"" << output_data->n_comp() << "\" ";
    }
    file    << "format=\"" << formats[this->variant_type_] << "\"";
 
    if ( this->variant_type_ == VTKVariant::VARIANT_ASCII ) {
        // ascii output
        file << ">" << endl;
        //file << std::fixed << std::setprecision(10); // Set precision to max
        output_data->print_ascii_all(file, start);
        file << "\n</DataArray>" << endl;
    } else {
        // binary output is stored to appended_data_ stream
        double range_min, range_max;
        output_data->get_min_max_range(range_min, range_max);
        file    << " offset=\"" << appended_data_.tellp() << "\" ";
        file    << "RangeMin=\"" << range_min << "\" RangeMax=\"" << range_max << "\"/>" << endl;
        if ( this->variant_type_ == VTKVariant::VARIANT_BINARY_UNCOMPRESSED ) {
            output_data->print_binary_all( appended_data_, true, start );
        } else { // ZLib compression
            stringstream uncompressed_data, compressed_data;
            output_data->print_binary_all( uncompressed_data, false, start );
            this->compress_data(uncompressed_data, compressed_data);
            appended_data_ << compressed_data.str();
        }
    }
 
}
 
 
void OutputVTK::compress_data(stringstream &uncompressed_stream, stringstream &compressed_stream) {
    // size of block of compressed data.
    static const size_t BUF_SIZE = 32 * 1024;
 
    string uncompressed_string = uncompressed_stream.str();  // full uncompressed string
    zlib_ulong uncompressed_size = uncompressed_string.size();    // size of uncompressed string
    stringstream compressed_data;                            // helper stream stores blocks of compress data
 
    zlib_ulong count_of_blocks = (uncompressed_size + BUF_SIZE - 1) / BUF_SIZE;
    zlib_ulong last_block_size = (uncompressed_size % BUF_SIZE);
    compressed_stream.write(reinterpret_cast<const char*>(&count_of_blocks), sizeof(unsigned long long int));
    compressed_stream.write(reinterpret_cast<const char*>(&BUF_SIZE), sizeof(unsigned long long int));
    compressed_stream.write(reinterpret_cast<const char*>(&last_block_size), sizeof(unsigned long long int));
 
    for (zlib_ulong i=0; i<count_of_blocks; ++i) {
        // get block of data for compression
        std::string data_block = uncompressed_string.substr(i*BUF_SIZE, BUF_SIZE);
        zlib_ulong data_block_size = data_block.size();
 
        std::vector<uint8_t> buffer;
        uint8_t temp_buffer[BUF_SIZE];
 
        // set zlib object
        z_stream strm;
        strm.zalloc = 0;
        strm.zfree = 0;
        strm.next_in = reinterpret_cast<uint8_t *>(&data_block[0]);
        strm.avail_in = data_block_size;
        strm.next_out = temp_buffer;
        strm.avail_out = BUF_SIZE;
 
        // compression of data
        deflateInit(&strm, Z_BEST_COMPRESSION);
        while (strm.avail_in != 0) {
            int res = deflate(&strm, Z_NO_FLUSH);
            ASSERT_EQ(res, Z_OK).error();
            if (strm.avail_out == 0) {
                buffer.insert(buffer.end(), temp_buffer, temp_buffer + BUF_SIZE);
                strm.next_out = temp_buffer;
                strm.avail_out = BUF_SIZE;
            }
        }
        int deflate_res = Z_OK;
        while (deflate_res == Z_OK) {
            if (strm.avail_out == 0) {
                buffer.insert(buffer.end(), temp_buffer, temp_buffer + BUF_SIZE);
                strm.next_out = temp_buffer;
                strm.avail_out = BUF_SIZE;
            }
            deflate_res = deflate(&strm, Z_FINISH);
        }
        ASSERT_EQ(deflate_res, Z_STREAM_END).error();
        buffer.insert(buffer.end(), temp_buffer, temp_buffer + BUF_SIZE - strm.avail_out);
        deflateEnd(&strm);
 
        // store compress data and its size to streams
        std::string str(buffer.begin(), buffer.end());
        zlib_ulong compressed_data_size = str.size();
        compressed_stream.write(reinterpret_cast<const char*>(&compressed_data_size), sizeof(unsigned long long int));
        compressed_data << str;
    }
    // push compress data to returned stream
    compressed_stream << compressed_data.str();
}
 
 
void OutputVTK::write_vtk_field_data(OutputDataFieldVec &output_data_vec)
{
    for(OutputDataPtr data :  output_data_vec)
        if( ! data->is_dummy())
            write_vtk_data(data);
}
 
 
 
 
void OutputVTK::write_vtk_data_names(ofstream &file,
        OutputDataFieldVec &output_data_vec)
{
    if (output_data_vec.empty()) return;
 
    file << "Scalars=\"";
    for(OutputDataPtr data :  output_data_vec )
        if (data->n_comp() == ElementDataCacheBase::N_SCALAR
            && ! data->is_dummy())
                file << data->field_input_name() << ",";
    file << "\" ";
 
    file << "Vectors=\"";
    for(OutputDataPtr data :  output_data_vec )
        if (data->n_comp() == ElementDataCacheBase::N_VECTOR
            && ! data->is_dummy())
                file << data->field_input_name() << ",";
    file << "\" ";
 
    file << "Tensors=\"";
    for(OutputDataPtr data :  output_data_vec )
        if (data->n_comp() == ElementDataCacheBase::N_TENSOR
            && ! data->is_dummy())
                file << data->field_input_name() << ",";
    file << "\"";
}
 
 
void OutputVTK::write_vtk_node_data(void)
{
    ofstream &file = this->_data_file;
 
    // merge node and corner data
    OutputDataFieldVec node_corner_data(output_data_vec_[NODE_DATA]);
    node_corner_data.insert(node_corner_data.end(),
            output_data_vec_[CORNER_DATA].begin(), output_data_vec_[CORNER_DATA].end());
 
    if( ! node_corner_data.empty() ) {
        /* Write <PointData begin */
        file << "<PointData ";
        write_vtk_data_names(file, node_corner_data);
        file << ">" << endl;
 
        /* Write data on nodes */
        this->write_vtk_field_data(output_data_vec_[NODE_DATA]);
 
        /* Write data in corners of elements */
        this->write_vtk_field_data(output_data_vec_[CORNER_DATA]);
 
        /* Write PointData end */
        file << "</PointData>" << endl;
    }
}
 
 
void OutputVTK::write_vtk_element_data(void)
{
    ofstream &file = this->_data_file;
 
    auto &data_map = this->output_data_vec_[ELEM_DATA];
    if (data_map.empty()) return;
 
    /* Write CellData begin */
    file << "<CellData ";
    write_vtk_data_names(file, data_map);
    file << ">" << endl;
 
    /* Write own data */
    this->write_vtk_field_data(data_map);
 
    /* Write PointData end */
    file << "</CellData>" << endl;
}
 
 
void OutputVTK::write_vtk_native_data(void)
{
    ofstream &file = this->_data_file;
 
    auto &data_map = this->output_data_vec_[NATIVE_DATA];
    if (data_map.empty()) return;
 
    /* Write Flow123dData begin */
    file << "<Flow123dData ";
    write_vtk_data_names(file, data_map);
    file << ">" << endl;
 
    /* Write own data */
    for(OutputDataPtr output_data : data_map) {
        file  << "<DataArray type=\"Float64\" ";
        file  << "Name=\"" << output_data->field_input_name() <<"\" ";
        file  << "format=\"" << formats[this->variant_type_] << "\" ";
        file  << "dof_handler_hash=\"" << output_data->dof_handler_hash() << "\" ";
        file  << "n_dofs_per_element=\"" << output_data->n_dofs_per_element() << "\"";
        //file  << " fe_type=\"" << output_data->fe_type() << "\"";
 
        if ( this->variant_type_ == VTKVariant::VARIANT_ASCII ) {
            // ascii output
            file << ">" << endl;
            //file << std::fixed << std::setprecision(10); // Set precision to max
            output_data->print_ascii_all(file);
            file << "\n</DataArray>" << endl;
        } else {
            // binary output is stored to appended_data_ stream
            double range_min, range_max;
            output_data->get_min_max_range(range_min, range_max);
            file    << " offset=\"" << appended_data_.tellp() << "\" ";
            file    << "RangeMin=\"" << range_min << "\" RangeMax=\"" << range_max << "\"/>" << endl;
            if ( this->variant_type_ == VTKVariant::VARIANT_BINARY_UNCOMPRESSED ) {
                output_data->print_binary_all( appended_data_ );
            } else { // ZLib compression
                stringstream uncompressed_data, compressed_data;
                output_data->print_binary_all( uncompressed_data, false );
                this->compress_data(uncompressed_data, compressed_data);
                appended_data_ << compressed_data.str();
            }
        }
    }
 
    /* Write Flow123dData end */
    file << "</Flow123dData>" << endl;
}
 
 
void OutputVTK::write_vtk_vtu_tail(void)
{
    ofstream &file = this->_data_file;
 
    file << "</UnstructuredGrid>" << endl;
    if ( this->variant_type_ != VTKVariant::VARIANT_ASCII ) {
        // appended data of binary compressed output
        file << "<AppendedData encoding=\"raw\">" << endl;
        // appended data starts with '_' character
        file << "_" << appended_data_.str() << endl;
        file << "</AppendedData>" << endl;
    }
    file << "</VTKFile>" << endl;
}
 
 
void OutputVTK::write_vtk_vtu(void)
{
    ofstream &file = this->_data_file;
 
    /* Write header */
    this->write_vtk_vtu_head();
 
    /* Write Piece begin */
    file << "<Piece NumberOfPoints=\"" << this->nodes_->n_values()
              << "\" NumberOfCells=\"" << this->offsets_->n_values()-1 <<"\">" << endl;
 
    /* Write VTK Geometry */
    file << "<Points>" << endl;
        write_vtk_data(this->nodes_);
    file << "</Points>" << endl;
 
    /* Write VTK Topology */
    file << "<Cells>" << endl;
        write_vtk_data(this->connectivity_);
        write_vtk_data(this->offsets_, 1);
        auto types = fill_element_types_data();
        write_vtk_data( types );
    file << "</Cells>" << endl;
 
    /* Write VTK scalar and vector data on nodes to the file */
    this->write_vtk_node_data();
 
    /* Write VTK data on elements */
    this->write_vtk_element_data();
 
    /* Write own VTK native data (skipped by Paraview) */
    this->write_vtk_native_data();
 
    /* Write Piece end */
    file << "</Piece>" << endl;
 
    /* Write tail */
    this->write_vtk_vtu_tail();
}
 
 
 
int OutputVTK::write_head(void)
{
    /* Output to PVD file is implemented only in the first process */
    if(this->rank_ != 0) {
        return 0;
    }
 
    LogOut() << __func__ << ": Writing output file (head) " << this->_base_filename << " ... ";
 
    this->_base_file << "<?xml version=\"1.0\"?>" << endl;
    this->_base_file << "<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\">" << endl;
    this->_base_file << "<Collection>" << endl;
 
    LogOut() << "O.K.";
 
    return 1;
}
 
 
int OutputVTK::write_tail(void)
{
    /* Output to PVD file is implemented only in the first process */
    if(this->rank_ != 0) {
        return 0;
    }
 
    LogOut() << __func__ << ": Writing output file (tail) " << this->_base_filename << " ... ";
 
    this->_base_file << "</Collection>" << endl;
    this->_base_file << "</VTKFile>" << endl;
 
    LogOut() << "O.K.";
 
    return 1;
}