sfocus.c

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/* 
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of this software and associated documentation files (the "Software"), to deal
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in all copies or substantial portions of the Software.

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 */


#include "extern.h"

double last_focus_fit = 0.0;

/* Process a multi spectral line focus; assumes scan is already loaded */
int  specFocusOne(noint, nfoc, feed)
int noint, nfoc, feed;
{
  int    i, j, n, ret, delta, nchan, expectedPos, maxi, save_ps;
  int    start, end, npts, bchans;
  char   cmdBuf[256];
  double focusp[MAX_SPEC_FOCUS], peaks[MAX_SPEC_FOCUS];
  double maxG, aa1[4], sig[MAX_SPEC_FOCUS];

  /* These routines assume the line is in the center; need to allow otherwise */
  if(env->sf_fitcenter != 0)
  {
    expectedPos = env->sf_fitcenter;
    st_report("Using User supplied Center Channel: %d", expectedPos);
  }
  else
  {
    expectedPos = noint / 2; /* halfway through bandpass??? */
  }

  if(env->sf_fitmhz == 0.0)
  {
    env->sf_fitmhz = 20.0;
    st_report("Using Line Width: %f", env->sf_fitmhz);
  }
  else
  {
    st_report("Using User supplied Line Width: %f", env->sf_fitmhz);
  }

  if(env->sf_bchans)
  {
    bchans = env->sf_bchans;
  }
  else
  {
    bchans = 40;
  }

  delta = (int)((env->sf_fitmhz / fabs(h0->head.freqres) ) / 4.0);

  st_report("specFocusOne(): noint = %d, nfoc = %d, expectedPos = %d, delta = %d", 
                                        noint, nfoc, expectedPos, delta);

  /* Automatically set baselines to 40 channels on the ends of each expected spectra */
  /* Zero out the current baselines */
  bzero((char *)&env->baselines[0], sizeof(env->baselines));

  env->baselines[0][0]   =       1;
  env->baselines[0][1]   =  bchans;
  for(i=1;i<nfoc;i++)
  {
    env->baselines[i][0] = (i * noint) - bchans;
    env->baselines[i][1] = (i * noint) + bchans;
  }

  env->baselines[nfoc][0] = h0->head.noint - bchans;
  env->baselines[nfoc][1] = h0->head.noint -      1;

  env->bmark = 1;

  tellBaselines();

  strcpy(cmdBuf, "show"); /* Replot with baselines visible */
  parseCmd(cmdBuf);
  xdelay(1000000);              /* Give plot time to show */

  env->markers    =  noint;     /* Show breaks between spectra */
  env->mshow      =  1;         /* Markers show */
  env->bmark      =  1;         /* Show Baseline regions */
  env->zline      =  1;         /* Show Zero Line */
  env->bsmoothing =  1;         /* poly baseline shape */

  if(!env->nfit)
  {
    env->nfit       =  1;       /* linear baseline fitting */
  }

  strcpy(cmdBuf, "gracefit");
  parseCmd(cmdBuf);
  xdelay(1000000);              /* Give plot time to show */

  strcpy(cmdBuf, "rmbase");
  parseCmd(cmdBuf);
  xdelay(1000000);              /* Give plot time to show */

  strcpy(cmdBuf, "show");               /* Replot with baselines visible */
  parseCmd(cmdBuf);
  xdelay(1000000);              /* Give plot time to show */

  if(isSet(PF_P_FLAG))
  {
    sprintf(cmdBuf, "make /c /g /d sfocus_data.%.2f.png", h0->head.scan);
    parseCmd(cmdBuf);
  }

  maxG = 0.0;
  maxi = 0;

  npts = 0;

  if(env->sf_start)
  {
    start = env->sf_start;
  }
  else
  {
    start = 0;
  }

  if(env->sf_end)
  {
    end = env->sf_end;
  }
  else
  {
    end = nfoc;
  }

  for(i=start;i<end;i++)
  {
    nchan = expectedPos + (noint * i);

    peaks[i] = 0.0;
    n = 0;
    for(j=(nchan-delta);j<(nchan+delta);j++)  /* Average up the delta*2 channels about the center */
    {
      peaks[i] += h0->yplot1[j];
      n++;
    }

    focusp[i] = h0->head.focusr - (floor((double)nfoc / 2.0) * h0->head.wl) + (double)i * h0->head.wl;
    peaks[i] /= (double)n;

    if(peaks[i] > maxG)
    {
      maxG = peaks[i];
      maxi = i;
    }

    st_report("[%2d]: %f %f", i, focusp[i], peaks[i]);

    sig[i] = 1.0;

    npts++;
  }

  /* Steal the continuum focus structure so xgraphics will plot the results */
  clearFillContStruct(&h0->head, npts, "Focus", "Ta* (K)");

  st_report("Fitting a %d Point Gauss to Peak: %f, @ %f, HP = %f", npts, maxG, focusp[maxi], h0->head.wl * 6.0);
  aa1[0] = 0.0;
  aa1[1] = maxG;
  aa1[2] = h0->head.focusr;                     /* Center Focus */
  aa1[3] = h0->head.wl * 6.0;

  ret = gauss_fit(&focusp[start], &peaks[start], &sig[start], npts-1, aa1, isSet(PF_V_FLAG)); /* Fit a gaussian curve to  peaks */

  if(ret != 1)
  {
    st_report("gauss_fit() returned: %d", ret);
  }

  st_report("Gaussian Peak:   %7.2f K",  aa1[1]);
  st_report("Gaussian Center: %7.2f",    aa1[2]);
  st_report("Gaussian FWHM:   %7.2f mm", aa1[3]);

  last_focus_fit = aa1[2];

  for(i=0;i<npts;i++)
  {
    cont_plain_send.xdata[i] = (float)focusp[start+i];
    cont_plain_send.ydata[i] = (float)peaks[start+i];
  }

  if(feed == 0)
  {
    env->plotwin   = 15;
  }
  else
  {
    env->plotwin   = 16;
  }

  env->yscale    = Y_AUTO_SCALE;

  save_ps = env->plotstyle;
  env->plotstyle = PLOT_STYLE_LINEPTS;

  env->zline     = 0;

  if(xgraphic)
  {
    sendCont(SEND_PLAIN);
    xdelay(1000000);            /* Give plot time to show */
  }

  plotGauss(&focusp[start], npts, aa1, &h0->head, 1);
  xdelay(1000000); /* Give plot time to show */

  env->plotstyle = save_ps;

  if(isSet(PF_P_FLAG))
  {
    sprintf(cmdBuf, "make /c /g /d sfocus_gauss.%.2f.png", h0->head.scan);
    parseCmd(cmdBuf);
  }

  return(0);
}

/* SFocus analysis:

   The Spec Focus comes in as an array of bandpasses, each at a different
   focus position.

   openpar[6] contains the number of focus positions. Maximum of 15;

   Procedure:

   1) Fetch the scan;
   2) Copy it to h8 to save it.
   3) Move the n'th / 2 array into h0->yplot[];
   4) Show it and fit a gauss
   5) Wait for xgraphics to reply on yaxis.
   6) Fix the yaxis to min/max
   7) for(i=0;i<n;i++)
      {
        bcopy(h8->yplot1[noint*i], h0->yplot1[0], noint * sizeof(float));

        show();

        peak();

        gauss();  /a

        save();
      }

*/

int doSfocus()
{
  int    i, ret, noint, nfoc;
  int    feed;
  char   monBuf[256], cmdBuf[256];
  double scan;

  if(args->ntokens < 2)
  {
    printH_FlagHelp(args->firstArg);
  }

  if(strlen(args->secondArg))
  {
    scan = atof(args->secondArg);
  }
  else
  {
    st_fail("Missing Scan Number");
    printH_FlagHelp(args->firstArg);

    return(1);
  }

  saveEnv();

  env->focus_fit_1 = env->focus_fit_2 = 0.0;

  for(i=0;i<2;i++)
  {
    ret = read_scan(scan, env->filename, h0->yplot1, &h0->head, 0);

    if(ret <= 0)
    {
      st_fail("doSfocus(): Scan %.2f, not found", scan);

      restoreEnv();

      return(1);
    }

    noint = (int)h0->head.noint;
    nfoc  = (int)h0->head.openpar[6];

    if(i == 0)
    {
      env->plotwin = 0;
    }
    else
    {
      env->plotwin = 1;
    }

    sprintf(cmdBuf, "show /f");
    parseCmd(cmdBuf);

    xdelay(1000000); /* Give plot time to show */

    specFocusOne(noint, nfoc, i);

    feed = getFeed(h0->head.scan);

    if((feed%2))                                /* odd channel */
    {
      env->focus_fit_1 = last_focus_fit;
    }
    else                                        /* even channel */
    {
      env->focus_fit_2 = last_focus_fit;
    }

    if(isSet(PF_2_FLAG))
    {
      scan += 0.02;
    }
    else
    {
      scan += 0.01;
    }
  }

  sprintf(monBuf, "DISPLAY FIT_AX01 %f FIT_AX02 %f FIT_AX0AVG %f", env->focus_fit_1, env->focus_fit_2, (env->focus_fit_1 + env->focus_fit_2) / 2.0);
  st_report("Results: %s", monBuf);

  if(isSet(PF_T_FLAG))
  {
    if(monitorSock)
    {
      st_report("To MONITOR: %s", monBuf);

      sock_send(monitorSock, monBuf);
    }
    else
    {
      st_fail("monitor sockect not defined");
    }
  }

  restoreEnv();

  return(0);
}