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mktree.cpp
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mktree.cpp
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///////////////////////////////////////////////////////////////
//
// This program demonstrates how to read the output of LCM and
// put them in a ROOT file
//
// ROOT is free data analysis framework built on C++.
//
// See http://root.cern.ch for more information about ROOT
//
// You need both the ROOT library and the LCM source code
// to compile the program.
//
// Assuming you have the LCM source code in directory "src"
// and a working root software installed, then you can compile
// the program using the following command
//
// g++ -o mktree mktree.cpp src/*.cpp -O2 $(root-config --cflags --glibs)
//
// Usage:
// ./mktree volt.dat volt.root
//
// where "volt.dat" is the input file, which is the LCM output file,
// and "volt.root" is the root file to be created.
// The third argument is optional. If not given, the root file
// would be the same as the input file with the extension
// changed to ".root"
/////////////////////////////////////////////////////////////
#include <cstdio>
#include <iostream>
#include <string>
#include <map>
#include <omp.h>
#include "TNamed.h"
#include "TFile.h"
#include "TTree.h"
#include "TH1F.h"
#include "TVirtualFFT.h"
#include "src/simulation.h"
using namespace std;
using std::string;
using std::map;
//get the directory of the given file
string get_dir(const string& fpath, const string& path_sep = "/\\")
{
std::size_t found = fpath.find_last_of(path_sep);
if (found == string::npos) {
return string("."); //current directory
}
else {
return(fpath.substr(0, found));
}
}
string get_name(const string& fpath, const string& path_sep = "/\\")
{
string fname(fpath);
std::size_t found = fpath.find_last_of(path_sep);
if (found != string::npos) {
fname = fpath.substr(found + 1, string::npos);
}
found = fname.find_last_of(".");
if (found != string::npos) {
return fname.substr(0, found);
}
else {
return fname;
}
}
Int_t main(Int_t argc, char* argv[])
{
if (argc != 2 & argc != 3) {
cerr << "usage: " << argv[0] << " volt_data_file" << endl;
exit(-1);
}
FILE *fp = fopen(argv[1], "r");
if (fp == NULL) {
cerr << "ERROR! failed to open file '" << argv[1] << "' !" << endl;
exit(-1);
}
map<string, string> fileInfo;
//read and processing the header
{
char *buff = new char[1024];
fread(buff, sizeof(char), 1024, fp);
string str = buff;
vector<string> parts;
strsplit(str, "\n", parts);
Int_t pos1, pos2;
string paraName, paraVal;
for (vector<string>::iterator it = parts.begin(); it != parts.end(); ++it) {
*it = strtrim(remove_comments(*it));
if (it->size() == 0) continue;
pos1 = it->find("=");
pos2 = it->find(";");
if (pos1 > pos2) {
cerr << "ERROR! cannnot recognise the line " << *it << endl;
fclose(fp);
exit(-1);
}
paraName = upperstr(strtrim(it->substr(0, pos1)));
paraVal = upperstr(strtrim(it->substr(pos1 + 1, pos2 - pos1 - 1)));
fileInfo[paraName] = paraVal;
}
delete[] buff;
}
Int_t ng_num, elmt_num;
Int_t section_num;
Int_t cfg_pos, cfg_len;
Int_t num_size, block_size, block_num;
Int_t data_pos, data_len;
//proccessing the header
{
if ((!str2int(fileInfo["NEUR_NUM"], ng_num)) || ng_num < 0) {
if ((!str2int(fileInfo["NG_NUM"], ng_num)) || ng_num < 0) {
cerr << "ERROR! cannot recognise the value for 'NEUR_NUM' or 'NG_NUM': NEUR_NUM = '" <<
fileInfo["NEUR_NUM"] << "', NG_NUM = " << fileInfo["NG_NUM"] << "!" << endl;
fclose(fp);
exit(-1);
}
}
if ((!str2int(fileInfo["ELMT_NUM"], elmt_num)) || elmt_num < 0) {
cerr << "ERROR! cannot recognise the value for 'ELMT_NUM': '" << fileInfo["ELMT_NUM"] << "'!" << endl;
fclose(fp);
exit(-1);
}
if ((!str2int(fileInfo["CFG_POS"], cfg_pos)) || cfg_pos < 0) {
cerr << "ERROR! cannot recognise the value for 'CFG_POS': '" << fileInfo["CFG_POS"] << "'!" << endl;
fclose(fp);
exit(-1);
}
if ((!str2int(fileInfo["CFG_LEN"], cfg_len)) || cfg_len < 0) {
cerr << "ERROR! cannot recognise the value for 'CFG_LEN': '" << fileInfo["CFG_LEN"] << "'!" << endl;
fclose(fp);
exit(-1);
}
if ((!str2int(fileInfo["NUM_SIZE"], num_size)) || num_size < 0) {
cerr << "ERROR! cannot recognise the value for 'NUM_SIZE': '" << fileInfo["NUM_SIZE"] << "'!" << endl;
fclose(fp);
exit(-1);
}
if (num_size != sizeof(float)) {
cerr << "ERROR! Data type is not right. Only float type data are supported! num_size = " << num_size << endl;
fclose(fp);
exit(-1);
}
if ((!str2int(fileInfo["BLOCK_SIZE"], block_size)) || block_size < 0) {
cerr << "ERROR! cannot recognise the value for 'BLOCK_SIZE': '" << fileInfo["BLOCK_SIZE"] << "'!" << endl;
fclose(fp);
exit(-1);
}
if ((!str2int(fileInfo["BLOCK_NUM"], block_num)) || block_num < 0) {
cerr << "ERROR! cannot recognise the value for 'BLOCK_NUM': '" << fileInfo["BLOCK_NUM"] << "'!" << endl;
fclose(fp);
exit(-1);
}
if ((!str2int(fileInfo["DATA_POS"], data_pos)) || (data_pos < 0)) {
cerr << "ERROR! cannot recognise the valure for 'DATA_POS': " << fileInfo["DATA_POS"] << "! " << endl;
fclose(fp);
exit(-1);
}
if ((!str2int(fileInfo["DATA_LEN"], data_len)) || (data_len < 0)) {
cerr << "ERROR! cannot recognise the valure for 'DATA_LEN': " << fileInfo["DATA_LEN"] << "! " << endl;
fclose(fp);
exit(-1);
}
Int_t curr_pos = ftell(fp); // save current position
fseek(fp, 0, SEEK_END); // go the end of the file
Int_t end_pos = ftell(fp); // length of the file
if ((end_pos - data_pos + 2) / block_size < block_num) {
block_num = (end_pos - data_pos + 2) / block_size;
cerr << "WARNING! it seems the data blocks in '" << argv[1] << "' the file is smaller than it claims!" << endl;
cerr << " " << block_num << " blocks are found in the file. data_pos = " << data_pos << ", file_size = " << end_pos << "." << endl;
fclose(fp);
exit(-1);
}
fseek(fp, curr_pos, SEEK_SET);
}
//
//
//The following section parse the parameter configuration section
//and save the parameter name and value pair to th variable modelInfo
LCM lcm;
map<string, string> modelInfo;
//read the parameter section, and use that to initialise a LCM model
{
char *cfg = new char[cfg_len + 1];
std::fill(cfg, cfg + cfg_len + 1, '\0');
fseek(fp, cfg_pos, SEEK_SET);
fread(cfg, sizeof(char), cfg_len, fp);
read_param(cfg, modelInfo);
map<string, string> paraList = modelInfo;
for (map<string, string>::iterator it = paraList.begin(); it != paraList.end(); ++it) {
if ((it->first).substr(0, 5) == string("SIMU.")) {
paraList.erase(it);
it = paraList.begin();
}
}
lcm.set_param(paraList);
if (!lcm.init()) {
cerr << "ERROR! Initialising LCM failed!" << endl;
exit(-1);
}
if (lcm.ng_num() != ng_num || lcm.elmt_num() != elmt_num) {
cout << "ERROR! Info in header section is not consistent with that in config section!" << endl;
exit(-1);
}
//cout<<lcm.print()<<endl;
delete[] cfg;
}
string fpath;
if (argc == 3) {
fpath.assign(argv[2]);
}
else {
fpath.assign(argv[1]);
#if defined(_WIN32) || defined(_WIN64)
fpath = get_dir(fpath) + ("\\") + get_name(fpath) + (".root");
#else
fpath = get_dir(fpath) + ("/") + get_name(fpath) + (".root");
#endif
}
cout << "INFO: save data to " << fpath << endl;
TFile *hfile = new TFile(fpath.c_str(), "RECREATE", "Neuronal firing rates from LCM", 5);
if (hfile->IsZombie()) {
cout << "ERROR: cannot create file '" << fpath.c_str() << "' for writting." << endl;
exit(-1);
}
//
//The following section save the content in modelInfo
//to the root file
TNamed *pList = new TNamed[modelInfo.size()];
hfile->mkdir("param");
hfile->cd("param");
Int_t idx = 0;
for (map<string, string>::iterator it = modelInfo.begin(); it != modelInfo.end(); (++it), (++idx)) {
pList[idx].SetNameTitle((it->first).c_str(), (it->second).c_str());
pList[idx].Write();
}
hfile->cd("/");
/////////////////////////////////////////////////////
//
//In the following section, a tree is created to
//store information about the model and filled with
//only one entry
//
Int_t nrow = lcm.grid_row();
Int_t ncol = elmt_num / nrow;
Int_t volt_num = ng_num * elmt_num;
Int_t mid_elmt = (nrow / 2) * ncol + ncol / 2;
Int_t *idx_neur = new Int_t[volt_num];
Int_t *idx_elmt = new Int_t[volt_num];
for (Int_t idx = 0; idx < volt_num; ++idx) {
idx_neur[idx] = idx % ng_num;
idx_elmt[idx] = idx / ng_num;
}
TString neur_name;
Float_t *neur_density = new Float_t[ng_num];
Int_t *neur_layer = new Int_t[ng_num];
Int_t *neur_type = new Int_t[ng_num];
for (Int_t idx = 0; idx < ng_num; ++idx) {
if (idx != 0) {
neur_name += TString(";");
}
neur_name += (TString::Format("%d-", idx) + TString(lcm.neur_group(idx).name()));
neur_density[idx] = lcm.neur_group(idx).density();
neur_layer[idx] = lcm.neur_group(idx).layer();
neur_type[idx] = lcm.neur_group(idx).type();
}
Int_t layer_num = lcm.layer_num();
TString layer_name;
for (Int_t idx = 0; idx < layer_num; ++idx) {
if (idx != 0) {
layer_name += TString(";");
}
layer_name += (TString::Format("%d-", idx) + TString(lcm.layer(idx).name()));
}
TString excit_inhib = TString::Format("%d-EXCIT;%d-INHIB", cEXCIT, cINHIB);
TTree *tr1 = new TTree("model_info", "LCM information");
tr1->Branch("nneur", &ng_num, "nneur/I");
tr1->Branch("ncol", &ncol, "ncol/I");
tr1->Branch("nrow", &nrow, "nrow/I");
tr1->Branch("nelmt", &elmt_num, "nelmt/I");
tr1->Branch("nvolt", &volt_num, "nvolt/I"); // volt_num == ng_num * elmt_num;
tr1->Branch("nlayer", &layer_num, "nlayer/I");
tr1->Branch("mid_elmt", &mid_elmt, "mid_elmt/I");
tr1->Branch("layer_name", (void *)layer_name.Data(), "layer_name/C", 1024);
tr1->Branch("neur_name", (void *)neur_name.Data(), "neur_name/C", 1024);
tr1->Branch("excit_inhib", (void *)excit_inhib.Data(), "excit_inhib/C", 1024);
tr1->Branch("neur_density", neur_density, "neur_density[nneur]/F");
tr1->Branch("neur_layer", neur_layer, "neur_layer[nneur]/I");
tr1->Branch("neur_type", neur_type, "neur_type[nneur]/I");
tr1->Branch("idx_neur", idx_neur, "idx_neur[nvolt]/I");
tr1->Branch("idx_elmt", idx_elmt, "idx_elmt[nvolt]/I");
tr1->Fill();
tr1->Write();
/////////////////////////////////////////////////////////
//
Float_t nneur_E = 0.;
Float_t nneur_I = 0.;
for (Int_t idx = 0; idx < ng_num; ++idx) {
if (neur_type[idx] == cEXCIT) {
nneur_E += neur_density[idx];
}
else {
nneur_I += neur_density[idx];
}
}
//convert to percentage
for (Int_t idx = 0; idx < ng_num; ++idx) {
if (neur_type[idx] == cEXCIT) {
neur_density[idx] /= nneur_E;
}
else {
neur_density[idx] /= nneur_I;
}
}
/////////////////////////////////////////////////////////
//
//In the following section, the voltage information is read
//and convert into firing rates, both the voltage and FR
//information are stored in a tree
//
//
char *pos;
Float_t tau;
Float_t *volt = new Float_t[volt_num];
Float_t *FR = new Float_t[volt_num];
Float_t *mFR_E = new Float_t[elmt_num];
Float_t *mFR_I = new Float_t[elmt_num];
TTree *tr2 = new TTree("neur_volts", "neuron voltages and firing rates");
tr2->Branch("tau", &tau, "tau/F"); //branch for evolution time
tr2->Branch("nvolt", &volt_num, "nvolt/I");
tr2->Branch("nelmt", &elmt_num, "nelmt/I");
tr2->Branch("volt", volt, "volt[nvolt]/F");
tr2->Branch("FR", FR, "FR[nvolt]/F");
tr2->Branch("mFR_E", mFR_E, "mFR_E[nelmt]/F");
tr2->Branch("mFR_I", mFR_I, "mFR_I[nelmt]/F");
Int_t Nproc = omp_get_num_procs() / 2;//get the number of available processors without hyper-threading.
if (Nproc > 10) Nproc = 10;
omp_set_num_threads(Nproc);//set the number of processors.
omp_set_nested(0);
omp_set_dynamic(1);
char ch;
Int_t ineur, ibgn, ielmt;
ibgn = mid_elmt * ng_num;
for (Int_t iblk = 0; iblk < block_num; ++iblk) {
fseek(fp, data_pos + iblk*block_size, SEEK_SET);
fread(&tau, num_size, 1, fp); //read tau
fread(volt, num_size, volt_num, fp); //read voltage data
fread(&ch, sizeof(char), 1, fp); //read ending '\0'
if (ch != '\0') {
cerr << "ERROR! A inappropriately ended data block found!" << endl;
cerr << " block# = " << iblk << ", pos = " << ftell(fp) << endl;
break;
}
for (ielmt = 0; ielmt < elmt_num; ++ielmt) {
mFR_E[ielmt] = 0.;
mFR_I[ielmt] = 0.;
}
#pragma omp parallel for
for (Int_t ielmt = 0; ielmt < elmt_num; ++ielmt) {
Int_t idx = ielmt * ng_num;
for (Int_t ineur = 0; ineur < ng_num; ++ineur) {
FR[idx] = lcm.neur_group(ineur).eqn_firing(volt[idx]);
if (neur_type[ineur] == cEXCIT) {
mFR_E[ielmt] += (FR[idx] * neur_density[ineur]);
}
else {
mFR_I[ielmt] += (FR[idx] * neur_density[ineur]);
}
++idx;
}
}
tr2->Fill();
}
tr2->Write();
hfile->Close();
delete hfile;
delete[] pList;
delete[] idx_neur;
delete[] idx_elmt;
delete[] neur_density;
delete[] neur_layer;
delete[] neur_type;
delete[] volt;
delete[] FR;
delete[] mFR_E;
delete[] mFR_I;
fclose(fp);
}