spikegen_from_file.cpp

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/* * Copyright (c) 2016 Regents of the University of California. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
*    notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright
*    notice, this list of conditions and the following disclaimer in the
*    documentation and/or other materials provided with the distribution.
*
* 3. The names of its contributors may not 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 OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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*
* *********************************************************************************************** *
* CARLsim
* created by: (MDR) Micah Richert, (JN) Jayram M. Nageswaran
* maintained by:
* (MA) Mike Avery <averym@uci.edu>
* (MB) Michael Beyeler <mbeyeler@uci.edu>,
* (KDC) Kristofor Carlson <kdcarlso@uci.edu>
* (TSC) Ting-Shuo Chou <tingshuc@uci.edu>
* (HK) Hirak J Kashyap <kashyaph@uci.edu>
*
* CARLsim v1.0: JM, MDR
* CARLsim v2.0/v2.1/v2.2: JM, MDR, MA, MB, KDC
* CARLsim3: MB, KDC, TSC
* CARLsim4: TSC, HK
* CARLsim5: HK, JX, KC
*
* CARLsim available from http://socsci.uci.edu/~jkrichma/CARLsim/
* Ver 12/31/2016
*/
#include <spikegen_from_file.h>
 
#include <carlsim.h>
//#include <user_errors.h>      // fancy user error messages
 
#include <stdio.h>              // fopen, fread, fclose
#include <string.h>             // std::string
#include <assert.h>             // assert
 
// #define VERBOSE
 
SpikeGeneratorFromFile::SpikeGeneratorFromFile(std::string fileName, int offsetTimeMs) {
    fileName_ = fileName;
    fpBegin_ = NULL;
 
    nNeur_ = -1;
    szByteHeader_ = -1;
    offsetTimeMs_ = offsetTimeMs;
 
    // move unsafe operations out of constructor
    openFile();
    init();
}
 
SpikeGeneratorFromFile::~SpikeGeneratorFromFile() {
    if (fpBegin_ != NULL) {
        fclose(fpBegin_);
    }
    fpBegin_ = NULL;
}
 
void SpikeGeneratorFromFile::loadFile(std::string fileName, int offsetTimeMs) {
    // close previously opened file (if any)
    if (fpBegin_ != NULL) {
        fclose(fpBegin_);
    }
    fpBegin_ = NULL;
 
    // update file name and open
    fileName_ = fileName;
    offsetTimeMs_ = offsetTimeMs;
    openFile();
    init();
}
 
// rewind file pointers to beginning
void SpikeGeneratorFromFile::rewind(int offsetTimeMs) {
    offsetTimeMs_ = offsetTimeMs;
 
    // reset all iterators
    spikesIt_.clear();
    for (int i=0; i<nNeur_; i++) {
        spikesIt_.push_back(spikes_[i].begin());
    }
}
 
void SpikeGeneratorFromFile::openFile() {
    std::string funcName = "openFile("+fileName_+")";
    fpBegin_ = fopen(fileName_.c_str(),"rb");
    UserErrors::assertTrue(fpBegin_!=NULL, UserErrors::FILE_CANNOT_OPEN, funcName, fileName_);
 
    // \TODO there should be a common/standard way to read spike files
    // \FIXME: this is a hack...to get the size of the header section
    // needs to be updated every time header changes
    FILE* fp = fpBegin_;
    szByteHeader_ = 4*sizeof(int)+1*sizeof(float);
    fseek(fp, sizeof(int)+sizeof(float), SEEK_SET); // skipping signature+version
 
    // get number of neurons from header
    nNeur_ = 1;
    int grid;
    for (int i=1; i<=3; i++) {
        size_t result = fread(&grid, sizeof(int), 1, fp);
        UserErrors::assertTrue(result == 1, UserErrors::FILE_CANNOT_READ, funcName, fileName_);
        nNeur_ *= grid;
    }
 
    // make sure number of neurons is now valid
    assert(nNeur_>0);
}
 
void SpikeGeneratorFromFile::init() {
    assert(nNeur_>0);
 
    // allocate spike vector
    // we organize AER format into a 2D spike vector: first dim=neuron, second dim=spike times
    // then we just need to maintain an iterator for each neuron to know which spike to schedule next
    spikes_.clear();
    for (int i=0; i<nNeur_; i++) {
        spikes_.push_back(std::vector<int>());
    }
 
    // read spike file
    FILE* fp = fpBegin_;
    fseek(fp, szByteHeader_, SEEK_SET); // skip header section
 
    std::string funcName = "readFile("+fileName_+")";
    int tmpTime = -1;
    int tmpNeurId = -1;
    size_t result1, result2;
 
    while (!feof(fp)) {
        result1 = fread(&tmpTime, sizeof(int), 1, fp); // i-th time
        //UserErrors::assertTrue(result == 1, UserErrors::FILE_CANNOT_READ, funcName, fileName_);
        result2 = fread(&tmpNeurId, sizeof(int), 1, fp); // i-th nid
        //UserErrors::assertTrue(result == 1, UserErrors::FILE_CANNOT_READ, funcName, fileName_);
        if (result1 + result2 == 2) // validate the size of reading
            spikes_[tmpNeurId].push_back(tmpTime); // add spike time to 2D vector
    }
 
#ifdef VERBOSE
    for (int neurId=0; neurId<1; neurId++) {
        printf("[%d]: ",neurId);
        for (int i=0; i<spikes_[neurId].size(); i++) {
            printf("%d ",spikes_[neurId][i]);
        }
        printf("\n");
    }
#endif
 
    // initialize iterators
    rewind(offsetTimeMs_);
}
 
int SpikeGeneratorFromFile::nextSpikeTime(CARLsim* sim, int grpId, int nid, int currentTime, int lastScheduledSpikeTime, int endOfTimeSlice) {
    assert(nNeur_>0);
    assert(nid < nNeur_);
 
    if (spikesIt_[nid] != spikes_[nid].end()) {
        // if there are spikes left in the vector ...
 
        if (*(spikesIt_[nid])+offsetTimeMs_ < endOfTimeSlice) {
            // ... and if the next spike time is in the current scheduling time slice:
#ifdef VERBOSE
            if (nid==0) {
            printf("[%d][%d]: currTime=%u, lastTime=%u, endOfTime=%u, offsetTimeMs=%u, nextSpike=%u\n", grpId, nid,
                currentTime, lastScheduledSpikeTime, endOfTimeSlice, offsetTimeMs_,
                (unsigned int) (*(spikesIt_[nid])+offsetTimeMs_));
            }
#endif
            // return the next spike time and update iterator
            return (unsigned int)(*(spikesIt_[nid]++)+offsetTimeMs_);
        }
    }
 
    // if the next spike time is not a valid number, return a large positive number instead
    // this will signal CARLsim to break the nextSpikeTime loop
    return -1; // large positive number
}