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DataTools.c
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DataTools.c
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#include "GeneralIncludes.h"
#include "DataTools.h"
//#include "Synapse.h"
#include "SpikeTrains.h"
/* Checkpoint_init:
1. Load parameters
2. openLogFile() (now in load params())
3. Reserve memory for array of synapses
4. Load Reset values
5. Reserve memory for members of Synapse(s)
*/
Synapse* checkpoint_init(int argc, char *argv[], Synapse *syn){
char *checkpoint_filename, *restart;//, old_checkpoint_filename[100];
FILE *checkpoint_fp;
char outfile[FILE_NAME_LENGTH];
int i;
// Setup global variable of whether checkpointing is enabled
if (! (checkpoint_filename = getenv("SYNAPSE_CHECKFILE")) ){
checkpointing = 0;
}
else{
checkpointing = 1;
}
if (! (restart = getenv("SYNAPSE_RESTART")) ){
printf("No previous checkpoint set, starting afresh.\n");
loadSimulationParameters(argc, argv);
// Memory allocation for array of synapses
syn = (Synapse *) malloc( no_synapses * sizeof(Synapse));
if (syn == NULL){
perror("Memory allocation failure (syn array)\n");
fprintf(logfile, "ERROR: Memory allocation failure (syn array)\n");
}
else{
fprintf(logfile, "syn array successfully assigned %d synapses\n", no_synapses);
}
// fflush(logfile);
synapse_memory_init(syn);
for (i = 0; i < no_synapses; i++){
syn[i].rho[siT] = initial_rho;
syn[i].c[siT] = initial_c;
}
// for (i = 0; i < no_synapses; i++){
// fprintf(logfile, "DEBUG:: checkpoint_init(1): syn(%d).c(0): %lf\n", i, syn[i].c[0]);
// }
// For checkpointing, must add headers separately to output files
if ( checkpointing ){
for (i = 0; i < no_synapses; i++){
//sprintf(outfile, "output/01_syn_%.3d.dat", syn[i].ID);
sprintf(outfile, outfilepattern, syn[i].ID);
printf("writing...%s\n", outfile);
createOutputFileHeader(outfile, &syn[i], siT, dCpre, dCpost, dThetaD, dThetaP, dGammaD, dGammaP, dSigma, iPreSpikeDelay, iTau, iTauC, dRhoFixed, poisson_param, initial_random_seed);
}
}
}
else{
if (! (checkpoint_filename = getenv("SYNAPSE_CHECKFILE")) ){
fprintf(stderr, "Error: no checkpoint file for the restart job.\n");
exit(1);
}
else{
printf("Restarting the job from %s.\n", checkpoint_filename);
if(! (checkpoint_fp = fopen(checkpoint_filename, "r")) ){
perror(checkpoint_filename);
exit(2);
}
else{
loadSimulationParameters(argc, argv);
// Memory allocation for array of synapses
syn = (Synapse *) malloc( no_synapses * sizeof(Synapse));
if (syn == NULL){
perror("Memory allocation failure (syn array)\n");
fprintf(logfile, "ERROR: Memory allocation failure (syn array)\n");
}
else{
fprintf(logfile, "syn array successfully assigned\n");
}
synapse_memory_init(syn);
// Attempt to load from checkpoint file
if ( (checkpoint_load(checkpoint_fp, syn) > 0) ){
fprintf(stderr, "Error reading from restart file %s.\n", checkpoint_filename);
exit(3);
}
else{
printf("Reading from restart file succeeded.\n");
}
fclose(checkpoint_fp);
}
}
}
//time_of_last_save = siT;
// for (i = 0; i < no_synapses; i++){
// for (j = 0; j < simulation_duration; j++)
// fprintf(logfile, "DEBUG:: checkpoint_init(2): syn(%d).c(%d): %lf\n", i, j, syn[i].c[j]);
// }
// fflush(logfile);
return syn;
}
// On failure return 0, otherwise return (meaningful?) value > 0
// call loadSimulationParameters() and synapse_memory_init() before checkpoint_load()
int checkpoint_load(FILE *checkpoint_fp, Synapse *syn){
char paramName[FILE_NAME_LENGTH];
double paramValue;
int syn_index;
int i;
printf("Loading from checkpoint file.\n");
while (!feof(checkpoint_fp)) {
if (fscanf(checkpoint_fp, "%s %lf\n", paramName, ¶mValue) != 2){
fprintf(logfile, "Error reading previous spike times (a)\n");
break;
}
printf("Read(a): %s %f\n", paramName, paramValue);
if (!strcmp(paramName, "SIT")){
printf("Previous siT: %d\n", (int) paramValue);
siT = (int) paramValue;
time_of_last_save = siT;
}
else if (!strcmp(paramName, "RANDOM_SEED")){
printf("Previous random_seed: %ld\n", (long) paramValue);
random_seed = (int) paramValue;
}
else if (!strcmp(paramName, "SYNAPSE")){
syn_index = (int) paramValue;
printf("Loading Synapse(%d)\n", syn_index);
for (i = 0; i < 2; i++){
if (fscanf(checkpoint_fp, "%s %lf\n", paramName, ¶mValue) != 2){
fprintf(logfile, "Error reading previous spike times (b)\n");
break;
}
printf("Read(b): %s %f\n", paramName, paramValue);
if (!strcmp(paramName, "LAST_C")){
printf("Previous c(t): %f\n", paramValue);
initial_c = paramValue;
syn[syn_index].c[siT] = initial_c;
// printf("DEBUG:: syn[syn_index].c[siT]: %lf\n", syn[syn_index].c[siT]);
}
else if (!strcmp(paramName, "LAST_RHO")){
printf("Previous rho(t): %f\n", paramValue);
initial_rho = paramValue;
syn[syn_index].rho[siT] = initial_rho;
}
}
// Attempt to read spike times
if (fscanf(checkpoint_fp, "%s ", paramName) != 1){
fprintf(logfile, "Error reading previous spike times (c)\n");
break;
}
printf("Read(d): %s\n", paramName);
if (!strcmp(paramName, "SPIKES")){
for (i = 0; i < (iPreSpikeDelay+1); i++){
if (fscanf(checkpoint_fp, "%lf ", ¶mValue) != 1){
fprintf(logfile, "Error reading previous spike times (d)\n");
break;
}
printf("Read(e): %d\n", (int) paramValue);
syn[syn_index].preT[(siT-iPreSpikeDelay+i)] = (int) paramValue;
//printf("DEBUG:: syn[syn_index].preT[(siT-iPreSpikeDelay+i)]: %d\n", syn[syn_index].preT[(siT-iPreSpikeDelay+i)]);
}
fscanf(checkpoint_fp, "\n");
}
// if (fscanf(checkpoint_fp, "%s %lf\n", paramName, ¶mValue) != 2)
// break;
// printf("Read(c): %s %f\n", paramName, paramValue);
// if (!strcmp(paramName, "LAST_C")){
// printf("Previous c(t): %f\n", paramValue);
// initial_c = paramValue;
// syn[syn_index].c[siT] = initial_c;
//// printf("DEBUG:: syn[syn_index].c[siT]: %lf\n", syn[syn_index].c[siT]);
// }
// else if (!strcmp(paramName, "LAST_RHO")){
// printf("Previous rho(t): %f\n", paramValue);
// initial_rho = paramValue;
// syn[syn_index].rho[siT] = initial_rho;
//// printf("DEBUG:: syn[syn_index].rho[siT]: %lf\n", syn[syn_index].rho[siT]);
// }
}
}
//fclose(checkpoint_fp);
printf("DEBUG:: exiting checkpoint_load()\n");
// for(i = 0; i < no_synapses; i++){
// for (j = 0; j < simulation_duration; j++){
// printf("DEBUG:: syn(%d).preT(%d) %d\n", i, j, syn[i].preT[j] );
// }
// }
return 0;
}
int checkpoint_save(Synapse *syn){
char *checkpoint_name, *restart, old_checkpoint_name[FILE_NAME_LENGTH];
FILE *checkpoint_fp;
char outfile[FILE_NAME_LENGTH];
int i, j;
if (! (checkpoint_name = getenv ("SYNAPSE_CHECKFILE"))) {
fprintf (logfile, "Checkpointing not enabled...skipping\n");
}
else {
// Rename old checkpoint file
if ( (restart = getenv("SYNAPSE_RESTART")) ) {
strcpy (old_checkpoint_name, checkpoint_name);
strcat (old_checkpoint_name, ".old");
fprintf (logfile, "Renaming old checkpoint restart file to %s\n", old_checkpoint_name);
if (0 > rename (checkpoint_name, old_checkpoint_name)) {
perror (old_checkpoint_name);
exit (4);
}
}
// Save progress so far to output file
fprintf(logfile, "Saving progress so far to %s\n", outfilearray);
// Output to files loop
for (i = 0; i < no_synapses; i++){
//sprintf(outfile, "output/01_syn_%.3d.dat", syn[i].ID);
sprintf(outfile, outfilepattern, syn[i].ID);
printf("writing...%s\n", outfile);
saveSynapseProgressToFile(outfile, &syn[i], siT);
}
// Save restart data to checkpoint file
fprintf (logfile, "Saving checkpoint data on %s\n", checkpoint_name);
if (! (checkpoint_fp = fopen (checkpoint_name, "w"))) {
perror (checkpoint_name);
exit (5);
}
else {
fprintf(checkpoint_fp, "SIT %d\n", siT);
fprintf(checkpoint_fp, "RANDOM_SEED %ld\n", random_seed);
for (i = 0; i < no_synapses; i++){
fprintf(checkpoint_fp, "SYNAPSE %d\n", i);
fprintf(checkpoint_fp, "LAST_C %lf\n", syn[i].c[siT]);
fprintf(checkpoint_fp, "LAST_RHO %lf\n", syn[i].rho[siT]);
fprintf(checkpoint_fp, "SPIKES ");
for (j = (siT-iPreSpikeDelay); j <= siT; j++){
if (j >= 0){
fprintf(checkpoint_fp, " %d", syn[i].preT[j]);
}
}
fprintf(checkpoint_fp, "\n");
}
fclose (checkpoint_fp);
}
}
return 0;
}
int saveSynapseProgressToFile(char* filename, void *obj, int end_time ){
FILE *fp;
int i;
Synapse * syn = (Synapse *)obj;
fprintf(logfile, "Opening file for saving: %s\n", filename);
fp = fopen(filename, "a");
if (fp == NULL){
perror("Error in saveSynapseProgressToFile()");
}
else{
fprintf(logfile, "Saving to file: %s\n", filename);
printf("DEBUG:: before\n");
for (i = (time_of_last_save+1); i <= end_time; i++){
fprintf(fp, "%d %f %f %u %u\n", i, (*syn).rho[i], (*syn).c[i], (*syn).preT[i], (*syn).postT[i]);
printf("DEBUG: saving progress %d %f %f %u %u\n", i, (*syn).rho[i], (*syn).c[i], (*syn).preT[i], (*syn).postT[i]);
}
//fprintf(fp,"\n\n");
printf("DEBUG:: after\n");
fclose(fp);
fprintf(logfile, "Completed saving\n");
time_of_last_save = end_time;
}
return 0;
}
int createOutputFileHeader(char* filename, void *obj, int duration, double dCpre, double dCpost, double dThetaD, double dThetaP, double dGammaD, double dGammaP, double dSigma, int iPreSpikeDelay, int iTau, int iTauC, double dRhoFixed, double poisson_param, long initial_random_seed){
FILE *fp;
Synapse * syn = (Synapse *)obj;
fprintf(logfile, "Opening file for saving: %s\n", filename);
fp = fopen(filename, "a");
if (fp == NULL){
perror("Error in saveSynapseOutputFile()");
}
else{
fprintf(logfile, "Saving to file: %s\n", filename);
fprintf(fp, "\n\n# Params:\n# Cpre: %f, Cpost: %f, thetaD: %f, thetaP: %f, gammaD: %f, gammaP: %f, sigma: %f, Delay: %d, tau: %d, tauC: %d, rhoF: %f, poisson param: %f, seed: %ld\n", dCpre, dCpost, dThetaD, dThetaP, dGammaD, dGammaP, dSigma, iPreSpikeDelay, iTau, iTauC, dRhoFixed, poisson_param, initial_random_seed);
fprintf(fp,"#\n# Synaptic output, Synapse(%d):\n# t rho c preT postT\n", (*syn).ID);
fclose(fp);
fprintf(logfile, "Completed saving\n");
}
return 0;
}
int saveSynapseOutputFile(char* filename, void *obj, int duration, double dCpre, double dCpost, double dThetaD, double dThetaP, double dGammaD, double dGammaP, double dSigma, int iPreSpikeDelay, int iTau, int iTauC, double dRhoFixed, double poisson_param, long initial_random_seed){
FILE *fp;
int i;
Synapse * syn = (Synapse *)obj;
fprintf(logfile, "Opening file for saving: %s\n", filename);
fp = fopen(filename, "a");
if (fp == NULL){
perror("Error in saveSynapseOutputFile()");
}
else{
fprintf(logfile, "Saving to file: %s\n", filename);
fprintf(fp, "\n\n# Params:\n# Cpre: %f, Cpost: %f, thetaD: %f, thetaP: %f, gammaD: %f, gammaP: %f, sigma: %f, Delay: %d, tau: %d, tauC: %d, rhoF: %f, poisson param: %f, seed: %ld\n", dCpre, dCpost, dThetaD, dThetaP, dGammaD, dGammaP, dSigma, iPreSpikeDelay, iTau, iTauC, dRhoFixed, poisson_param, initial_random_seed);
fprintf(fp,"#\n# Synaptic output, Synapse(%d):\n# t rho c preT postT\n", (*syn).ID);
for (i = 0; i <= duration; i++){
fprintf(fp, "%d %f %0.10lf %u %u\n", i, (*syn).rho[i], (*syn).c[i], (*syn).preT[i], (*syn).postT[i]);
}
fclose(fp);
fprintf(logfile, "Completed saving\n");
}
return 0;
}
void loadSimulationParameters(int argc, char *argv[]){
FILE* paramsfile;
char paramName[FILE_NAME_LENGTH];
double paramValue;
strcpy(logfilearray, "output/logfile.log");
logfilename = logfilearray;
strcpy(outfilearray, "output/01_syn_%.3d.dat");
outfilepattern = outfilearray;
train_fn = train1;
siT = 0;
siID = 0;
time_of_last_save = -1;
if (argc < 2){
printf("No command-line arguments passed....loading defaults.\n");
printf("arg0 is %s\n", argv[0]);
simulation_duration = 100;
no_synapses = 1;
initial_c = 0;
initial_rho = 0;
initial_random_seed = (-13);
random_seed = initial_random_seed;
iTau = 150000; // measured in ms (equivalent to 150sec)
iTauC = 20; // measured in ms
dRhoFixed = 0.5;
dCpre = 1.0;
dCpost = 4.0;
dThetaD = 1.0;
dThetaP = 2.0;
dGammaD = 50;
dGammaP = 100;
dSigma = 3.50;
iPreSpikeDelay = 19;
poisson_param = 1.0/1000;
}
else{
printf("arg[1] is %s....attempting to open it as parameters file.\n", argv[1]);
paramsfile = fopen(argv[1], "r");
if (paramsfile == NULL){
perror("Error in loadSimulationParameters()");
}
else{
printf("Loading from file: %s\n", argv[1]);
while (!feof(paramsfile)) {
if (fscanf(paramsfile, "%s %lf\n", paramName, ¶mValue) != 2)
break;
printf("Read: %s %f\n", paramName, paramValue);
if (!strcmp(paramName, "SIMULATION_DURATION")){
simulation_duration = paramValue;
}
else if (!strcmp(paramName, "NO_SYNAPSES")){
no_synapses = paramValue;
}
else if (!strcmp(paramName, "INITIAL_C")){
initial_c = paramValue;
}
else if (!strcmp(paramName, "INITIAL_RHO")){
initial_rho = paramValue;
}
else if (!strcmp(paramName, "INITIAL_RANDOM_SEED")){
initial_random_seed = paramValue;
random_seed = paramValue;
}
else if (!strcmp(paramName, "TAU")){
iTau = (int) paramValue;
}
else if (!strcmp(paramName, "TAU_C")){
iTauC = (int) paramValue;
}
else if (!strcmp(paramName, "RHO_FIXED")){
dRhoFixed = paramValue;
}
else if (!strcmp(paramName, "C_PRE")){
dCpre = paramValue;
}
else if (!strcmp(paramName, "C_POST")){
dCpost = paramValue;
}
else if (!strcmp(paramName, "THETA_D")){
dThetaD = paramValue;
}
else if (!strcmp(paramName, "THETA_P")){
dThetaP = paramValue;
}
else if (!strcmp(paramName, "GAMMA_D")){
dGammaD = paramValue;
}
else if (!strcmp(paramName, "GAMMA_P")){
dGammaP = paramValue;
}
else if (!strcmp(paramName, "SIGMA")){
dSigma = paramValue;
}
else if (!strcmp(paramName, "PRE_SPIKE_DELAY")){
iPreSpikeDelay = (int) paramValue;
}
else if (!strcmp(paramName, "TRAIN_FUNCTION")){
if ((int) paramValue == 1){
train_fn = train1;
}
else if ((int) paramValue == 2){
train_fn = train2;
}
else if ((int) paramValue == 3){
train_fn = train3;
}
else if ((int) paramValue == 4){
train_fn = train4;
}
else if ((int) paramValue == 5){
train_fn = train5;
}
// - Pasted from (my) Pfister code
else if ((int) paramValue == 6){
train_fn = train6;
}
else if ((int) paramValue == 7){
train_fn = train7;
}
else if ((int) paramValue == 8){
train_fn = train8;
}
else if ((int) paramValue == 9){
train_fn = train9;
}
else if ((int) paramValue == 10){
train_fn = train10;
}
else if ((int) paramValue == 11){
train_fn = train11;
}
else if ((int) paramValue == 12){
train_fn = train12;
}
else if ((int) paramValue == 13){
train_fn = train13;
}
else if ((int) paramValue == 14){
train_fn = train14;
}
else if ((int) paramValue == 15){
train_fn = train15;
}
else if ((int) paramValue == 16){
train_fn = train16;
}
else if ((int) paramValue == 17){
train_fn = train17;
}
else if ((int) paramValue == 18){
train_fn = train18;
}
else if ((int) paramValue == 19){
train_fn = train19;
}
else if ((int) paramValue == 20){
train_fn = train20;
}
else if ((int) paramValue == 21){
train_fn = train21;
}
else if ((int) paramValue == 22){
train_fn = train22;
}
else if ((int) paramValue == 23){
train_fn = train23;
}
else if ((int) paramValue == 24){
train_fn = train24;
}
else if ((int) paramValue == 25){
train_fn = train25;
}
// - End of paste from (my) Pfister code
else if ((int) paramValue == 26){
train_fn = train26;
}
else if ((int) paramValue == 27){
train_fn = train27;
}
printf("DEBUG: train function loaded from param file\n");
}
else if (!strcmp(paramName, "POISSON_PARAM")){
poisson_param = paramValue;
}
}
fclose(paramsfile);
}
if (argc > 2){
printf("argv[2] is %s....attempting to use it as log file.\n", argv[2]);
if (!strcmp(argv[2], "stdout")){
strcpy(logfilearray, "stdout");
}
else{
strcpy(logfilearray, "output/");
strcat(logfilearray, argv[2]);
}
printf("Log file name: %s\n", logfilename);
}
if (argc > 3){
printf("argv[3] is %s....attempting to use it as output file pattern.\n", argv[3]);
strcpy(outfilearray, "output/");
strcat(outfilearray, argv[3]);
//outfilepattern = argv[3];
printf("Output file pattern: %s\n", outfilepattern);
}
}
// Make sure that directory 'output' exists
if(mkdir("output",(S_IRUSR | S_IWUSR | S_IXUSR)) == -1){
if (errno == EEXIST){
printf("Directory 'output' already exists.\n");
}
else{
perror("Error creating directory 'output'");
}
}
// Open a log file for writing
logfile = openLogFile(logfilename);
fprintf(logfile, "\n\n---------------------\n New Run\n---------------------\n");
}
int printToLog(FILE* fp, char* message){
//printf("LOG: Saving message: %s\n", message);
fprintf(fp, "%s", message);
//printf("LOG: Completed saving\n");
return 0;
}
FILE* openLogFile(char* filename){
FILE *fp;
if(!strcmp(filename, "stdout")){
fp = stdout;
}
else{
fp = fopen(filename, "a");
}
if (fp == NULL){
perror("Error in openLogFile()");
}
else{
printf("LOG: Log file opened for writing: %s\n", filename);
}
return fp;
}
int closeLogFile(FILE* fp){
fclose(fp);
return 0;
}
//// I'm only playing around here, was trying to
//// define object type as a parameter, turns out
//// I'd just be rewriting the basic libraries.
//int loadDataFile(char* filename, void *obj){
// FILE *fp;
//
// printf("Opening file for loading: %s\n", filename);
// fp = fopen(filename, "r");
// if (fp == NULL){
// perror("Error in loadDataFile()");
// }
// else{
// printf("Loading from file: %s\n", filename);
// fscanf(fp, "%s\n", obj);
// fclose(fp);
// }
//
// printf("Loaded data: %s", (char *)obj);
//
// return 0;
//}
//
//// Note to self: when passing a (void *) argument, reassignment
//// to a local variable is unavoidable otherwise uncertain
//// compiler behaviour occurs (can't explain why)
//int saveOutputFile(char* filename, void *obj){
// FILE *fp;
// //double * local_obj = (double *)obj;
// int * local_obj = (int *)obj;
//
//
// printf("Opening file for saving: %s\n", filename);
// fp = fopen(filename, "a");
// if (fp == NULL){
// perror("Error in saveOutputFile()");
// }
// else{
// printf("Saving to file: %s\n", filename);
// fprintf(fp,"Data value: %d\n", *local_obj);
// fclose(fp);
// }
//
// // double
//// printf("output:%f\n", local_obj);
//// printf("value:%d\n", local_obj);
//// printf("local p value:%f\n", *local_obj);
//// printf("final value:%f\n", (double *)obj);
//
// // int
// printf("output:%d\n", local_obj);
// printf("value:%d\n", local_obj);
// printf("local p value:%d\n", *local_obj);
// printf("final value:%d\n", (int *)obj);
//
// return 0;
//}