--- a
+++ b/HRV.src/filtnn.c
@@ -0,0 +1,287 @@
+/* filtnn.c		Joe Mietus		Apr 1 2011 */
+
+/* filtnn.c		Joe Mietus		Oct 7 2008 */
+/* getline renamed to lineget May 18 2010 */
+
+/*
+filtnn :
+Usage: filtnn [options] filt hwin
+  Reads 2 (y,ann) or 3 (x,y,ann) columns from stdin and
+  filters NN intervals by marking intervals not within `filt'
+  range from the average of intervals
+  within a window `hwin' distance on either side of
+  current interval.
+  NEED TO DO A `sort -n' ON FILTERED SERIES TO RESTORE TIME ORDER
+  options are :
+  [-n] : print ratio of nnout to nnin to rrin
+  [-x min max] : exclude date outside min - max
+  [-p] : print excluded data at start/end of hwin buffer
+  [-C ann] : change annotation of excluded points to ann (default: X)
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#define MAXSTR 256
+#define MAXWIN 1024
+
+char *prog, line[MAXSTR], tmp[MAXSTR], ann[MAXWIN+1];
+int ncols;
+static double t, x[MAXWIN+1], y[MAXWIN+1];
+FILE *fp;
+
+
+main(argc, argv)
+int argc;
+char * argv[];
+{
+    char c, lastann;
+    int hwin, win, i, j, k, cflag, xflag, pflag, nflag, rrin, nnin, nnout;
+    double filt, filtmin, filtmax, min, max, mtmp, sum, av;
+
+    c = 'X';
+    cflag = xflag = pflag = nflag = rrin = nnin = nnout = 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 'n': nflag = 1;
+                      break;
+            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 'p': pflag = 1;
+                      break;
+            case 'C': cflag = 1;
+	              c = *argv[++i];
+                      break;
+            default:  usage();
+                      exit(1);
+        }
+    }
+
+    filtmax = 1.0 + filt;
+    filtmin = 1.0 - filt;
+
+    i = 0;
+    if (fgets(line, MAXSTR, stdin) == NULL) {
+	fprintf(stderr, "%s : no data read\n", prog);
+	exit(2);
+    }
+    if (sscanf(line, "%lf %lf %c %s", &x[i], &y[i], &ann[i], tmp) == 4) {
+	fprintf(stderr, "%s : incorrectly formatted data\n", prog);
+	exit(2);
+    }
+    else if (sscanf(line, "%lf %lf %c", &x[i], &y[i], &ann[i]) == 3) {
+        ncols = 3;
+    }
+    else if (sscanf(line, "%lf %c %s", &y[i], &ann[i], tmp) == 3) {
+	fprintf(stderr, "%s : incorrectly formatted data\n", prog);
+	exit(2);
+    }
+    else if (sscanf(line, "%lf %c", &y[i], &ann[i]) == 2) {
+        x[i] = t = y[i];
+        ncols = 2;
+    }
+    else {
+	fprintf(stderr, "%s : incorrectly formatted data\n", prog);
+	exit(2);
+    }
+
+    rrin++;
+    lastann = ann[i];
+    if (pflag)
+	cprintline(i, c);
+
+    while (i<=win) {
+        if (lineget(i) == EOF) {
+	    fprintf(stderr, "%s : insufficient data\n", prog);
+            exit(2);
+	}
+        rrin++;
+
+	if (ann[i] != 'N' || lastann != 'N') {
+	    if (pflag)
+	        printline(i);
+            lastann = ann[i];
+	}
+        else if (xflag && (y[i]<min || y[i]>max)) {
+	    if (pflag)
+	        cprintline(i, c);
+            lastann = ann[i];
+        }
+        else {
+	    if (pflag && i<hwin)
+	       cprintline(i, c);
+	    nnin++;
+            lastann = ann[i];
+	    i++;
+	}
+    }
+
+    j = hwin;
+
+    for (i=0; i<=win; i++)
+        sum += y[i];
+    sum -= y[j];
+    av = sum/win;
+    sum += y[j] - y[0];
+
+    if (y[j] <= filtmax*av && y[j] >= filtmin*av)
+        nnout++;
+    else
+        ann[j] = c;
+    printline(j);
+
+    i = 0;
+
+    while (lineget(i) != EOF) {
+        rrin++;
+
+	if (ann[i] != 'N' || lastann != 'N') {
+	    printline(i);
+            lastann = ann[i];
+	}
+        else if (xflag && (y[i]<min || y[i]>max)) {
+	    cprintline(i, c);
+            lastann = ann[i];
+        }
+        else {
+	    nnin++;
+	    if (++j > win)
+	        j = 0;
+
+	    sum += y[i];
+	    sum -= y[j];
+	    av = sum/win;
+	    lastann = ann[i];
+	    if (++i > win)
+		i = 0;
+	    sum += y[j] - y[i];
+
+	    if (y[j] <= filtmax*av && y[j] >= filtmin*av) {
+	        printline(j);
+	        nnout++;
+	    }
+	    else
+	        cprintline(j, c);
+	}
+    }
+
+    if (pflag)
+        for (i=0; i<hwin; i++) {
+            if (++j > win)
+                j = 0;
+            cprintline(j, c);
+        }
+
+    if (nflag)
+        fprintf(stderr, "nnout : nnin : rrin = %d : %d : %d = %g : %g = %g\n", 
+		nnout, nnin, rrin, (double)nnout/nnin, (double)nnin/rrin,
+		(double)nnout/rrin);
+
+    exit(0);
+}
+
+
+
+lineget(i)
+int i;
+{
+    int j;
+    static int n = 2;
+
+    if (fgets(line, MAXSTR, stdin) == NULL)
+        return(EOF);
+
+    if (ncols == 2) {
+        if ((j = sscanf(line, "%lf %c %s", &y[i], &ann[i], tmp)) != 2) {
+            fprintf(stderr, "%s: incorrectly formatted data : ", prog);
+	    fprintf(stderr, "line = %d\n", n);
+	    exit(2);
+        }
+	t += y[i];
+	x[i] = t;
+    }
+    else if (ncols == 3) {
+        if ((j = sscanf(line, "%lf %lf %c %s", &x[i], &y[i], &ann[i], tmp)) != 3) {
+            fprintf(stderr, "%s: incorrectly formatted data : ", prog);
+	    fprintf(stderr, "line = %d\n", n);
+	    exit(2);
+        }
+    }
+
+    n++;
+
+    return(j);
+}
+
+
+printline(i)
+int i;
+{
+    if (ncols == 3)
+        printf("%.9g ", x[i]);
+    printf("%.8g %c\n", y[i], ann[i]);
+}
+
+
+cprintline(i, c)
+int i;
+char c;
+{
+    if (ncols == 3)
+        printf("%.9g ", x[i]);
+    printf("%.8g %c\n", y[i], c);
+}
+
+
+usage()
+{
+    fprintf(stderr, "Usage: %s [options] filt hwin\n", prog);
+    fprintf(stderr, " Reads 2 (y,ann) or 3 (x,y,ann) columns from stdin and\n");
+    fprintf(stderr, " filters NN intervals by marking intervals not within `filt'\n");
+    fprintf(stderr, " range from the average of intervals\n");
+    fprintf(stderr, " within a window `hwin' distance on either side of\n");
+    fprintf(stderr, " current interval.\n");
+    fprintf(stderr, " NEED TO DO A `sort -n' ON FILTERED SERIES");
+    fprintf(stderr, " TO RESTORE TIME ORDER\n\n");
+    fprintf(stderr, " options are :\n");
+    fprintf(stderr, " [-n] : print ratio of nnout to nnin to rrin\n");
+    fprintf(stderr, " [-x min max] : exclude date outside min - max\n");
+    fprintf(stderr, " [-p] : print excluded data at start/end of hwin buffer\n");
+    fprintf(stderr, " [-C ann] : change annotation of excluded points to ann");
+    fprintf(stderr, " (default: X)\n");
+}