1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463
|
/*
gbbin (ver. 5.6) -- A program to bin data
Copyright (C) 1998-2018 Giulio Bottazzi
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
(version 2) as published by the Free Software Foundation;
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include "tools.h"
int main(int argc,char* argv[]){
double **data=NULL; /* array of values */
size_t rows=0,columns=0;
size_t steps=10;
size_t binum;
int numpres;
char *splitstring = strdup(" \t");
double wmin,wmax;
/* otpions */
char * const output_opts[] = {"xmean","xstd","xmin","xmax","xmedian","ymean","yadev","ystd","yvar","yskew","ykurt","ymin","ymax","ymedian","num",NULL};
size_t outnum;
size_t *outtype;
int o_verbose=0;
int o_printbinned = 0;
int o_window=0; /* if the windows to bin is provided */
/* variable to handle data splitting */
size_t printnum = 0;
size_t *printcolumn=NULL;
/* variables for reading command line options */
int opt;
/* set default output */
outnum=2;
outtype = (size_t *) my_alloc(2*sizeof(size_t));
outtype[0]=0;
outtype[1]=5;
/* COMMAND LINE PROCESSING */
/* read the command line */
while((opt=getopt_long(argc,argv,"vn:hF:O:xyc:w:",gb_long_options, &gb_option_index))!=EOF){
if(opt==0){
gbutils_header(argv[0],stdout);
exit(0);
}
else if(opt=='?'){
fprintf(stderr,"option %c not recognized\n",optopt);
return(-1);
}
else if(opt=='F'){
/*set the fields separator string*/
free(splitstring);
splitstring = strdup(optarg);
}
else if(opt=='n'){
/*set the number of steps*/
steps = (size_t) atoi(optarg);
}
else if(opt=='v'){
/*increase verbosity*/
o_verbose = 1;
}
else if(opt=='c'){
/* set the columns whose elements are required */
char *stmp1=strdup (optarg);
char *stmp2;
char *stmp3=stmp1;
o_printbinned = 1;
while( (stmp2=strsep (&stmp1,",")) != NULL && strlen(stmp2)>0 ){
printnum++;
printcolumn = (size_t *) my_realloc((void *) printcolumn,printnum*sizeof(size_t));
printcolumn[printnum-1]= (size_t) atoi(stmp2);
}
free(stmp3);
}
else if(opt=='x'){
/* print binned x values */
o_printbinned = 1;
printnum++;
printcolumn = (size_t *) my_realloc((void *) printcolumn,printnum*sizeof(size_t));
printcolumn[printnum-1]=1;
}
else if(opt=='y'){
/* print binned y values */
o_printbinned = 1;
printnum++;
printcolumn = (size_t *) my_realloc((void *) printcolumn,printnum*sizeof(size_t));
printcolumn[printnum-1]=2;
}
else if(opt=='O'){
/* set the output type */
char *subopts,*subvalue=NULL;
/* clear default settings */
outnum=0;
free(outtype); outtype=NULL;
/* define new output */
subopts = optarg;
while (*subopts != '\0'){
int itmp1 = getsubopt(&subopts, output_opts, &subvalue);
outnum++;
outtype = (size_t *) my_realloc((void *)outtype,outnum*sizeof(size_t));
if(itmp1 == -1){/* Unknown suboption. */
fprintf (stderr,"ERROR (%s): Unknown output type `%s'\n",
GB_PROGNAME,subvalue);
exit(1);
}
else
outtype[outnum-1]=(size_t) itmp1;
}
}
else if(opt=='w'){
/*set the binning window */
char *stmp1=strdup (optarg);
char *stmp2;
char *stmp3=stmp1;
stmp2=strsep (&stmp1,",");
if(strlen(stmp2)>0 && stmp1 != NULL && strlen(stmp1)>0){
wmin=atof(stmp2);
wmax=atof(stmp1);
}
else
fprintf(stderr,"ERROR (%s): provide comma separated min and max. Try option -h.\n",GB_PROGNAME);
free(stmp3);
o_window=1;
}
else if(opt=='h'){
/*print short help*/
fprintf(stdout,"Compute binned statistics. Data are read from standard input as records \n");
fprintf(stdout,"(X,Y1,Y2,...). Equipopulated bins are built with respect to the first field\n");
fprintf(stdout,"X. Option -O decide which statistics are printed for each bin. With options\n");
fprintf(stdout,"-x, -y or -c elements in different bins are split in different columns. \n");
fprintf(stdout,"\nUsage: %s [options]\n\n",argv[0]);
fprintf(stdout,"Options:\n");
fprintf(stdout," -n set the number of equipopulated bins (default 10) \n");
fprintf(stdout," -w min,max set manually the binning window. Ignored with -x,-y and -c \n");
fprintf(stdout," -O set the output with a comma separated list of variables: xmean, xmin, \n");
fprintf(stdout," xmax, xstd, xmedian, ymean, yadev, ystd, yvar, yskew, ykurt, ymin, \n");
fprintf(stdout," ymax, ymedian, num (default xmean, ymean) \n");
fprintf(stdout," -c# the values in column # are split in different columns; # can be a comma\n");
fprintf(stdout," separated list of columns \n");
fprintf(stdout," -x equivalent to -c 1 \n");
fprintf(stdout," -y equivalent to -c 2 \n");
fprintf(stdout," -F specify the input fields separators (default \" \\t\") \n");
fprintf(stdout," -v verbose mode\n");
fprintf(stdout,"Examples:\n");
fprintf(stdout," gbbin -n 20 < file split the records (line) in 20 bins according to first \n");
fprintf(stdout," field. Print the average value of the bin entries for \n");
fprintf(stdout," each column. If 'file' has 3 columns, the output has \n");
fprintf(stdout," twenty rows and three columns.\n");
fprintf(stdout," gbbin -O ymedian < file bin the records with respect to the first value and\n");
fprintf(stdout," print the median value of the other columns in each bin\n");
fprintf(stdout," gbbin -c 3 < file the binned values of the third columns are printed on \n");
fprintf(stdout," separate columns. The output has ten columns.\n");
exit(0);
}
}
/* END OF COMMAND LINE PROCESSING */
/* initialize global variables */
initialize_program(argv[0]);
/* load data: data[column][row] */
loadtable(&data,&rows,&columns,0,splitstring);
if(columns==2)
sort2(data[0],data[1],rows,2);
else if(columns>2)
sortn(data,columns,rows,0,2);
else{
fprintf(stdout,
"ERROR (%s): Provide at least two columns of input\n",GB_PROGNAME);
exit(1);
}
/* compute the size of the bins */
binum=rows/steps; /* number of points per bin */
numpres=rows%steps; /* number of residual points */
/* ++++++++++++++++++++++++++++ */
if(o_verbose == 1){
size_t i;
fprintf(stdout,"#read rows %zd\n",rows);
fprintf(stdout,"#read columns %zd\n",columns);
fprintf(stdout,"#number of bins %zd\n",steps);
fprintf(stdout,"#x support [%f,%f]\n",data[0][0],data[0][rows-1]);
fprintf(stdout,"#Output: ");
if(outnum==0){
fprintf(stdout,"%s %s\n",output_opts[0],output_opts[4]);
}
else{
for(i=0;i<outnum;i++)
fprintf(stdout,"%s ",output_opts[outtype[i]]);
fprintf(stdout,"\n");
}
}
/* ++++++++++++++++++++++++++++ */
if(o_printbinned == 0){ /* option -O */
size_t i,h,j;
double **stats;
size_t startindex=0,actualbinum;
/* set to 1 if the median has to be computed */
char o_xmedian,o_ymedian=0;
/* allocate space for the results of stat */
stats = (double **) my_alloc(columns*sizeof(double *));
for(i=0;i<columns;i++)
stats[i] = (double *) my_alloc(9*sizeof(double));
/* check if median for x and ys should be computed */
for(i=0;i<outnum;i++)
if(outtype[i]==4){
o_xmedian=1;
break;
}
for(i=0;i<outnum;i++)
if(outtype[i]==13){
o_ymedian=1;
break;
}
for(i=0;i<steps;i++){
/* chose the number of observations */
if(o_window == 1){/* windows width preset */
const double xmax= wmin+(wmax-wmin)*(i+1)/steps;
/* initially remove too small observations */
if(i==0){
for(j=startindex;j<rows;j++){
if(data[0][j] >= wmin)
break;
}
if(j>startindex) startindex=j;
}
/* chose the limit index of the observations in the windows */
actualbinum=0;
for(j=startindex;j<rows;j++){
if(data[0][j] <= xmax)
actualbinum++;
else
break;
}
}
else{/* equipopulated bins */
if(i==0){
actualbinum=binum+numpres/2;
}
else if(i==steps-1){
actualbinum=binum+numpres-numpres/2;
}
else{
actualbinum=binum;
}
}
/* compute stats for x values (first column) */
moment_short(data[0]+startindex,actualbinum,stats[0],stats[0]+1,stats[0]+2,stats[0]+3);
if(o_xmedian==1){ /* need to compute the median */
double* vals = (double *) my_alloc(actualbinum*sizeof(double));
for (j=0;j<actualbinum;j++)
vals[j]=data[0][startindex+j];
qsort(vals,actualbinum,sizeof(double),sort_by_value);
stats[0][8] = (actualbinum%2 ==0 ? .5*(vals[actualbinum/2-1]+vals[actualbinum/2]) : vals[(actualbinum-1)/2]);
free(vals);
}
/* compute stats for y values (from the second columns) */
for(h=1;h<columns;h++){
moment(data[h]+startindex,actualbinum,
stats[h],stats[h]+1,stats[h]+2,stats[h]+3,
stats[h]+4,stats[h]+5,stats[h]+6,stats[h]+7);
if(o_ymedian==1){ /* need to compute the median */
double* vals = (double *) my_alloc(actualbinum*sizeof(double));
for (j=0;j<actualbinum;j++)
vals[j]=data[h][startindex+j];
qsort(vals,actualbinum,sizeof(double),sort_by_value);
stats[h][8] = (actualbinum%2 ==0 ? .5*(vals[actualbinum/2-1]+vals[actualbinum/2]) : vals[(actualbinum-1)/2]);
free(vals);
}
}
/*
output options
0 "xmean"
1 "xstd"
2 "xmin"
3 "xmax"
4 "xmedian"
5 "ymean"
6 "yadev"
7 "ystd"
8 "yvar"
9 "yskew"
10 "ykurt"
11 "ymin"
12 "ymax"
13 "ymedian"
14 "num"
statistics in array 'stat'
0 "mean"
1 "adev"
2 "std"
3 "var"
4 "skew"
5 "kurt"
6 "min"
7 "max"
8 "median"
returned by moments
0 ave
1 adev
2 sdev
3 var
4 skew
5 curt
6 min
7 max
returned by moments_short
0 ave
1 sdev
2 min
3 max
*/
/* output */
for(j=0;j<outnum-1;j++)
if(outtype[h]==14) /* number of observations */
printf(FLOAT_SEP, (double) actualbinum );
else if(outtype[j]<4) /* x values stat */
printf(FLOAT_SEP,stats[0][outtype[j]]);
else if(outtype[j]==4) /* x median */
printf(FLOAT_SEP,stats[0][8]);
else
for(h=1;h<columns;h++) /* y values stat */
printf(FLOAT_SEP,stats[h][outtype[j]-5]);
if(outtype[outnum-1]==14) /* number of observations */
printf(FLOAT_NL, (double) actualbinum);
else if(outtype[outnum-1]<4) /* x values stat */
printf(FLOAT_NL,stats[0][outtype[j]]);
else if(outtype[j]==4) /* x median */
printf(FLOAT_SEP,stats[0][8]);
else{
for(h=1;h<columns-1;h++) /* y values stat */
printf(FLOAT_SEP,stats[h][outtype[outnum-1]-5]);
printf(FLOAT_NL,stats[columns-1][outtype[outnum-1]-5]);
}
startindex+=actualbinum;
}
/* deallocate stat */
for(i=0;i<columns;i++) free(stats[i]);
free(stats);
}
else{/* options -c, -x or -y */
size_t i,j,h;
/* check that the column spec are OK */
for(h=0;h<printnum;h++)
if(printcolumn[h]>columns){
fprintf(stdout,
"ERROR (%s): Col spec %zd larger than number of col\n",
GB_PROGNAME,printcolumn[h]);
exit(1);
}
for(j=0;j<binum;j++){
for(i=0;i<steps;i++)
for(h=0;h<printnum;h++)
printf(FLOAT_SEP,data[printcolumn[h]-1][j+i*binum]);
printf("\n");
}
for(j=binum;j<binum+numpres/2;j++){
for(h=0;h<printnum;h++)
printf(FLOAT_SEP,data[printcolumn[h]-1][j]);
for(i=0;i<steps-2;i++)
for(h=0;h<printnum;h++)
printf(EMPTY_SEP,"nan");
if(steps>1)
for(h=0;h<printnum;h++)
printf(FLOAT_SEP,data[printcolumn[h]-1][j+(steps-1)*binum]);
printf("\n");
}
for(j=binum+numpres/2;j<binum+numpres-numpres/2;j++){
for(i=0;i<steps-1;i++)
for(h=0;h<printnum;h++)
printf(EMPTY_SEP,"nan");
for(h=0;h<printnum;h++)
printf(FLOAT_SEP,data[printcolumn[h]-1][j+(steps-1)*binum]);
printf("\n");
}
}
return(0);
}
|