mk_mech.cpp

/*
Copyright (c) 2016, Blue Brain Project
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   this list of conditions and the following disclaimer.
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   may be used to endorse or promote products derived from this software
   without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
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*/

#include <string.h>
#include <map>
#include <string>
#include "coreneuron/nrnconf.h"
#include "coreneuron/nrnoc/multicore.h"
#include "coreneuron/nrnoc/membdef.h"
#include "coreneuron/nrnoc/nrnoc_decl.h"
#include "coreneuron/nrniv/nrniv_decl.h"
#include "coreneuron/nrniv/nrn_assert.h"
#include "coreneuron/utils/sdprintf.h"
#include "coreneuron/mech/cfile/cabvars.h"

static char banner[] = "Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015";

namespace coreneuron {
int nrn_nobanner_;

int nrn_need_byteswap;
// following copied (except for nrn_need_byteswap line) from NEURON ivocvect.cpp
#define BYTEHEADER   \
    uint32_t _II__;  \
    char* _IN__;     \
    char _OUT__[16]; \
    int BYTESWAP_FLAG = 0;
#define BYTESWAP(_X__, _TYPE__)                                 \
    BYTESWAP_FLAG = nrn_need_byteswap;                          \
    if (BYTESWAP_FLAG == 1) {                                   \
        _IN__ = (char*)&(_X__);                                 \
        for (_II__ = 0; _II__ < sizeof(_TYPE__); _II__++) {     \
            _OUT__[_II__] = _IN__[sizeof(_TYPE__) - _II__ - 1]; \
        }                                                       \
        (_X__) = *((_TYPE__*)&_OUT__);                          \
    }

std::map<std::string, int> mech2type;

/// Read meta data about the mechanisms and allocate corresponding mechanism management data
/// structures
void mk_mech(const char* datpath) {
    char fnamebuf[1024];
    sd_ptr fname = sdprintf(fnamebuf, sizeof(fnamebuf), "%s/%s", datpath, "bbcore_mech.dat");
    FILE* f;
    f = fopen(fname, "r");

    if (f == NULL) {
        fprintf(stderr, "Error: couldn't find bbcore_mech.dat file in the dataset directory \n");
        fprintf(
            stderr,
            "       Make sure to pass full directory path of dataset using -d DIR or --datpath=DIR \n");
    }

    nrn_assert(f);

    char version[256];
    fscanf(f, "%s\n", version);
    check_bbcore_write_version(version);

    //  printf("reading %s\n", fname);
    int n = 0;
    nrn_assert(fscanf(f, "%d\n", &n) == 1);

    /// Allocate space for mechanism related data structures
    alloc_mech(n);

    /// Read all the mechanisms and their meta data
    for (int i = 2; i < n; ++i) {
        char mname[100];
        int type = 0, pnttype = 0, is_art = 0, is_ion = 0, dsize = 0, pdsize = 0;
        nrn_assert(fscanf(f, "%s %d %d %d %d %d %d\n", mname, &type, &pnttype, &is_art, &is_ion,
                          &dsize, &pdsize) == 7);
        nrn_assert(i == type);
#ifdef DEBUG
        printf("%s %d %d %d %d %d %d\n", mname, type, pnttype, is_art, is_ion, dsize, pdsize);
#endif
        std::string str(mname);
        memb_func[type].sym = (Symbol*)strdup(mname);
        mech2type[str] = type;
        pnt_map[type] = (char)pnttype;
        nrn_prop_param_size_[type] = dsize;
        nrn_prop_dparam_size_[type] = pdsize;
        nrn_is_artificial_[type] = is_art;
        if (is_ion) {
            double charge = 0.;
            nrn_assert(fscanf(f, "%lf\n", &charge) == 1);
            // strip the _ion
            char iname[100];
            strcpy(iname, mname);
            iname[strlen(iname) - 4] = '\0';
            // printf("%s %s\n", mname, iname);
            ion_reg(iname, charge);
        }
        // printf("%s %d %d\n", mname, nrn_get_mechtype(mname), type);
    }

    // an int32_t binary 1 is at this position. After reading can decide if
    // binary info in files needs to be byteswapped.
    int32_t x;
    nrn_assert(fread(&x, sizeof(int32_t), 1, f) == 1);
    nrn_need_byteswap = 0;
    if (x != 1) {
        BYTEHEADER;
        nrn_need_byteswap = 1;
        BYTESWAP(x, int32_t);
        nrn_assert(x == 1);
    }

    fclose(f);

    if (nrnmpi_myid < 1 && nrn_nobanner_ == 0) {
        fprintf(stderr, " \n");
        fprintf(stderr, " %s\n", banner);
        fprintf(stderr, " %s\n", nrn_version(1));
        fprintf(stderr, " \n");
        fflush(stderr);
    }
    /* will have to put this back if any mod file refers to diam */
    //	register_mech(morph_mech, morph_alloc, (Pfri)0, (Pfri)0, (Pfri)0, (Pfri)0, -1, 0);

    /// Calling _reg functions for the default mechanisms from the file mech/cfile/cabvars.h
    for (int i = 0; mechanism[i]; i++) {
        (*mechanism[i])();
    }

    /// Calling the rest of additional Neurodamus or other _reg functions from the file mod_func.c
    /// (built during the config time from mech/mod_func.c.pl)
    modl_reg();
}

/// Get mechanism type by the mechanism name
int nrn_get_mechtype(const char* name) {
    std::string str(name);
    std::map<std::string, int>::const_iterator mapit;
    mapit = mech2type.find(str);
    if (mapit == mech2type.end())
        return -1;  // Could not find the mechanism
    return mapit->second;
}

const char* nrn_get_mechname(int type) {
    for (std::map<std::string, int>::iterator i = mech2type.begin(); i != mech2type.end(); ++i) {
        if (type == i->second) {
            return i->first.c_str();
        }
    }
    return NULL;
}
}  // namespace coreneuron