nrn_filehandler.hpp

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/*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================.
*/
 
#pragma once
 
#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <cmath>
#include <sys/stat.h>
 
#include "coreneuron/io/nrnsection_mapping.hpp"
#include "coreneuron/permute/node_permute.h"
#include "coreneuron/sim/multicore.hpp"
#include "coreneuron/utils/nrn_assert.h"
 
namespace coreneuron {
/** Encapsulate low-level reading of coreneuron input data files.
 *
 * Error handling is simple: abort()!
 *
 * Reader will abort() if native integer size is not 4 bytes.
 *
 * All automatic allocations performed by read_int_array()
 * and read_dbl_array() methods use new [].
 */
 
// @todo: remove this static buffer
const int max_line_length = 1024;
 
class FileHandler {
    std::fstream F;                        //!< File stream associated with reader.
    std::ios_base::openmode current_mode;  //!< File open mode (not stored in fstream)
    int chkpnt;                            //!< Current checkpoint number state.
    int stored_chkpnt;                     //!< last "remembered" checkpoint number state.
    /** Read a checkpoint line, bump our chkpnt counter, and assert equality.
     *
     * Checkpoint information is represented by a sequence "checkpt %d\n"
     * where %d is a scanf-compatible representation of the checkpoint
     * integer.
     */
    void read_checkpoint_assert();
 
    // FileHandler is not copyable.
    FileHandler(const FileHandler&) = delete;
    FileHandler& operator=(const FileHandler&) = delete;
 
  public:
    FileHandler()
        : chkpnt(0)
        , stored_chkpnt(0) {}
 
    explicit FileHandler(const std::string& filename);
 
    /** Preserving chkpnt state, move to a new file. */
    void open(const std::string& filename, std::ios::openmode mode = std::ios::in);
 
    /** Is the file not open */
    bool fail() const {
        return F.fail();
    }
 
    static bool file_exist(const std::string& filename);
 
    /** nothing more to read */
    bool eof();
 
    /** Query chkpnt state. */
    int checkpoint() const {
        return chkpnt;
    }
 
    /** Explicitly override chkpnt state. */
    void checkpoint(int c) {
        chkpnt = c;
    }
 
    /** Record current chkpnt state. */
    void record_checkpoint() {
        stored_chkpnt = chkpnt;
    }
 
    /** Restored last recorded chkpnt state. */
    void restore_checkpoint() {
        chkpnt = stored_chkpnt;
    }
 
    /** Parse a single integer entry.
     *
     * Single integer entries are represented by their standard
     * (C locale) text representation, followed by a newline.
     * Extraneous characters following the integer but preceding
     * the newline are ignore.
     */
    int read_int();
 
    /** Parse a neuron mapping count entries
     *
     * Reads neuron mapping info which is represented by
     * gid, #sections, #segments, #section lists
     */
    void read_mapping_count(int* gid, int* nsec, int* nseg, int* nseclist);
 
    /** Reads number of cells in parsing file */
    void read_mapping_cell_count(int* count);
 
    /** Parse a neuron section segment mapping
     *
     * Read count no of mappings for section to segment
     */
    template <typename T>
    int read_mapping_info(T mapinfo,
                          NrnThreadMappingInfo* ntmapping,
                          std::shared_ptr<CellMapping> cmap,
                          const NrnThread& nt) {
        std::string line;
        std::getline(F, line);
 
        std::istringstream iss(line);
        std::string name_str;
        int nsec = 0;
        int nseg = 0;
        size_t total_lfp_factors = 0;
        int offset_count = 0;
        iss >> name_str >> nsec >> nseg >> total_lfp_factors >> offset_count;
        nrn_assert(!iss.fail());
 
        if (offset_count > 0) {
            cmap->electrode_offsets.resize(offset_count);
            for (int k = 0; k < offset_count; k++) {
                iss >> cmap->electrode_offsets[k];
            }
            nrn_assert(!iss.fail());
        }
 
        mapinfo->type = section_type_from_string(name_str);
 
        if (nseg) {
            auto sec = read_vector<int>(nseg);
            auto seg = read_vector<int>(nseg);
 
            if (nt._permute) {
                node_permute(seg.data(), seg.size(), nt._permute);
            }
 
            std::vector<double> lfp_factors;
            if (total_lfp_factors > 0) {
                lfp_factors = read_vector<double>(total_lfp_factors);
            }
 
            for (int i = 0; i < nseg; i++) {
                mapinfo->add_segment(sec[i], seg[i]);
                ntmapping->add_segment_id(seg[i]);
                if (total_lfp_factors > 0) {
                    const auto num_electrodes = cmap->num_electrodes();
                    nrn_assert(count_if(lfp_factors.begin(), lfp_factors.end(), [](double d) {
                                   return std::isnan(d);
                               }) == 0);
                    auto begin = lfp_factors.begin() + i * num_electrodes;
                    cmap->add_segment_lfp_factor(seg[i], begin, begin + num_electrodes);
                }
            }
        }
        return nseg;
    }
 
    /** Defined flag values for parse_array() */
    enum parse_action { read, seek };
 
    /** Generic parse function for an array of fixed length.
     *
     * \tparam T the array element type: may be \c int or \c double.
     * \param p pointer to the target in memory for reading into.
     * \param count number of items of type \a T to parse.
     * \param action whether to validate and skip (\c seek) or
     *    copy array into memory (\c read).
     * \return the supplied pointer value.
     *
     * Error if \a count is non-zero, \a flag is \c read, and
     * the supplied pointer \p is null.
     *
     * Arrays are represented by a checkpoint line followed by
     * the array items in increasing index order, in the native binary
     * representation of the writing process.
     */
    template <typename T>
    inline T* parse_array(T* p, size_t count, parse_action flag) {
        if (count > 0 && flag != seek)
            nrn_assert(p != 0);
 
        read_checkpoint_assert();
        switch (flag) {
        case seek:
            F.seekg(count * sizeof(T), std::ios_base::cur);
            break;
        case read:
            F.read((char*) p, count * sizeof(T));
            break;
        }
 
        nrn_assert(!F.fail());
        return p;
    }
 
    // convenience interfaces:
 
    /** Read an integer array of fixed length. */
    template <typename T>
    inline T* read_array(T* p, size_t count) {
        return parse_array(p, count, read);
    }
 
    /** Allocate and read an integer array of fixed length. */
    template <typename T>
    inline T* read_array(size_t count) {
        return parse_array(new T[count], count, read);
    }
 
    template <typename T>
    inline std::vector<T> read_vector(size_t count) {
        std::vector<T> vec(count);
        parse_array(vec.data(), count, read);
        return vec;
    }
 
    /** Close currently open file. */
    void close();
 
    /** Write an 1D array **/
    template <typename T>
    void write_array(T* p, size_t nb_elements) {
        nrn_assert(F.is_open());
        nrn_assert(current_mode & std::ios::out);
        write_checkpoint();
        F.write((const char*) p, nb_elements * (sizeof(T)));
        nrn_assert(!F.fail());
    }
 
    /** Write a padded array. nb_elements is number of elements to write per line,
     * line_width is full size of a line in nb elements**/
    template <typename T>
    void write_array(T* p,
                     size_t nb_elements,
                     size_t line_width,
                     size_t nb_lines,
                     bool to_transpose = false) {
        nrn_assert(F.is_open());
        nrn_assert(current_mode & std::ios::out);
        write_checkpoint();
        T* temp_cpy = new T[nb_elements * nb_lines];
 
        if (to_transpose) {
            for (size_t i = 0; i < nb_lines; i++) {
                for (size_t j = 0; j < nb_elements; j++) {
                    temp_cpy[i + j * nb_lines] = p[i * line_width + j];
                }
            }
        } else {
            memcpy(temp_cpy, p, nb_elements * sizeof(T) * nb_lines);
        }
        // AoS never use padding, SoA is translated above, so one write
        // operation is enought in both cases
        F.write((const char*) temp_cpy, nb_elements * sizeof(T) * nb_lines);
        nrn_assert(!F.fail());
        delete[] temp_cpy;
    }
 
    template <typename T>
    FileHandler& operator<<(const T& scalar) {
        nrn_assert(F.is_open());
        nrn_assert(current_mode & std::ios::out);
        F << scalar;
        nrn_assert(!F.fail());
        return *this;
    }
 
  private:
    /* write_checkpoint is callable only for our internal uses, making it accesible to user, makes
     * file format unpredictable */
    void write_checkpoint() {
        F << "chkpnt " << chkpnt++ << "\n";
    }
};
}  // namespace coreneuron