UVES_tmpfit.c

/****************************************************************************
Temporary routine to fit some gaussians in pixel space to raw 860L settings
****************************************************************************/

#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "UVES_popler.h"
#include "fit.h"
#include "memory.h"
#include "const.h"
#include "error.h"

int UVES_tmpfit(spectrum *spec, params *par) {

  double swl=0.0,ewl=0.0;
  double chisq=0.0,ochisq=INFIN,alambda=0.0;
  double half=0.0;
  double wl[2397]={
    3043.06528200,
    3043.24890200,
    3043.93001900,
    3045.06817100,
    3048.23309300,
    3049.09238700,
    3050.81588800,
    3051.79288800,
    3058.42628400,
    3060.43895700,
    3060.90547300,
    3065.93001300,
    3066.23627200,
    3066.41205100,
    3067.72940900,
    3071.93725800,
    3072.11501200,
    3073.80395000,
    3075.05652900,
    3076.40918800,
    3077.33906600,
    3077.71716600,
    3077.93184800,
    3079.88746000,
    3080.21704300,
    3081.98100100,
    3082.50471200,
    3085.02557900,
    3086.56672000,
    3093.40153600,
    3098.72687700,
    3100.79721500,
    3101.68984000,
    3107.02613600,
    3110.02090400,
    3111.28068900,
    3112.08906300,
    3117.68401000,
    3120.88084200,
    3123.15807700,
    3124.38739100,
    3125.20912700,
    3126.05316200,
    3127.20824100,
    3129.97405600,
    3133.61965500,
    3134.42574400,
    3136.21608200,
    3137.63262000,
    3139.01719800,
    3140.27202800,
    3142.83560500,
    3145.63699100,
    3146.04336800,
    3147.44860600,
    3153.21819900,
    3155.83018100,
    3156.40064800,
    3158.61734400,
    3159.07226400,
    3159.70722200,
    3163.71524100,
    3164.48156300,
    3165.29105100,
    3169.32849200,
    3169.66800700,
    3171.27547700,
    3172.11120200,
    3173.42665400,
    3173.70457000,
    3174.20434000,
    3174.83929400,
    3176.16708000,
    3178.24330400,
    3179.04819100,
    3180.19375400,
    3181.03711200,
    3182.64252800,
    3184.61495900,
    3186.17170100,
    3191.61678600,
    3193.15976900,
    3193.36888400,
    3193.78099400,
    3195.68913700,
    3204.32088500,
    3210.30882500,
    3211.19431900,
    3214.07466400,
    3216.99791300,
    3220.35085100,
    3221.86410500,
    3222.39788900,
    3225.00528700,
    3225.41105300,
    3226.11900700,
    3227.47045500,
    3229.00959300,
    3230.86796300,
    3232.30618000,
    3235.83998500,
    3236.57341300,
    3237.23233200,
    3238.11574700,
    3238.93431000,
    3240.94704000,
    3241.10795000,
    3243.68807900,
    3244.04343900,
    3244.44880900,
    3244.88150700,
    3245.99421100,
    3247.21852200,
    3248.89383400,
    3249.34312800,
    3251.91591000,
    3252.96441300,
    3253.68386100,
    3254.06732300,
    3256.27385400,
    3256.69540600,
    3257.16205100,
    3259.06086900,
    3262.66845400,
    3263.18278100,
    3264.12161300,
    3267.00245400,
    3272.02680000,
    3275.06759700,
    3275.26005300,
    3275.64335900,
    3282.61657400,
    3282.97957100,
    3285.51481800,
    3286.58291200,
    3287.78930100,
    3288.16027400,
    3290.59962000,
    3291.73944900,
    3292.31152000,
    3294.24523700,
    3294.75323500,
    3297.37483100,
    3304.23836000,
    3307.22825700,
    3309.13585200,
    3319.34191200,
    3320.47631900,
    3322.09332200,
    3324.75270600,
    3325.12075200,
    3325.96580500,
    3326.46525900,
    3327.19316700,
    3327.71276000,
    3330.47700700,
    3333.12899800,
    3335.47418200,
    3337.87035700,
    3338.59802600,
    3341.39887200,
    3341.74064200,
    3344.31011000,
    3346.55599900,
    3349.32947000,
    3350.92383500,
    3353.94847300,
    3354.17960500,
    3355.10613100,
    3355.25871600,
    3359.06010000,
    3360.37355000,
    3362.67625600,
    3365.97886200,
    3367.58222900,
    3372.33473900,
    3373.05675500,
    3374.97489400,
    3378.57337900,
    3380.57023200,
    3380.85954100,
    3383.58610600,
    3386.50066000,
    3387.92055300,
    3389.03736200,
    3389.64054100,
    3390.36812200,
    3392.03495700,
    3393.42149400,
    3393.99295400,
    3395.98618600,
    3396.72780100,
    3397.51611400,
    3403.00595400,
    3405.55838100,
    3406.83855100,
    3407.83018400,
    3408.74988300,
    3417.49779400,
    3418.77551500,
    3419.17330300,
    3420.37360800,
    3423.12907200,
    3423.98968100,
    3426.74266700,
    3428.99918100,
    3429.38927000,
    3430.12733000,
    3432.58308700,
    3433.55539600,
    3437.30709500,
    3438.95033100,
    3439.39875100,
    3440.60580800,
    3441.36469700,
    3441.52679200,
    3445.21727800,
    3445.74415200,
    3446.54745600,
    3449.28707600,
    3450.94751800,
    3451.70237200,
    3452.68207300,
    3454.09496300,
    3455.27262400,
    3456.44173100,
    3457.43399300,
    3458.14134200,
    3458.45864400,
    3461.01867900,
    3461.21725100,
    3462.85056500,
    3463.71971000,
    3466.33295000,
    3466.89680500,
    3468.21979900,
    3469.34545400,
    3469.92080400,
    3470.56749100,
    3471.95933000,
    3476.74714000,
    3477.70426000,
    3478.46354200,
    3478.76883000,
    3480.05252900,
    3481.00298400,
    3484.08000400,
    3485.67673700,
    3487.31547500,
    3487.84367100,
    3488.83385500,
    3489.18415200,
    3490.87295900,
    3491.24371000,
    3491.53560100,
    3496.81071600,
    3497.68606500,
    3498.62101600,
    3501.45594800,
    3505.49413800,
    3506.13279300,
    3506.64579400,
    3509.77791900,
    3514.38736300,
    3516.35450600,
    3516.82430800,
    3518.40402400,
    3519.99336400,
    3521.05948100,
    3521.25991800,
    3523.50615000,
    3523.75854800,
    3524.17873100,
    3524.53647100,
    3527.00051900,
    3528.41165800,
    3529.38597300,
    3530.51478000,
    3531.45056100,
    3532.98488700,
    3536.63281100,
    3536.97675400,
    3537.15975800,
    3539.32230600,
    3539.58727600,
    3539.84008900,
    3541.61591400,
    3541.96969900,
    3543.14694400,
    3544.48769000,
    3545.59518900,
    3545.84313900,
    3547.91748700,
    3548.51404100,
    3549.59594400,
    3550.29244100,
    3551.40192300,
    3553.11032500,
    3554.30551700,
    3555.70463300,
    3556.90377100,
    3561.03014300,
    3565.60425400,
    3566.37180700,
    3567.26381000,
    3569.82047500,
    3570.35771500,
    3571.00922000,
    3572.06723700,
    3573.21964700,
    3577.59939600,
    3578.35562500,
    3578.94976300,
    3580.99123700,
    3582.00913500,
    3582.35442400,
    3584.17563800,
    3588.44023200,
    3589.74950300,
    3591.45241400,
    3594.11116100,
    3594.72164700,
    3594.98561600,
    3595.61773600,
    3597.49552200,
    3598.11997700,
    3599.72401800,
    3600.43232700,
    3601.50888400,
    3601.77159400,
    3603.20420700,
    3605.19366100,
    3606.52160700,
    3608.88167300,
    3609.44518700,
    3611.16046100,
    3611.81304200,
    3612.42748000,
    3612.86664700,
    3615.13275700,
    3615.85034800,
    3616.17779600,
    3618.36336600,
    3618.59697200,
    3619.39097100,
    3624.47200700,
    3625.62803800,
    3631.86301900,
    3634.21356400,
    3635.94336800,
    3636.56673000,
    3638.64447100,
    3639.44697400,
    3642.24900400,
    3642.57291600,
    3643.51234500,
    3643.82500700,
    3645.95585100,
    3648.85524100,
    3650.20460300,
    3652.53722500,
    3654.46178600,
    3656.04946100,
    3656.69383500,
    3657.05540000,
    3658.80873300,
    3659.62938600,
    3665.18116200,
    3666.98114200,
    3667.62184200,
    3668.39017200,
    3671.00415200,
    3672.30029700,
    3672.52178900,
    3673.79355700,
    3674.89101300,
    3675.13720400,
    3675.56757500,
    3675.78932600,
    3675.95927900,
    3676.68968700,
    3677.08881200,
    3679.13433300,
    3679.54443400,
    3679.71049500,
    3680.06045000,
    3683.49316600,
    3687.67004700,
    3687.98414300,
    3690.62386900,
    3691.41174900,
    3691.61410900,
    3692.56641700,
    3695.28896800,
    3695.97375800,
    3697.03085600,
    3697.19398900,
    3697.74364800,
    3698.10617900,
    3699.88080900,
    3700.76537900,
    3700.97823300,
    3702.86383300,
    3703.77432500,
    3704.33735900,
    3706.76726100,
    3711.30411000,
    3713.89210500,
    3715.56065300,
    3715.86155300,
    3719.43472800,
    3721.82545000,
    3723.28981700,
    3725.39321500,
    3727.61201400,
    3727.90275700,
    3729.30813600,
    3732.98542900,
    3733.67243800,
    3734.86380000,
    3737.51253500,
    3737.88894500,
    3740.85513200,
    3741.18305700,
    3742.92339300,
    3745.65912200,
    3747.53903200,
    3752.56897300,
    3752.79042000,
    3754.28840400,
    3754.59305700,
    3755.21213700,
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    3780.14888400,
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    3785.28040100,
    3785.60019200,
    3786.38202300,
    3786.88256500,
    3790.79485700,
    3794.15125100,
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    3799.85757600,
    3800.19800900,
    3802.14830300,
    3804.69863900,
    3807.87449100,
    3809.45574600,
    3809.83504000,
    3810.49970500,
    3810.99532700,
    3812.39738800,
    3813.06760100,
    3815.56599900,
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    3818.68552900,
    3820.79266700,
    3821.43079100,
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    3823.99034500,
    3825.67237700,
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    3828.38462200,
    3830.06061300,
    3830.77360300,
    3834.67840100,
    3835.71117400,
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    3844.18617300,
    3844.73082800,
    3847.61992700,
    3850.58080900,
    3852.13529100,
    3854.51086900,
    3862.05219500,
    3863.40591700,
    3868.52812200,
    3869.66336800,
    3872.13700400,
    3873.14794100,
    3873.82242200,
    3874.24380000,
    3874.86196500,
    3875.64618300,
    3879.26884600,
    3879.64411600,
    3883.76835300,
    3885.40384500,
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    3891.72602200,
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    3893.65195500,
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    3895.41922600,
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    3900.87848700,
    3901.15222000,
    3901.66212600,
    3903.10241500,
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    3907.54323700,
    3910.77345400,
    3913.64500900,
    3914.16232300,
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    10045.31239700};
  double a[5];
  double **x=NULL,**lim=NULL,**covar=NULL,**alpha=NULL;
  int    fval=0,lval=0,widx=0;
  int    i=0,j=0,k=0,l=0;
  int    ia[5]={1,1,1,1,1};

  if (strncmp(spec->abfile,"thar_sci_860_01_l.fits",22)) return 1;

  /* Loop over all orders */
  for (l=0; l<spec->nor; l++) {
    /* Check first to see if order is useful */
    if (spec->or[l].nuse>=MINUSE) {
      /* Find first valid pixel in raw array */
      i=0; while (spec->or[l].st[i]<1) i++; fval=i;
      /* Find last valid pixel in raw array */
      i=spec->or[l].np-1; while (spec->or[l].st[i]<1) i--; lval=i;
      /* Find starting and ending wavelengths of order */
      swl=(fval) ? spec->or[l].vhrwl[fval-1] : spec->or[l].fvhlwl;
      ewl=spec->or[l].vhrwl[lval];
      /* Loop over lab wavelengths and fit those which lie in order's
	 wavelength range */
      for (i=0; i<2397; i++) {
	if (wl[i]>swl && wl[i]<ewl) {
	  /* Allocate memory to fitting matrices */
	  if ((x=dmatrix(9,1))==NULL)
	    errormsg("UVES_tmpfit(): Cannot allocate memory for x matrix\n\
\tof size %dx%d",9,1);
	  if ((lim=dmatrix(5,2))==NULL)
	    errormsg("UVES_tmpfit(): Cannot allocate memeory for lim matrix\n\
\tof size %dx%d",5,2);
	  if ((covar=dmatrix(5,5))==NULL)
	    errormsg("UVES_tmpfit(): Cannot allocate memeory for covar matrix\n\
\tof size %dx%d",5,5);
	  if ((alpha=dmatrix(5,5))==NULL)
	    errormsg("UVES_tmpfit(): Cannot allocate memeory for alpha matrix\n\
\tof size %dx%d",5,5);
	  /* Fill limits matrix */
	  lim[0][0]=0.01; lim[0][1]=INFIN;
	  lim[1][0]=0.0; lim[1][1]=10000.0;
	  lim[2][0]=1.0; lim[2][1]=10.0;
	  lim[3][0]=-5.e5; lim[3][1]=5.e5;
	  lim[4][0]=-5.e5; lim[4][1]=5.e5;
	  /* Find pixel nearest to lab wavelength */
	  widx=idxdval(&(spec->or[l].vhrwl[fval]),lval-fval+1,wl[i]); widx+=fval;
	  /* Find pixel near widx with maximum flux */
	  widx+=idxdmax(&(spec->or[l].fl[widx-1]),3)-1;
	  /* Initialise fitting array */
	  for (j=0; j<9; j++) x[j][0]=(double)(widx-4+j);
	  /** Initialize fitting parameters **/
	  /* Starting continuum level is mean of 4 outer pixels */
	  a[4]=(spec->or[l].fl[widx-4]+spec->or[l].fl[widx-3]+
		spec->or[l].fl[widx+4]+spec->or[l].fl[widx+3])/4.0;
	  /* Starting position is flux-weighted mean position of inner 3 pixels */
	  a[1]=((spec->or[l].fl[widx-1]-a[4])*(double)(widx-1)+
		(spec->or[l].fl[widx]-a[4])*(double)(widx)+
		(spec->or[l].fl[widx+1]-a[4])*(double)(widx+1))/
	    (spec->or[l].fl[widx-1]+spec->or[l].fl[widx]+spec->or[l].fl[widx+1]-
	     3.0*a[4]);
	  if ((int)(a[1]+0.5)!=widx) a[1]=(float)widx;
	  /* Starting slope is calculated from average of outer pixels */
	  a[3]=(spec->or[l].fl[widx+4]+spec->or[l].fl[widx+3]-
		spec->or[l].fl[widx-4]-spec->or[l].fl[widx-3])/7.0;
	  /* Starting intensity is taken relative to continuum */
	  a[0]=(MAX(0.0,(spec->or[l].fl[widx]-a[4]))); half=a[0]/2.0+a[4];
	  /* Starting width is calculated by testing the data itself */
	  for (j=widx-4; j<widx+4; j++) if (spec->or[l].fl[j]>half) break;
	  for (k=j+1; k<=widx+4; k++) if (spec->or[l].fl[k]<half) break;
	  a[2]=(double)(k-j)/C_FWHMSIG;
	  /* if (l==13 && wl[i]==7865.969) */
	  /*
	  fprintf(stdout,"0: %lf %lf %lf %lf %lf %lf\n",a[0],a[1]+1.0,a[2],a[4],
		  a[3],UVES_wpol(spec,l,a[1],par));
	  */
	  /** Do Gaussian fit to data **/
	  alambda=-1.0;
	  for (j=0,ochisq=INFIN; j<MRQNMAX; j++) {
	    if (!mrqmin(x,&(spec->or[l].fl[widx-4]),&(spec->or[l].er[widx-4]),9,
			1,a,lim,ia,NULL,5,covar,alpha,&chisq,&alambda,
			mrqfit_gauss))
	      errormsg("UVES_tmpfit(): Error fitting line %d at x=%lf",i+1,wl[i]);
	    if (chisq<ochisq && (ochisq-chisq)/chisq<5.e-3) break;
	    ochisq=chisq;
	  }
	  if (j==MRQNMAX)
	    warnmsg("UVES_tmpfit(): More than %d iterations required\n\
\tto fit line %d at x=%lf",MRQNMAX,i+1,wl[i]);
	  alambda=0.0;
	  if (!mrqmin(x,&(spec->or[l].fl[widx-4]),&(spec->or[l].er[widx-4]),9,1,
		      a,lim,ia,NULL,5,covar,alpha,&chisq,&alambda,mrqfit_gauss))
	    errormsg("UVES_tmpfit(): Error fitting line %d at x=%lf",i+1,wl[i]);
	  /*
	  fprintf(stdout,"1: %lf %lf %lf %lf %lf\n",a[0],a[1]+1.0,a[2],a[4],a[3]);
	  */
	  /* if (l==13 && wl[i]==7865.969) {
	  fprintf(stdout,"%d %14.8lf %14.8lf %14.8lf %14.8lf %14.8lf %14.8lf \
%14.8lf %11.8lf\n",
		  l,swl,ewl,x[0][0],x[8][0],a[1]+1.0,wl[i],
		  UVES_wpol(spec,l,a[1],par),wl[i]-UVES_wpol(spec,l,a[1],par));
	  fprintf(stdout,"%lf %lf %lf %lf %lf\n",a[0],a[1]+1.0,a[2],a[3],a[4]);
	  }
	  */
	  /*
	  fprintf(stdout,"%lf %lf %lf\n",wl[i],UVES_wpol(spec,l,a[1],par),
		  wl[i]-UVES_wpol(spec,l,a[1],par));
	  */
	  free(*x); free(x); free(*lim); free(lim); free(*covar); free(covar);
	  free(*alpha); free(alpha);
	}
      }
    }
  }
      
  return 1;

}