--- a
+++ b/HRV.src/filt.c
@@ -0,0 +1,277 @@
+/* filt.c		Joe Mietus		Apr 1 2011 */
+
+/* filt.c		Joe Mietus		Oct 7 2008 */
+/* getline renamed to lineget May 18 2010 */
+
+/*
+filt :
+Usage: filt filt hwin [options]
+  Reads 1 (y) or 2 (x,y) columns from stdin and
+  filters outliers by deleting those intervals outside
+  of `filt' range of the average within a window
+  `hwin' distance on either side of the
+  current interval.
+  options are :
+  [-x min max] : exclude date outside min - max
+  [-n] : print ratio of nout to nin
+  [-p file] : print excluded points to file
+              not including start/end hwin buffer
+  excluded points may not be printed in time
+  sequential order if -x opption is used
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+
+#define MAXSTR 256
+#define MAXWIN 1024
+
+char *prog, line[MAXSTR], tmp[MAXSTR];
+int ncols;
+static double x[MAXWIN+1], y[MAXWIN+1];
+FILE *fp;
+
+
+main(argc, argv)
+int argc;
+char * argv[];
+{
+    int hwin, win, i, j, k, nin, nout;
+    int xflag, nflag, pflag;
+    double filt, filtmin, filtmax, min, max, mtmp, sum, av;
+
+    xflag = 0;
+    nflag = pflag = nin = nout = 0;
+    sum = 0.0;
+    prog = argv[0];
+
+    if (argc < 3) {
+        usage();
+	exit(1);
+    }
+
+    i = 1;
+    if ((filt = atof(argv[i])) <= 0) {
+            fprintf(stderr, "%s: filt must be greater than 0\n",
+                    prog);
+            exit(2);
+    }
+    if ((hwin = atoi(argv[++i])) <= 0) {
+            fprintf(stderr, "%s: hwin must be integer greater than 0\n",
+                    prog);
+            exit(2);
+    }
+    if ((win = 2*hwin) > MAXWIN) {
+            fprintf(stderr, "%s: max hwin = %d\n", prog, MAXWIN/2);
+            exit(2);
+    }
+
+    for ( ; ++i < argc && *argv[i] == '-'; ) {
+        switch(argv[i][1]) {
+            case 'x': if (i+3 > argc) {
+	                  usage();
+			  exit(1);
+		      }
+	              min = atof(argv[++i]);
+	              max = atof(argv[++i]);
+                      if (min > max) {
+		          mtmp = min;
+			  min = max;
+			  max = mtmp;
+                      }
+	              xflag = 1;
+                      break;
+            case 'n': nflag = 1;
+                      break;
+            case 'p': if ((fp = fopen(argv[++i], "w")) == NULL)
+	                  fprintf(stderr, "%s : Can't open %s\n",
+				  argv[0], argv[i]);
+		      else
+			  pflag = 1;
+                      break;
+            default:  usage();
+                      exit(1);
+        }
+    }
+
+    i = 0;
+    if (fgets(line, MAXSTR, stdin) == NULL) {
+	fprintf(stderr, "%s : no data read\n", prog);
+	exit(2);
+    }
+    if (sscanf(line, "%lf %lf %s", &x[i], &y[i], tmp) == 3) {
+	fprintf(stderr, "%s : incorrectly formatted data\n", prog);
+	exit(2);
+    }
+    else if (sscanf(line, "%lf %lf", &x[i], &y[i]) == 2) {
+        ncols = 2;
+    }
+    else if (sscanf(line, "%lf %s", &x[i], tmp) == 2) {
+	fprintf(stderr, "%s : incorrectly formatted data\n", prog);
+	exit(2);
+    }
+    else if (sscanf(line, "%lf", &y[i]) == 1) {
+        ncols = 1;
+	x[0] = 0;
+    }
+    else {
+	fprintf(stderr, "%s : incorrectly formatted data\n", prog);
+	exit(2);
+    }
+
+    nin++;
+    if (pflag)
+        fprintline(i);
+
+    i++;
+    while (i<=win) {
+        if (lineget(i) == EOF) {
+	    fprintf(stderr, "%s : insufficient data\n", prog);
+            exit(2);
+	}
+        nin++;
+
+        if (xflag && (y[i]<min || y[i]>max)) {
+	    if (pflag)
+	        fprintline(i);
+        }
+        else {
+            if (pflag && i<hwin)
+	        fprintline(i);
+            i++;
+        }
+    }
+
+    i = 0;
+    j = hwin;
+
+    for (i=0; i<=win; i++)
+        sum += y[i];
+    sum -= y[j];
+    av = sum/win;
+    sum += y[j] - y[0];
+
+    filtmax = filtmin = filt * av;
+
+    if (y[j] <= av+filtmax && y[j] >= av-filtmin) {
+        printline(j);
+        nout++;
+    }
+    else if (pflag)
+        fprintline(j);
+
+    i = 0;
+
+    while (lineget(i) != EOF) {
+        nin++;
+
+	if (xflag && (y[i]<min || y[i]>max)) {
+	    if (pflag)
+                fprintline(i);
+	}
+        else {
+            if (++j > win)
+                j = 0;
+
+            sum += y[i] - y[j];
+	    av = sum/win;
+            if (++i > win)
+                i = 0;
+	    sum += y[j] - y[i];
+
+            filtmax = filtmin = filt * av;
+
+            if (y[j] <= av+filtmax && y[j] >= av-filtmin) {
+	        printline(j);
+                nout++;
+            }
+	    else {
+	        if (pflag)
+                    fprintline(j);
+            }
+	}
+    }
+
+    if (pflag) {
+        for (i=0; i<hwin; i++) {
+            if (++j > win)
+                j = 0;
+            fprintline(j);
+	}
+    }
+
+    if (nflag)
+        fprintf(stderr, "nout : nin = %d : %d = %g\n", 
+		nout, nin, (double)nout/nin);
+
+    exit(0);
+}
+
+
+
+lineget(i)
+int i;
+{
+    int j;
+    static int n = 1;
+
+    if (fgets(line, MAXSTR, stdin) == NULL)
+        return(EOF);
+
+    if (ncols == 1) {
+        if ((j = sscanf(line, "%lf %s", &y[i], tmp)) != 1) {
+            fprintf(stderr, "%s: incorrectly formatted data : ", prog);
+	    fprintf(stderr, "line = %d\n", n+1);
+	    exit(2);
+        }
+	x[i] = n;
+    }
+    else if (ncols == 2) {
+        if ((j = sscanf(line, "%lf %lf %s", &x[i], &y[i], tmp)) != 2) {
+            fprintf(stderr, "%s: incorrectly formatted data : ", prog);
+	    fprintf(stderr, "line = %d\n", n+1);
+	    exit(2);
+        }
+    }
+
+    n++;
+
+    return(j);
+}
+
+
+printline(i)
+int i;
+{
+    if (ncols == 2)
+        printf("%.9g ", x[i]);
+    printf("%g\n", y[i]);
+}
+
+
+fprintline(i)
+int i;
+{
+    if (ncols == 2)
+        fprintf(fp, "%.9g ", x[i]);
+    fprintf(fp, "%g\n", y[i]);
+}
+
+
+usage()
+{
+    fprintf(stderr, "Usage: %s filt hwin [options]\n", prog);
+    fprintf(stderr, " Reads 1 (y) or 2 (x,y) columns from stdin and\n");
+    fprintf(stderr, " filters outliers by deleting those intervals outside\n");
+    fprintf(stderr, " of `filt' range of the average within a window\n");
+    fprintf(stderr, " `hwin' distance on either side of the\n");
+    fprintf(stderr, " current interval.\n\n");
+    fprintf(stderr, " options are :\n");
+    fprintf(stderr, " [-x min max] : exclude date outside min - max\n");
+    fprintf(stderr, " [-n] : print ratio of nout to nin\n");
+    fprintf(stderr, " [-p file] : print excluded points to file\n");
+    fprintf(stderr, "             not including start/end hwin buffer\n");
+    fprintf(stderr, " excluded points may not be printed in time\n");
+    fprintf(stderr, " sequential order if -x opption is used\n");
+}