Changeset 3778 for PP/trunk/BAP/GENBAP_AWW_2.TXT

Timestamp:

01/26/09 16:33:10 (4 years ago)

Author:

awwalter

Message:

 

File:

• PP/trunk/BAP/GENBAP_AWW_2.TXT (modified) (44 diffs)

PP/trunk/BAP/GENBAP_AWW_2.TXT

@@ -732 +732 @@
 
     // Padding parameters:
-    //      PADSEC(1 & 2) = length of the leading and trailing pad
-    //                      areas, in seconds.
+    //      PADSEC(1 & 2) = length of the leading and trailing pad areas, in seconds.
     public static double [] padsec = new double[2];
 
     //      TAPSEC(1 & 2) = taper length used with the datataper option.
-    //                Given as number of seconds in the taper.
-    //                Usually= 0.2.
+    //                      Given as number of seconds in the taper. Usually= 0.2.
     public static double [] tapsec = new double[2];
 
-    //      MTAPER(1 & 2) = tapering option, one for each end of the
-    //               time series.  Usually = 0.
+    //      MTAPER(1 & 2) = tapering option, one for each end of the time series. Usually = 0.
     //             = 0=> notaper,
     //             = 1=> zcross,
@@ -1568 +1565 @@
       int ndamp = BapRSI.rsiDamping.length;
       int nper = BapRSI.rsiPeriod.length;
-      nwant6 = 2*nper + nper*ndamp;
+      int nwant6 = 2*nper + nper*ndamp;
 
       //nwant = Math.max(nwant0,nwant1,nwant2,nwant3,nwant4,nwant5,nwant6);
@@ -1796 +1793 @@
          if (ndone<npandd) {
             System.out.printf(lunmsg, 2001) npandd, ndone, lenwrk;
-            warn("*");
+            BapUtil.warn("*");
             npandd = ndone;
             if (ndone>npadl+ndata) {
@@ -1972 +1969 @@
                   if (npadl!=0 || npadt!=0) {
                      System.out.printf(lunmsg, 2004) npadl, npadt;
-                     warn("*");
+                     BapUtil.warn("*");
                   }
                   LINCOR(lunusr, lunmsg, rp.dptim1,dpdelt,
@@ -2110 +2107 @@
 // cccccccccccccccccccc (end of BAP2/BAP)cccccccccccccccccccccccccccccccccc
 
-  WCOPY(work1,work2,npoint) {
-      float work1(npoint), work2(npoint);
-//   WCOPY is called from BAP2 to copy the contents of WORK1() into WORK2().
-//   Note that we would not need WCOPY or need to deal with 3 separate
-//         working arrays except that we may want to keep each array
-//         smaller than the 64K byte (=16K reals) segment limit in
-//         80x86 computers.  See comments in BAP.FOR for more info.
-      do 100 i =1,npoint;
-      work2(i)=work1(i);
-  100 continue;
+  //   WCOPY is called from BAP2 to copy the contents of WORK1() into WORK2().
+  //   Note that we would not need WCOPY or need to deal with 3 separate
+  //         working arrays except that we may want to keep each array
+  //         smaller than the 64K byte (=16K reals) segment limit in
+  //         80x86 computers.  See comments in BAP.FOR for more info.
+  WCOPY(float[] work1, float[] work2, npoint) {
+      System.arraycopy(work1, 0, work2, 0, npoint);
   }
 // cccccccccccccccccccc (end of WCOPY/BAP2/BAP) ccccccccccccccccccccccccccc
-//
+
+
 //   IDSTEP is called from BAP2 to write information about the current
 //          processing step to the run messages file and to the user
@@ -2176 +2171 @@
                   sb.append("    Better to reduce the sampling rate in the DECIM step, which is done after the INSCOR step. ***");
                   System.out.println(sb.toString());
-                  warn("*");
+                  BapUtil.warn("*");
                else if (rp.spsnew>rp.spsin && rp.spsin>0.0 && (!rp.mdo[BapSteps.khicut]) ) {
                   double x=rp.spsin/2.0;
@@ -2186 +2181 @@
                   sb.append("    But the HICUT step was *not* requested in this run.  ***%n"
                   System.out.printf(sb.toString(), x);
-                  warn("*");
+                  BapUtil.warn("*");
                }
             } else {
                System.out.println("*** ERROR, INTERP step is only applicable for an unevenly-sampled time series.\n" +
                  "    (This restriction may be removed in future versions.) Ending Run. ***");
-               warn("*");
+               BapUtil.warn("*");
             }
          }
@@ -2268 +2263 @@
             rp.jpad=1;
             System.out.printf("*** WARNING: JPAD=0 invalid when decimation is requested; jpad reset to %2d ***", rp.jpad);
-            warn("*");
+            BapUtil.warn("*");
 
          //  e) reset jpad if jpad = 4 is not required
@@ -2286 +2281 @@
                if (jwas!=5) {
                   System.out.printf("*** WARNING: jpad=%2d is invalid here, jpad reset to %2d ***%n", jwas, rp.jpad);
-                  warn("*");
+                  BapUtil.warn("*");
                }
             }
@@ -2352 +2347 @@
        "sampling rate is genuinely required here.)  ***");
 
-               warn("*");
+               BapUtil.warn("*");
             } else if (rp.mdo[BapSteps.kintrp] ) {
                StringBuffer sb = new StringBuffer(256);
@@ -2359 +2354 @@
                sb.append("    But BOTH interpolations have been requested in this BAP run! ***");
                System.out.println(sb.toString());
-               warn("*");
+               BapUtil.warn("*");
             }
          } else {
@@ -2367 +2362 @@
                doit=false;
                System.out.println("    ***    NO decimation performed when ndense < 2.");
-               warn("*");
+               BapUtil.warn("*");
             } else {
                x = outValue/outMode;
@@ -2381 +2376 @@
               System.out.printf( "    Unless HICUT was previously applied or no frequencies are greater than %12.5g Hz,%n", x);
               System.out.println("    the DECIMated time-series generated here will probably contain aliasing errors. ***");
-              warn("*");
+              BapUtil.warn("*");
          }
 
@@ -2415 +2410 @@
                rp.velfit=false;
                System.out.print("    *** WARNING: the VELFIT option does not apply when the LOCUT2 option is on. ***");
-               warn("*");
+               BapUtil.warn("*");
             }
             if (rp.motion!=1 && rp.motion!=4) rp.locut2=false;
@@ -2424 +2419 @@
                     "    *** WARNING: the LOCUT2 option does not apply when the LOCUT step is off or when MOTION is not = acc. ***"
                 );
-               warn("*");
+               BapUtil.warn("*");
             }
          } else {
@@ -2470 +2465 @@
                   System.out.printf(lunmsg, 2003);
  2003 System.out.print(" *** WARNING: the VELFIT option should usually not be used when the LOCUT step is applied. ***");
-                  warn("*");
+                  BapUtil.warn("*");
                }
             }
@@ -2489 +2484 @@
 // cccccccccccccccccccc (end of BAP/IDSTEP) ccccccccccccccccccccccccccccccc
 
-  warn(onec, lunusr,lunmsg) {
-      String onec;
-
-//   WARN: warn user by rining terminal bell and/or stopping, depending
-//         on the value of IWARN (in BAPINOUT.INC).
-//         IWARN = 3 => ring bell, tell user how to change IWARN,
-//                      then stop
-//         IWARN = 2 => IWARN = 3 if ONEC="*", = IWARN=1 otherwise
-//         IWARN = 1 => ring bell and return
-//         IWARN = 0 => return.
-
-//   On entry --
-//     ONEC   = "+" or "*" to indicate how severe the warning is,
-//                with "*" being more severe than "+".
-//     LUNUSR = boolean unit number for the user terminal.
-//     LUNMSG =  "                  for the run messages file.
-
-      include "bapsteps.inc";
-      include "bapinout.inc";
-
-      if (rp.iwarn!=0) bell(6);
-      if (rp.iwarn>2 || (rp.iwarn==2 && onec=="*")) {
-         System.out.printf(lunusr,1000);
-         if (lunusr!=lunmsg) {
-            System.out.printf(lunmsg,1001);
-            System.out.printf(lunmsg,1000);
-         }
-         BapUtil.woe(-2);
-      }
-      return;
-
- 1000 System.out.print(5x,"WARN=STOP.  If you wish processing to proceed despite the above warning,"
-      /17x,"reset WARN=BELLS in the BAP run parameters list, then", " rerun." /17x,"Ending Run.");
- 1001 System.out.print(" >>> 6 bells.");
-  }
-// cccccccccccccccccccc (end of warn) cccccccccccccccccccccccccccccccccccc
-
-//  SHOWZ: display info about the pad for DEBUG runs
-  showz (npadl,ndata,npadt, workA, npandd) {
-      float workA(npandd);
-      int idebug;
-      float debugr;
-      equivalence (debugr, idebug);
-
-      nfar = 0;
-      do 10 jjj=1,npadl;
-      debugr = workA(jjj);
-      if (idebug!=0) {
-         print *, " first non-zero value: i, v=",jjj,debugr;
-         nfar = npadl-jjj +300;
-         if (jjj<300) nfar=npadl;
-         goto 12;
-      }
- 10   continue;
-         print *, " NO non-zero leading pad values!";
-         nfar = npadl;
- 12   continue;
-      print *, " ";
-      do 20 jjj=npadl-nfar+1,npadl-nfar+600,50;
-      if (jjj <=0 || jjj>npandd) goto 20;
-      debugr = workA(jjj);
-      System.out.printf(" Debug r&h= %7d %15.7e %10x", jjj,debugr,idebug);
-   20 continue;
-      print *, " ";
-      do 30 jjj=npadl+ndata +nfar-1,
-                     npadl+ndata +nfar-601, -50;
-      if (jjj <=0 || jjj>npandd) goto 30;
-      debugr = workA(jjj);
-      System.out.printf(" Debug r&h= %7d %15.7e %10x", jjj,debugr,idebug);
-   30 continue;
-
-  200 continue;
-      print *, " ";
-      print *, " SHOWZ: npadl, ndata, npadt",npadl,ndata,npadt;
-      print *, "        npadl + ndata=", npadl+ndata;
-      print *, " ";
-      return;
-  }
-// cccccccccccccccccccc (end of showz) ccccccccccccccccccccccccccccccccccccc
+
 
   BAPSET(lunans,lunusr, lundsk,lundat, luntmp,luntm2) {
@@ -5136 +5053 @@
             n = min (130-27,ncout);
             System.out.printf(lunmsg,1020) fmtout, filnam(1:n);
-            warn("*");
+            BapUtil.warn("*");
          }
       }
@@ -6529 +6446 @@
 // cccccccccccccccccccc (end of QLBL/HDRLBL/BANNER) cccccccccccccccccccccc
 
-//   BAPSPS:  Linearly interpolate the BAP input time series to SPSNEW
-//            samples per second.
-//            Note that this subroutine does *not* apply any high-cut
-//            filter to remove alias errors.
+//   BAPSPS:  Linearly interpolate the BAP input time series to SPSNEW samples per second.
+//            Note that this subroutine does *not* apply any high-cut filter to remove alias errors.
 //   On entry--
 //     SPS      = input sample rate if workA() contains an evenly-sampled
@@ -6585 +6500 @@
       // I also have not decided whether or not to just ignore back-stepping samples in an unevenly-sampled input time series.
 
-      public static final boolean MOVET1=false;
-      public static final boolean IGBACK =false;
-
-      //   Sanity checks:
+      public static final boolean MOVET1 = false;
+      public static final boolean IGBACK = false;
+
+      // Sanity checks:
       if (BapConstants.small > rp.spsnew) BapUtil.woe(0);
       if (BapConstants.small > Math.abs(rp.spsnew-sps)) BapUtil.woe(0);
@@ -6643 +6558 @@
                }
             }
-            warn("*");
+            BapUtil.warn("*");
          }
       }
@@ -6684 +6599 @@
                  nwork -= 1;
                  System.out.printf(" *** Truncating time series at %13.5e s due to array size. Length of the array =%8d. ***%n", time, lenwrk);
-                 warn("*");
+                 BapUtil.warn("*");
                  break;
               }
@@ -6815 +6730 @@
       // Get the time interval at beginning and end of the t.s. in which to calculate mean value or llsqf line.
 
-      for (int ii=0; ii==1; ii++) {
+      for (int ii=0; ii<=1; ii++) {
 
         ibeg = Math.min( Math.max(0, ifromt(tskew[0+ii])), ilast );
@@ -6836 +6751 @@
             xy0 =BapLLSQF.y0;
 
-            for (int i=ibeg; i==iend; i++) {
+            for (int i=ibeg; i<=iend; i++) {
               workB[ib++] = (float) (worka[i] - xy0 - xslope*tfromi(i));    // B = A - (llsq fit line value) 
             }
@@ -6842 +6757 @@
           } else {
              // sum the values in the interval
-             for (int i=ibeg; i==iend; i++) {
+             for (int i=ibeg; i<=iend; i++) {
                xy0 = xy0 + worka[i];
              }
              xy0 = xy0/(iend-ibeg + 1); // mean value
 
-             for (int i=ibeg; i==iend; i++) {
+             for (int i=ibeg; i<=iend; i++) {
                workB[ib++]= (float) (worka[i] - xy0); // B = A - (mean value) 
              }
@@ -6887 +6802 @@
 //   Find the first and last zero-crossings in the WORK() array.
 //   On entry --
-//      SMIDGE, WORK(),NPTS
+//      SMIDGE, WORK()
 //   On return --
 //      IZC1 = first sample to retain w.r.t. first zero crossing
@@ -6895 +6810 @@
   int izc1 = -1;
   int izcn = -1;
-  int npts = 0;
-
-  public void calcZeroCrossings(double smidge, float[] work, int npts) {
+
+  public void calcZeroCrossings(double smidge, float[] work) {
+      calcZeroCrossings(smidge, work, 0, work.length-1);
+  }
+
+  public void calcZeroCrossings(double smidge, float[] work, int idatan) {
+      calcZeroCrossings(smidge, work, 0, idatan);
+  }
+
+  public void calcZeroCrossings(double smidge, float[] work, int idata1, int idatan) {
+
       int j = 0;
-      if (work[0]==0.f || Math.abs(work[0])<smidge) {
-         izc1=0;
-      } else if (npts>2) {
-        for (int i=2; i<npts-1; i++) {
-          if (work[i]*work[0] < 0.f) {
-            izc1=0;
+      double dx = Math.abs(smidge); 
+
+      int ndata = idatan-idata1+1;
+
+      float data1 = work[idata1];
+      float datan = work[idatan];
+
+      if ( Math.abs(data1) < dx) {
+         izc1= idata1;
+      } else if (ndata>2) {
+        for (int i=idata1+1; i <= idatan-1; i++) {
+          if (work[i]*data1 < 0.f) {
+            izc1=idata1;
             j=i;
             if (Math.abs(work[i-1]) < Math.abs(work[i])) j=i-1;
-            if (Math.abs(work[j]) < Math.abs(work[0])) izc1=i;
+            if (Math.abs(work[j]) < Math.abs(data1)) izc1=i;
             break;
           }
@@ -6913 +6843 @@
       }
 
-      if (work[npts-1]==0.f || Math.abs(work[npts-1])<smidge) {
-         izcn=npts-1;
-      } else if (npts>2 && izc1 < npts-1) {
-        for i= npts-2; i=Math.max(0, izc1-1), i--) {
-          if (work[i]*work[npts-1] < 0.f) {
-            izcn=npts-1;
+      if (Math.abs(datan) < dx) {
+         izcn=idatan;
+      } else if (ndata>2 && izc1 < idatan) {
+        for i= idatan-1; i >= Math.max(idata1, izc1-1), i--) {
+          if (work[i]*datan < 0.f) {
+            izcn=idatan;
             j=i;
             if (Math.abs(work[i+1]) < Math.abs(work[i])) j=i+1;
-            if (Math.abs(work[j]) < Math.abs(work[npts-1])) izcn=i;
+            if (Math.abs(work[j]) < Math.abs(datan)) izcn=i;
             break;
           }
         }
       }
+
   }
 // cccccccccccccccccccc (end of ZCROSS) ccccccccccccccccccccccccccccccccc
@@ -7011 +6942 @@
          y0 = BapLLSQF.y0;
       } else if (rp.mmean) {  // slope=0. and y0 is mean bias over fit interval
-         for (int i = ibegf; i==iendf; i++) {
+         for (int i = ibegf; i<=iendf; i++) {
              y0 += worka[i];
          }
@@ -7019 +6950 @@
       // Subtract the line
       if (slope ==0.0) {  // Remove constant/bias value
-        for (int i = ibegl; i==iendl; ii++) {
+        for (int i = ibegl; i<=iendl; ii++) {
             worka[i] = (float) (worka(i) - Y0);
         }
       } else { // remove line with slope
-        for (int i = ibegl; i==iendl; ii++) {
+        for (int i = ibegl; i<=iendl; ii++) {
             worka[i] = (float) (worka[i] - Y0 - slope*(dptim1 + dpdelt*i));
         }
@@ -7424 +7355 @@
          sb.append("    Leading/trailing pads truncated to %7d/%7d samples. ***%n");
          System.out.printf(sb.toString(), lenwrk, newpts, newz[0], newz[1]);
-         warn("*"); // throw Exception ?
+         BapUtil.warn("*"); // throw Exception ?
       } else if (rp.jpad==4 || rp.jpad==5) {
          nn = Math.round(newpts*ratio);
@@ -7440 +7371 @@
             if (morez[1] <0) BapUtil.woe(0);
             System.out.printf("    to %8d, " and %8d points. ***%n", morez[0], morez[1]);
-            warn("*"); // throw Exception ?
+            BapUtil.warn("*"); // throw Exception ?
          }
       }
@@ -7493 +7424 @@
 // cccccccccccccccccccc (end of PADLEN) ccccccccccccccccccccccccccccccccccc
 
-  BAPPAD(lunusr,lunmsg,mtaper,tapsec, sps,work,morelz,newlz,ndata,newtz, doit2) {
-      float    work(morelz+newlz+ndata+newtz);
-      float    tapsec(2);
-      int mtaper[1];
-      boolean doit2;
-
 //   BAPPAD pads the time series in WORK() with leading and trailing
 //          zeros, then smooths the discontinuity between the data and
 //          the pad areas according to the tapering option, MTAPER.
-
 //   On entry --
-//     LUNMSG   = lun for run messages  = user terminal or disk file.
-//     LUNUSR   =   "                   = user terminal.
 //     MTAPER() = tapering option, one for each end of the time-series:
 //              = 0=> notaper
-//              = 1=> zcross    = reset to zero all values for samples
-//                                that occur before the first zero
-//                                crossing or after the last zero
-//                                crossing
-//              = 2=> datataper = apply a cosine taper at the end of
-//                                the time series.
-//     TAPSEC() = taper length used with the datataper option, in
-//                  seconds.  TAPSEC indicates the number of points to
-//                  be used in the taper, excluding the endpoints at
-//                  taper-factor = 0.0 and at taper-factor = 1.0.
+//              = 1=> zcross    = reset to zero all sample values, before the first and after the last, zero crossing
+//              = 2=> datataper = apply a cosine taper at the ends of the time series.
+//     TAPSEC() = taper length used with the datataper option, in seconds.
+//                TAPSEC determines the number of points to be used in the taper, excluding endpoints 
+//                taper-factor = 0.0 and at taper-factor = 1.0 (ie. ntaper = secs*sps-2).
 //     SPS      = sampling rate
-//     WORK()   = array containing a time-series plus free space for
-//                  padding.  The unpadded input time series is in
-//                  locations 1 thru NDATA.
-//     MORELZ   = empty space to be left at the beginning of the padded
-//                  time series.  (Will be used in the second padding
-//                  step)
+//     WORK()   = array containing a time-series plus free space for padding.
+//                The unpadded input time series is in locations 0 thru NDATA-1.
+//     MORELZ   = empty space to be left at the beginning of the padded time series for a second padding step.
 //     NEWLZ    = number of zeros requested for the leading pad.
-//     NDATA    = number of samples (beginning at WORK(1)) in the
-//                  input time series.
+//     NDATA    = number of samples (beginning at WORK[0]) in the input time series.
 //     NEWTZ    = number of zeros requested for the trailing pad.
-
-//     NOTES:
-//       - Before calling BAPPAD, the caller must make certain that
-//         there is enough space in WORK() to contain NEWLZ+NDATA+NEWTZ
-//         samples.
-//       - NEWLZ and NEWTZ may =0 if tapering is wanted, without the
-//         padding.  (As might be appropriate when VELFIT=true)
-
+//
+//       - Before calling BAPPAD, WORK array must be long enough to contain NEWLZ+NDATA+NEWTZ samples.
+//       - NEWLZ and NEWTZ may =0 if tapering is wanted, without the padding. (As might be appropriate when VELFIT=true)
 //   On return --
-//     WORK()   = contains the padded time series in locations MORELZ +1
-//                  thru MORELZ + newlz + NDATA + newtz.
-//     DOIT2    = false if there really was not any padding or tapering
-//                  applied to the time series.
-
-      include "bapconst.inc";
-      include "tempcs.inc";
-      public static final double pi =3.1415926535;
-      float ntaper(2);
-      boolean shift;
-
-      lztot = newlz+morelz;
-      doit2 = true;
+//     WORK  = contains the padded time series in index locations MORELZ thru MORELZ+newlz+NDATA+newtz-1.
+
+public class BapPad {
+
+  // Returns false if no padding or tapering was applied to the time series.
+  public boolean pad(int[] mtaper, float[] tapsec, double sps, float[] work, int morelz, int newlz, int ndata, int newtz) {
+
+      // Input work(morelz+newlz+ndata+newtz);
+
+      boolean doit2 = true;
+
       if (newlz==0 && newtz==0) {
-         if (rp.mtaper[0]==0 && rp.mtaper[1]==0) {
-            System.out.printf(lunmsg,1000);
-            if (lunusr!=lunmsg) System.out.printf(lunusr,1000);
-         }
          if (rp.mtaper[0]<=0 && rp.mtaper[1]<=0) {
+            System.out.println("No padding requested (NEWLZ=NEWTZ=0).");
             doit2 = false;
-            if (morelz<=0) return;
-         }
-      }
-
-      ntaper[0] = Math.max(0, Math.round(rp.tapsec[0]*sps) -2);
-      ntaper[1] = Math.max(0, Math.round(rp.tapsec[1]*sps) -2);
-
-       data1 = work(1);
-       datan = work(ndata);
-      idata1 = lztot + 1;
-      idatan = lztot + ndata;
-
-//   Shift the time series forward in WORK(), to leave room for the
-//      leading pad.
-
-      shift  = true;
-      if (lztot<=0) shift=false;
-      smidge = 0.;
-      do 120 i = idatan,idata1, -1;
-      if (shift) work[i] = work(i-lztot);
-      if (Math.abs(work[i]) > smidge) smidge = Math.abs(work[i]);
-  120 continue;
-      if (!doit2) return;
+            if (morelz<=0) return false; // no taper and no extra zeroes requested for later padding so we're done
+         }
+      }
+
+      // If adding zeroes, shift the data time series forward (to right) in WORK array, leaving room for the leading pad.
+      int lztot = newlz+morelz;
+      idata1 = lztot; // first sample index
+      idatan = lztot + ndata-1; // last sample index
+      boolean shift = (lztot > 0) ? true : false;
+
+      double smidge = 0.;
+      for (int i = idatan; i>=idata1; i--) {
+        if (shift) work[i] = work[i-lztot];
+        if (Math.abs(work[i]) > smidge) smidge = Math.abs(work[i]);
+      }
+
+      if (! doit2) return false; // no tapers and newlz=newtz=0
+
+      // Set smidge as a fractional part of the largest absolute data offset 
       smidge = BapConstants.small*smidge;
 
-//   If the "ZCROSS" taper option was specified, find the first and last
-//   zero-crossings in the time-series.
-
+      // If the "ZCROSS" taper option was specified, find the first and last zero-crossings in the time-series.
+/*
       izc1=-1;
       izcn=-1;
-      if (rp.mtaper[0]==1 || rp.mtaper[1]==1) {
+      float data1 = work[idata1];
+      float datan = work[idatan];
+      if (rp.mtaper[0]==1 || rp.mtaper[1]==1) { // 1= ZCROSS
          if (Math.abs(data1)<smidge) {
             izc1=idata1;
          } else if (ndata>2) {
-            do 31 i=idata1+1, idatan-1;
-            if (work[i]*data1<0.0) {
-               izc1=idata1;
-               j=i;
-               if (Math.abs(work(i-1)) < Math.abs(work[i])) j=i-1;
-               if (Math.abs(work(j)) < Math.abs(data1)) izc1=i;
-               goto 32;
+            for (i=idata1+1; i <= idatan-1; i++) {
+              if (work[i]*data1<0.f) {
+                izc1=idata1;
+                j=i;
+                if (Math.abs(work[i-1]) < Math.abs(work[i])) j=i-1;
+                if (Math.abs(work[j]) < Math.abs(data1)) izc1=i;
+                break;
+              }
             }
-   31       continue;
-   32       continue;
          }
          if (Math.abs(datan)<smidge) {
             izcn=idatan;
          } else if (ndata>2 && izc1 < idatan) {
-            do 33 i= idatan-1, Math.max(idata1,izc1-1), -1;
-            if (work[i]*datan<0.0) {
-               izcn=idatan;
-               j=i;
-               if (Math.abs(work(i+1)) < Math.abs(work[i])) j=i+1;
-               if (Math.abs(work(j)) < Math.abs(datan)) izcn=i;
-               goto 34;
+            for (int i= idatan-1; i >= Math.max(idata1, izc1-1); i--) {
+              if (work[i]*datan<0.f) {
+                 izcn=idatan;
+                 j=i;
+                 if (Math.abs(work[i+1]) < Math.abs(work[i])) j=i+1;
+                 if (Math.abs(work[j]) < Math.abs(datan)) izcn=i;
+                 break;
+              }
             }
-  33        continue;
-  34        continue;
-         }
-         if (izcn<=izc1 || izc1<0) {
-            System.out.printf(lunmsg,1101);
-            if (lunusr!=lunmsg) System.out.printf(lunusr,1101);
-            warn("*");
-            if ((rp.mtaper[0]==1 && rp.mtaper[1]==1) ||
-                (rp.mtaper[0]==1 && izc1==-1)     ||
-                (rp.mtaper[1]==1 && izcn==-1)    ) {
-// +++          BapUtil.woe(2)  +++ do we want to continue here or croak?
+         }
+*/
+         BapZCross.calcZeroCrossings(smidge, work, idata1, idatan);
+         izc1 = BapZcross.izc1;
+         izcn = BapZcross.izcn;
+
+         if (izcn <= izc1 || izc1 < 0) {
+            System.out.println(" *** The ZCROSS option should not be used with this data; it does not contain two zero crossings!***");
+            BapUtil.warn("*");
+            if ((rp.mtaper[0]==1 && rp.mtaper[1]==1) || (rp.mtaper[0]==1 && izc1==-1) || (rp.mtaper[1]==1 && izcn==-1)) {
+               // BapUtil.woe(2)  +++ do we want to continue here or croak?
                izc1 = idata1;
                izcn = idatan;
@@ -7631 +7531 @@
       }
 
-//   Begin Loop to pad and taper each end of the time-series.
-
-      do 500 ipad = 1,2;
-      itap = rp.mtaper[ipad];
-      nzdata = 0;
-      k2beg = 9;
-      if (ipad==1) {
-         tempcs(1:8) = "leading ";
-         tempcs(9:13)= "first";
-         k2end  = 13;
-         locbeg = 1;
-         locend = lztot;
-         npad   = newlz;
-         ilow   = idata1;
-         jdir   = -1;
-         if (itap==1) {
-            locend = izc1 -1;
-            nzdata = locend - lztot;
-         }
-      } else {
-         tempcs(1:8) = "trailing";
-         tempcs(9:12)= "last";
-         k2end  = 12;
-         locbeg = 1     + idatan;
-         locend = newtz + idatan;
-         npad   = newtz;
-         ilow   = idatan;
-         jdir   = 1;
-         if (itap==1) {
-            locbeg = izcn +1;
-            nzdata = idatan -izcn;
-         }
-      }
-
-//   a) Pad with zeros and, if requested, extend the zeros into the
-//      data area, up to the first zero crossing.
-
-      if (locbeg<locend) {
-         do 10 i= locbeg,locend;
-         work[i]= 0.0f;
-   10    continue;
-         System.out.printf(lunmsg,1002) npad, tempcs(1:8);
-         if (lunusr!=lunmsg) System.out.printf(lunusr,1002) npad, tempcs(1:8);
-         if (itap==1 && nzdata>0) {
-             System.out.printf(lunmsg,1030) tempcs(k2beg:k2end), nzdata;
-             if (lunusr!=lunmsg) System.out.printf(lunusr,1030) tempcs(k2beg:k2end), nzdata;
-         }
-      } else {
-         System.out.printf(lunmsg,1001) tempcs(1:8);
-         if (lunusr!=lunmsg) System.out.printf(lunusr,1001) tempcs(1:8);
-      }
-
-//   b) If requested, apply a cosine taper at both ends of the data area.
-//        (Math.cos(0)=1.0; Math.cos(pi/2) =0.0; Math.cos(pi)=-1.0)
-//      Apply the taper so the lowest point in the taper (0.0) falls at
-//        the first point in the pad.
-//      Note that NNN counts the number of interior points in the
-//        taper, excluding the endpoints at F=1.0 and F=0.0.  The
-//        endpoint at f=1.0 is at sample number IHIGH, the endpoint
-//        at f=0.0 is the first point in the pad.
-
-      if (itap==2) {
-         nnn= ntaper(ipad);
-         if (nnn>=1) {
-            System.out.printf(lunmsg,1010) tempcs(k2beg:k2end), nnn;
-            if (lunusr!=lunmsg) System.out.printf(lunusr,1010) tempcs(k2beg:k2end), nnn;
-            rstep = Math.PI/float(nnn+1);
-            ihigh = ilow -jdir*(nnn);
-            do 101 j=1,nnn;
-               f = 0.5*(1.0+Math.cos(rstep*float(j)));
-               i = ihigh + j*jdir;
-               work[i] = (float) (work[i] * f);
-  101       continue;
-         }
-      }
-
-//   End of loop.
-
-  500 continue;
-      return;
-
- 1000 System.out.print("No padding requested (MORELZ+NEWLZ=NEWTZ=0).");
- 1001 System.out.print("The time series has NOT been extended with %8s zeros.");
- 1002 System.out.print("The time series has been extended with %8d %8s zeros.");
- 1010 System.out.print("In addition, the %s %8d input samples were weighted with a cosine taper (values at the end approach zero).");
- 1030 System.out.print("In addition, the "%s %8d input samples were reset to zero." );
- 1101 System.out.print(" *** The ZCROSS option should not be used with this data; it does not contain two zero crossings!***"/);
+      float[] ntaper = new int[2];
+      ntaper[0] = Math.max(0, Math.round(rp.tapsec[0]*sps)-2);
+      ntaper[1] = Math.max(0, Math.round(rp.tapsec[1]*sps)-2);
+
+      String str1 = null;
+      String str2 = null;
+      // Begin Loop to pad and taper each end of the time-series.
+      int nzdata = 0;
+      int locbeg = 0;
+      int locend = 0;
+      int npad = 0;
+      int ilow = 0;
+      int jdir = 0;
+
+      for (int ipad = 0; ipad < 2; ipad++) {
+        itap = rp.mtaper[ipad];
+        nzdata = 0;
+        if (ipad==1) {
+           str1 = "leading";
+           str2 =  "first";
+           locbeg = 0;       // first array index
+           locend = lztot;   // total leading zeroes new+more in pad
+           // npad   = newlz;   // requested zeroes for lead pad -aww changed to below:
+           npad   = lztot;   // requested zeroes for lead pad plus secondary pad // added this -aww
+           ilow   = idata1;  // first data sample index
+           jdir   = -1;
+           if (itap==1) { // zcross
+              locend = izc1 - 1;        // out to 1st zero cross sample index - 1
+              nzdata = locend - lztot;  // data to zero before lead pad
+           }
+        } else {
+           str1 = "trailing";
+           str2 = "last";
+           locbeg = 1 + idatan;   // last data sample index +1 start of pad
+           locend = newtz+idatan; // index at end of trailing pad
+           npad   = newtz;        // requested zeroes for trailing pad
+           ilow   = idatan;       // last data sample index
+           jdir   = 1;
+           if (itap==1) {
+              locbeg = izcn + 1;      // from last zero crossing index + 1
+              nzdata = idatan - izcn; // data to zero before trailing pad
+           }
+        }
+
+        // Pad with zeros and, if requested, extend the zeros into the data area, up to the first zero crossing.
+        if (locbeg < locend) {
+           for (int i = locbeg; i<=locend; i++) {
+               work[i]= 0.f;
+           } 
+           System.out.printf("The time series has been extended with %8d %8s zeros.%n", npad, str1);
+           if (itap==1 && nzdata>0) {
+               System.out.printf("In addition, the "%s %8d input samples were reset to zero.%n", str2, nzdata);
+           }
+        } else {
+           System.out.printf("The time series has NOT been extended with %s zeros.%n", str1);
+        }
+
+        // If requested, apply a cosine taper at both ends of the data area (cos(0)=1, cos(pi/2)=0, cos(pi)=-1).
+        // Apply the taper so the lowest point in the taper (0.0) falls at the first point in the pad.
+        // Note that NNN counts the number of interior points in the taper, excluding the endpoints at F=1.0 and F=0.0. 
+        // The endpoint at f=1.0 is at sample number IHIGH, the endpoint at f=0.0 is the FIRST point in the pad past the data.
+        if (itap==2) {
+           nnn = ntaper(ipad);
+           if (nnn>=1) {
+              System.out.printf("In addition, the %s %8d input samples are weighted with a cosine taper (endpoints approach zero).%n", str2, nnn);
+              dw = Math.PI/float(nnn+1); // taper step
+              ihigh = ilow - jdir*(nnn); // index of sample with highest taper value
+
+              int i = 0;
+              for (int j=1; j<=nnn; j++) { // note endpoints excluded since values are 0. and 1.
+                 i= ihigh+(j*jdir);
+                 work[i] = (float) ( (.5 + .5*Math.cos(dw*j)) * work[i]);
+              }
+           }
+        }
+
+
+      } // End of loop.
+
+      return doit2;
+
   }
 // cccccccccccccccccccc (end of BAPPAD) ccccccccccccccccccccccccccccccccccc
@@ -7730 +7624 @@
 
   BAPPD2(float[] work, int newlz, int npadl, int ndata, int npadt, int newtz) {
-      // Input work length must be >= (newlz+npadl+ndata+npadt+newtz)
 
       if (newlz<=0 && newtz<=0) {
          System.out.println("No additional padding required.");
          return;
+      }
+
+      // Input work length must be >= (newlz+npadl+ndata+npadt+newtz)
+      if (work.length < (newlz+npadl+ndata+npadt+newtz)) {
+         System.out.println("BAPPD2 Error input work array length less than sum of data plus requested leading,trailing pads.");
       }
 
@@ -7741 +7639 @@
         float [] workB =  new float[npadl];
         System.arraycopy(work, newlz, workB, 0, workB.length);
-        BapZCross.calcZeroCrossings(0., work(newlz), npadl);
+        BapZCross.calcZeroCrossings(0., workB, npadl);
+        //BapZCross.calcZeroCrossings(0., work, newlz, npadl);
         izc = BapZCross.izc1; // should be zero if called b4 
       }
@@ -7763 +7662 @@
         System.arraycopy(work, nbeg, workB, 0, workB.length);
         BapZCross.calcZeroCrossings(0.0, workB, npadt);
+        //BapZCross.calcZeroCrossings(0.0, workB, nbeg, npadt);
         izc = BapZCross.izcn;
       }
@@ -8090 +7990 @@
          if (fh2 > 1.00001/(2*dpdelt) ) {
             System.out.printf(lunmsg, 1001) fh2, 1.0/dpdelt;
-            warn("*");
+            BapUtil.warn("*");
          }
          if (fh1+1.999 >fh2) {
             System.out.printf(lunmsg,1002) fh1, fh2;
-            warn("*");
+            BapUtil.warn("*");
          }
          if (pins > 1.0) {
             System.out.printf(lunmsg,1003) pins;
-            warn("*");
+            BapUtil.warn("*");
          }
          if (minsc) {
@@ -8149 +8049 @@
          if (fh1!= hitbeg || fh2!= hitend) {
             System.out.printf(lunmsg, 1006) fh1, fh2;
-            warn("*");
+            BapUtil.warn("*");
          }
 
@@ -8371 +8271 @@
 // ccccc (end of comments) ccccc
 
-  BIhip(array,ndata,fcut,dt,nfs) {
-      dimension array(ndata);
-      double dt,fcut;
-
 //   BIhip:  Bidirectional, high-pass Butterworth recursive filter.
-
 //   On entry --
 //     ARRAY()    contains the time series to be filtered.
@@ -8389 +8284 @@
 //     NFS      = rolloff parameter.
 //                rolloff = nfs*24 decibels/octave.
-
 //   On return --
 //     ARRAY()    contains filtered time-series.
-
-
 //   Subroutine History:
 //   ==================
@@ -8419 +8311 @@
 //     - removed array.inc and LARRAY.
 
-      DOUBLE cs,  pi, temp, ts, wcp;
-      DOUBLE f(11,3),a(11),b(11),c(11);
-
-      nfs1=nfs+1;
-      if (nfs>11) BapUtil.woe(0);
-      ts=dt;
-      //pi=3.1415926535;
-      wcp=Math.sin(fcut*Math.PI*ts)/Math.cos(fcut*Math.PI*ts);
-      do 5 k=1,nfs;
-      cs=Math.cos(float(2*(k+nfs)-1)*Math.PI/float(4*nfs));
-      a(k)=1./(1.+wcp*wcp-2.*wcp*cs);
-      b(k)=2.*(wcp*wcp-1.)*a(k);
-    5 c(k)=(1.+wcp*wcp+2.*wcp*cs)*a(k);
-      // ...perform convolution in two directions
-      do 30 ijk=1,2;
-      do 6 i=1,nfs1;
-      do 6 j=1,2;
-    6 f(i,j)=0.;
-      do 10 n=1,ndata;
-      f(1,3)=array(n);
-      do 14 i=1,nfs;
-      temp=a(i)*(f(i,3)-2.*f(i,2)+f(i,1));
-   14 f(i+1,3)=temp-b(i)*f(i+1,2)-c(i)*f(i+1,1);
-      do 16 i=1,nfs1;
-      do 16 j=1,2;
-   16 f(i,j)=f(i,j+1);
-   10 array(n)=f(nfs1,3);
-      nby2=int(float(ndata)/2.);
-      do 20 n=1,nby2;
-      num=ndata-n+1;
-      temp=array(n);
-      array(n)=array(num);
-   20 array(num)=temp;
-   30 continue;
-  }
+    float[] BIhip(float [] array, int ndata, double fcut, double dt, int nfs) {
+
+      int nfs1 = nfs+1;
+
+      double[][] f = new double [nfs1][3];
+      double[] a   = new double [nfs1];
+      double[] b   = new double [nfs1];
+      double[] c   = new double [nfs1];
+
+      if (nfs1>11) BapUtil.woe(0);
+
+      double ts = dt;
+      double wcp=Math.sin(Math.PI*ts*fcut)/Math.cos(Math.PI*ts*fcut);
+      double cs = 0;
+      for (int k=0; k<nfs; k++) {
+         cs=Math.cos(float(2*(k+nfs)-1)*Math.PI/float(4*nfs));
+         a[k]=1./(1.+wcp*wcp-2.*wcp*cs);
+         b[k]=2.*(wcp*wcp-1.)*a[k];
+         c[k]=(1.+wcp*wcp+2.*wcp*cs)*a[k];
+      }
+
+      double temp = 0.;
+      int ijk = 1;
+      while (ijk <= 2) { // ...perform convolution in two directions
+        ijk++
+
+        // zero out filter buffer
+        for (int i=0; i<nfs1; i++) {
+          for (int j=0, j<2; j++) {
+            f[i][j] = 0.;
+          }
+        }
+
+        // Determine filtered sample value
+        for (int n=0; n<ndata; n++) {
+          f[0][2]=array[n];
+          for (int i=0; i<nfs; i++) {
+            temp=a[i]*(f[i][2]-2.*f[i][1]+f[i][0]);
+            f[i+1][2]=temp-b[i]*f[i+1][1]-c[i]*f[i+1][0];
+          }
+
+          for (int i=0; i<nfs1; i++) {
+            for (int j=0; j<2; j++) {
+              f[i][j]=f[i][j+1];
+            }
+          }
+
+          array[n]=f[nfs1-1][2];
+        }
+
+        nby2=(int)(ndata/2); // what if ndata is not even ?
+        // from mid-array+1 to end of array, swap elements
+        for int n=0, n<nby2; n++) {
+          num=ndata-n+1;
+          temp=array[n];
+          array[n]=array[num];
+          array[num]=temp;
+        }
+      } // end of while
+    }
 // CCCCCCCCCCCCCCCCCCCC (END OF bihip) CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
 
 // CCCCCCCCCCCCCCCCCCCC (Begin DataSeries) CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
 public class DataSeries {
-    int ns = 0; 
-    double dx = 0.;
-    float [] x = null; 
+    int ns = 0;          // number of samples 
+    double dx = 0.;      // interval
+    float [] x = null;   // sample values 
 
     DataSeries(int ns) {
@@ -9048 +8965 @@
 // cccccccccccccccccccc (end of BapRSI) cccccccccccccccccccccccccccccc
 
-//   BapRSC = response-spectra calculating and reporting subroutine for
-//            program = BAP.
-//   BapRSI be called before BapRSC to create DAMP() and PERIOD() arrays.
+//   BapRSC = response-spectra calculating and reporting subroutine for program.
+//            call BapRSI before BapRSC to create DAMP() and PERIOD() arrays.
 //   On entry --
 //     printResp = true for printing response-spectra values, or false not to print
@@ -9561 +9477 @@
       for (int i = 1; i<=count; i++) System.out.print("\0007");
     }
+
+    // WARN: warn user by rining terminal bell and/or stopping, depending
+    //        on the value of IWARN (in BAPINOUT.INC).
+    //        IWARN = 3 => ring bell, tell user how to change IWARN, then stop
+    //        IWARN = 2 => IWARN = 3 if ONEC="*", = IWARN=1 otherwise
+    //        IWARN = 1 => beep and return
+    //        IWARN = 0 => return.
+    // On entry: 
+    //     ONEC   = "+" or "*" to indicate how severe the warning is,
+    //                with "*" being more severe than "+".
+    public void warn(String onec) {
+      if (rp.iwarn != 0) BapUtil.beep();
+      if (rp.iwarn>2 || (rp.iwarn==2 && onec=="*")) {
+        System.out.println("WARN=STOP. If you wish processing to proceed despite the above warning,");
+        System.out.println("reset WARN=BELLS in the run parameter properties, then rerun. Ending Run.");
+        BapUtil.woe(-2);
+      }
+    }
+
+    //  SHOWZ: display info about the pad for DEBUG runs
+    public void showz(int npadl, int ndata, int npadt, float[] workA, int npandd) {
+
+      if (workA.length < npandd) {
+         System.out.printf("ERROR showz work length=%8d > %8d=npandd%n", workA.length, npandd);
+         return;
+      }
+
+      int nfar = npadl+ndata+npadt;
+      if (nfar > npandd) {
+         System.out.printf("ERROR showz (npadl+ndata+npadt)=%8d > %8d=npandd%n", nfar, npandd);
+         return;
+      }
+
+      int idebug = 0;
+      float value = 0.f;
+
+      // Test leading
+      boolean notZero = true;
+      int icnt = 0;
+      int lastZero = 0;
+      for int j = 0; j<npadl; j++) {
+        value = workA(j);
+        if (value != 0.) {
+          if (notZero) {
+            System.out.printf("Showz: First non-zero leading pad value at index=%8d, npadl=%8d, value=%12.3g%n",j, npadl, value;
+            notZero = false;
+          }
+          lastZero = j;
+          icnt++
+        }
+      }
+      if (icnt > 0) System.out.printf("  non-zero leading pad value count=%8d, last zero index=%8d%n", icnt, lastZero);
+      else System.out.println("Showz: leading pad values all zero!");
+
+      // Test zero data
+      notZero = true;
+      icnt = 0;
+      lastZero = 0;
+      iend = npadl+ndata;
+      for int j = npadl; j<iend; j++) {
+        value = workA(j);
+        if (value != 0.) {
+          if (notZero) {
+            System.out.printf("Showz: First non-zero data value starts at index=%8d, startoff=%8d, value=%12.3g%n",j, j-npadl, value;
+            notZero = false;
+            break;
+          }
+        }
+      }
+      notZero = true;
+      icnt = 0;
+      lastZero = 0;
+      iend = npadl+ndata-1;
+      for int j = iend; j>=ipadl; j--) {
+        value = workA(j);
+        if (value != 0.) {
+          if (notZero) {
+            System.out.printf("Showz: First non-zero data value from end is at index=%8d, endoff=%8d, value=%12.3g%n",j, iend-j, value;
+            notZero = false;
+            break;
+          }
+        }
+      }
+
+      // Test trailing
+      notZero = true;
+      icnt = 0;
+      lastZero = 0;
+      iend = npadl+ndata+npadt; 
+      for int j = npadl+ndata; j<iend; j++) {
+        value = workA(j);
+        if (value != 0.) {
+          if (notZero) {
+            System.out.printf("Showz: first non-zero trailing pad value at index=%8d, npadl=%8d, value=%12.3g%n",j, npadt, value;
+            notZero = false;
+          }
+          lastZero = j;
+          icnt++
+        }
+      }
+      if (icnt > 0) System.out.printf("  non-zero trailing pad value count=%8d, last zero index=%8d%n", icnt, lastZero);
+      else System.out.println("Showz: trailing pad values all zero!");
+
+      return;
+    }
+// cccccccccccccccccccc (end of showz) ccccccccccccccccccccccccccccccccccccc
 }
 // cccccccccccccccccccc (end of BapUtil) cccccccccccccccccccccccccccccccc