void readColumn(unsigned col,
std::vector<T> &vals,
bool resize = false,
ndsize_t offset = 0) {
const std::string name = this->colName(col);
readColumn(name, vals, resize, offset);
}
int RemoveDistsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get names you want to keep
names = m->readAccnos(accnosfile);
if (m->control_pressed) { return 0; }
//read through the correct file and output lines you want to keep
if (phylipfile != "") { readPhylip(); }
if (columnfile != "") { readColumn(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
m->mothurOutEndLine();
m->mothurOut("Output File names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("phylip");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
}
itTypes = outputTypes.find("column");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveDistsCommand", "execute");
exit(1);
}
}
int main(int argc,char *argv[])
{
//////////////////////////////////////////////////////////////
//PROGRAM VARIBALES
//////////////////////////////////////////////////////////////
char datafile[FSIZE]="",fitfile[FSIZE]="";
char fitfunc[FSIZE]="",inipars[FSIZE]="";
real2 params[MAXPARAMS];
int numcols=0,colx=0,coly=0,cole=0;
int nfac=2;
int i,ndata;
//////////////////////////////////////////////////////////////
//INITIALIZE
//////////////////////////////////////////////////////////////
TITLE(stdout,'*',"FIT DATA TO A GIVEN FUNCTION");
//////////////////////////////////////////////////////////////
//SET OPTIONS AND USAGE
//////////////////////////////////////////////////////////////
SET_OPTIONS(":hvVf:F:u:p:n:x:y:e:N:");
SET_USAGE(
"=======================================================================================\n"
"Usage:\n\n"
"\t./program -f <datafile> [-F <fitfile>] -u <fit_function> [-p <initial_params>]\n"
"\t [-N <num_sampling_fitting_func>]\n"
"\t -n <numcols> -x <colx> -y <coly> [-e <cole>]\n"
"\n"
"Fit the 2D data described by <colx> and <coly> with errors <cole> using fitting function\n"
"<fit_function> as given by function file functions.hpp. The initial set of parameters\n"
"<initial_params> should be provided as a list of comma separated real values.\n"
"The result of the fit is stored in file <fitfile> where the fitted parameters, the \n"
"chisquare and the p-value are stored in the header. <fitfile> is a two column file with\n"
"the value of the fitted function at intermediate points (<num_sampling_fitting_func> x \n"
"number of fitted points).\n"
"=======================================================================================\n"
);
//////////////////////////////////////////////////////////////
//READ OPTIONS
//////////////////////////////////////////////////////////////
while(ITEROPTIONS){
switch(OPTION){
case 'f':
strcpy(datafile,optarg);
break;
case 'F':
strcpy(fitfile,optarg);
break;
case 'u':
strcpy(fitfunc,optarg);
break;
case 'p':
strcpy(inipars,optarg);
break;
case 'n':
numcols=atoi(optarg);
break;
case 'N':
nfac=atoi(optarg);
break;
case 'x':
colx=atoi(optarg);
break;
case 'y':
coly=atoi(optarg);
break;
case 'e':
cole=atoi(optarg);
break;
//========================================
//COMMON
//========================================
case 'v':
VERBOSITY=1;
break;
case 'V':
VERBOSITY=2;
break;
//DETECT ERRORS
OPTION_ERRORS;
}
}
//////////////////////////////////////////////////////////////
//VALIDATE OPTIONS
//////////////////////////////////////////////////////////////
if(isBlank(datafile)){
fprintf(stderr,"Error: No datafile was provided\n");
PRINT_USAGE;
EXIT;
}
if(!fileExists(datafile)){
fprintf(stderr,"Error: Datafile '%s' does not exist\n",datafile);
PRINT_USAGE;
EXIT;
}
if(isBlank(fitfile)){
sprintf(fitfile,"%s.fit",datafile);
}
if((ndata=countLines(datafile))==0){
fprintf(stderr,"Error: Datafile '%s' seems empty\n",datafile);
PRINT_USAGE;
EXIT;
}
if(numcols<1){
fprintf(stderr,"Error: The number of columns should be different from 0\n");
PRINT_USAGE;
EXIT;
}
if(colx==0){
colx=1;
}
if(coly==0){
coly=2;
}
if(isBlank(fitfunc)){
fprintf(stderr,"Error: No fit function was provided\n");
PRINT_USAGE;
EXIT;
}else{
getFunction(fitfunc);
}
if(isBlank(inipars)){
for(i=0;i<FNpars;i++){
if(i==FNpars-1)
strcat(inipars,"0.0");
else
strcat(inipars,"0.0,");
}
}
splitString(inipars,",",params);
//////////////////////////////////////////////////////////////
//REPORT INPUT INFORMATION
//////////////////////////////////////////////////////////////
if(VERBOSE(1)){
fprintf(stdout,"Datafile: %s\n",datafile);
fprintf(stdout,"Fitfile: %s\n",fitfile);
fprintf(stdout,"Fit function: %s\n",fitfunc);
fprintf(stdout,"Fit parameters: %s\n",inipars);
fprintf(stdout,"Test call: %s(%+14.7e;%s) = %+14.7e\n",
fitfunc,FXtest,inipars,FFunc(FXtest,params));
fprintf(stdout,"Number of columns: %d\n",numcols);
fprintf(stdout,"Columns x,y: %d,%d\n",colx,coly);
if(cole!=0)
fprintf(stdout,"Column error: %d\n",cole);
else
fprintf(stdout,"Errors assumed 1\n");
fprintf(stdout,"Factor of over sampling: %d\n",nfac);
}
//////////////////////////////////////////////////////////////
//PROGRAM
//////////////////////////////////////////////////////////////
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
//READING DATA
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fprintf(stdout,"Reading %d data points from datafile '%s'...\n",ndata,datafile);
real2 *X=readColumn(datafile,ndata,numcols,colx);
real2 *Y=readColumn(datafile,ndata,numcols,coly);
real2 *E;
if(cole)
E=readColumn(datafile,ndata,numcols,cole);
else{
E=(real2*)calloc(ndata,sizeof(real2));
for(int i=0;i<ndata;i++) E[i]=1.0;
}
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
//FITTING DATA
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
real2 chis,pval;
fprintf(stdout,"Fitting %d data points with function '%s'...\n",
ndata,fitfunc);
fitData(X,Y,E,ndata,FFunc,FNpars,params,chis,pval);
fprintf(stdout,"Fit succesful:\n");
fprintf(stdout,"\tBest fit parameters: ");
for(i=0;i<FNpars;i++)
fprintf(stdout,"%+14.7e ",params[i]);
fprintf(stdout,"\n");
fprintf(stdout,"\tChisquare: %+14.7e\n",chis);
fprintf(stdout,"\tP-val (nu = %d): %+14.7e\n",ndata,pval);
if(pval>0.05)
fprintf(stdout,"\tData is compatible with fitting function\n");
else
fprintf(stdout,"\tData cannot be fitted with function\n");
file fs=fileOpen(fitfile,"w");
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
//STORING
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fprintf(stdout,"Storing fit results...\n",fitfile);
fprintf(fs,"#Datafile: %s\n",datafile);
fprintf(fs,"#TotCols,ColX,ColY,ColE: %d %d %d %d\n",
numcols,colx,coly,cole);
fprintf(fs,"#FitFunction: %s\n",fitfunc);
fprintf(fs,"#Initial parameters: %s\n",inipars);
fprintf(fs,"#NumberDataPoints: %d\n",ndata);
fprintf(fs,"#FitParameters: ");
for(i=0;i<FNpars;i++)
fprintf(fs,"%+14.7e ",params[i]);
fprintf(fs,"\n");
fprintf(fs,"#Chisquare: %+14.7e\n",chis);
fprintf(fs,"#P-val: %+14.7e\n",pval);
fprintf(fs,"%-14s %-14s\n","#1:X","2:Y");
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
//SAMPLING FUNCTION
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fprintf(stdout,"Sampling fitting function...\n",fitfile);
real2 x,y;
real2 xini=X[0];
real2 dx=(X[ndata-1]-X[0])/(ndata*nfac);
for(i=0;i<=ndata*nfac;i++){
x=xini+i*dx;
y=FFunc(x,params);
fprintf(fs,"%+14.7e %+14.7e\n",x,y);
}
fprintf(stdout,"Fitting result stored in %s...\n",fitfile);
fclose(fs);
return 0;
}
