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version 1.14, 2013/07/04 02:16:52 version 1.43, 2021/05/26 04:45:48
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 /*=========================================== /*===========================================
  
    The following 14 functions calculate the following spaceweather indices:   The following functions calculate these spaceweather indices from the vector magnetic field data:
  
     USFLUX Total unsigned flux in Maxwells     USFLUX Total unsigned flux in Maxwells
     MEANGAM Mean inclination angle, gamma, in degrees     MEANGAM Mean inclination angle, gamma, in degrees
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     MEANPOT Mean photospheric excess magnetic energy density in ergs per cubic centimeter     MEANPOT Mean photospheric excess magnetic energy density in ergs per cubic centimeter
     TOTPOT Total photospheric magnetic energy density in ergs per cubic centimeter     TOTPOT Total photospheric magnetic energy density in ergs per cubic centimeter
     MEANSHR Mean shear angle (measured using Btotal) in degrees     MEANSHR Mean shear angle (measured using Btotal) in degrees
    CMASK The total number of pixels that contributed to the calculation of all the indices listed above
   
    And these spaceweather indices from the line-of-sight magnetic field data:
    USFLUXL Total unsigned flux in Maxwells
    MEANGBL Mean value of the line-of-sight field gradient, in Gauss/Mm
    CMASKL The total number of pixels that contributed to the calculation of USFLUXL and MEANGBL
    R_VALUE Karel Schrijver's R parameter
  
    The indices are calculated on the pixels in which the conf_disambig segment is greater than 70 and    The indices are calculated on the pixels in which the conf_disambig segment is greater than 70 and
    pixels in which the bitmap segment is greater than 30. These ranges are selected because the CCD    pixels in which the bitmap segment is greater than 30. These ranges are selected because the CCD
    coordinate bitmaps are interpolated.   coordinate bitmaps are interpolated for certain data (at the time of this CVS submit, all data
    prior to 2013.08.21_17:24:00_TAI contain interpolated bitmaps; data post-2013.08.21_17:24:00_TAI
    contain nearest-neighbor bitmaps).
  
    In the CCD coordinates, this means that we are selecting the pixels that equal 90 in conf_disambig    In the CCD coordinates, this means that we are selecting the pixels that equal 90 in conf_disambig
    and the pixels that equal 33 or 44 in bitmap. Here are the definitions of the pixel values:   and the pixels that equal 33 or 34 in bitmap. Here are the definitions of the pixel values:
  
    For conf_disambig:    For conf_disambig:
    50 : not all solutions agree (weak field method applied)    50 : not all solutions agree (weak field method applied)
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    Written by Monica Bobra 15 August 2012    Written by Monica Bobra 15 August 2012
    Potential Field code (appended) written by Keiji Hayashi    Potential Field code (appended) written by Keiji Hayashi
    Error analysis modification 21 October 2013
  
 ===========================================*/ ===========================================*/
 #include <math.h> #include <math.h>
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 //  To convert G to G*cm^2, simply multiply by the number of square centimeters per pixel. //  To convert G to G*cm^2, simply multiply by the number of square centimeters per pixel.
 //  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS). //  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS).
 //  (Gauss/pix^2)(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.cm/m)^2 //  (Gauss/pix^2)(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.cm/m)^2
 //  =(Gauss/pix^2)(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2  //  =Gauss*cm^2
 //  =(1.30501e15)Gauss*cm^2  
   
 //  The disambig mask value selects only the pixels with values of 5 or 7 -- that is,  
 //  5: pixels for which the radial acute disambiguation solution was chosen  
 //  7: pixels for which the radial acute and NRWA disambiguation agree  
  
 int computeAbsFlux(float *bz_err, float *bz, int *dims, float *absFlux, int computeAbsFlux(float *bz_err, float *bz, int *dims, float *absFlux,
                    float *mean_vf_ptr, float *mean_vf_err_ptr, float *count_mask_ptr, int *mask,                    float *mean_vf_ptr, float *mean_vf_err_ptr, float *count_mask_ptr, int *mask,
Line 78  int computeAbsFlux(float *bz_err, float
Line 84  int computeAbsFlux(float *bz_err, float
     int i=0;     int i=0;
     int j=0;     int j=0;
     int count_mask=0;     int count_mask=0;
     float sum=0.0;      double sum = 0.0;
     float err=0.0;      double err = 0.0;
     *absFlux = 0.0;     *absFlux = 0.0;
     *mean_vf_ptr = 0.0;     *mean_vf_ptr = 0.0;
  
Line 93  int computeAbsFlux(float *bz_err, float
Line 99  int computeAbsFlux(float *bz_err, float
                   if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                   if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                   if isnan(bz[j * nx + i]) continue;                   if isnan(bz[j * nx + i]) continue;
                   sum += (fabs(bz[j * nx + i]));                   sum += (fabs(bz[j * nx + i]));
                   //printf("i,j,bz[j * nx + i]=%d,%d,%f\n",i,j,bz[j * nx + i]);  
                   err += bz_err[j * nx + i]*bz_err[j * nx + i];                   err += bz_err[j * nx + i]*bz_err[j * nx + i];
                   count_mask++;                   count_mask++;
                 }                 }
Line 102  int computeAbsFlux(float *bz_err, float
Line 107  int computeAbsFlux(float *bz_err, float
      *mean_vf_ptr     = sum*cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;      *mean_vf_ptr     = sum*cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;
      *mean_vf_err_ptr = (sqrt(err))*fabs(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0); // error in the unsigned flux      *mean_vf_err_ptr = (sqrt(err))*fabs(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0); // error in the unsigned flux
      *count_mask_ptr  = count_mask;      *count_mask_ptr  = count_mask;
      printf("cdelt1=%f\n",cdelt1);  
      printf("rsun_obs=%f\n",rsun_obs);  
      printf("rsun_ref=%f\n",rsun_ref);  
      printf("CMASK=%g\n",*count_mask_ptr);  
      printf("USFLUX=%g\n",*mean_vf_ptr);  
      printf("sum=%f\n",sum);  
      printf("USFLUX_err=%g\n",*mean_vf_err_ptr);  
      return 0;      return 0;
 } }
  
Line 126  int computeBh(float *bx_err, float *by_e
Line 124  int computeBh(float *bx_err, float *by_e
     int i=0;     int i=0;
     int j=0;     int j=0;
     int count_mask=0;     int count_mask=0;
     float sum=0.0;      double sum = 0.0;
     *mean_hf_ptr = 0.0;     *mean_hf_ptr = 0.0;
  
     if (nx <= 0 || ny <= 0) return 1;     if (nx <= 0 || ny <= 0) return 1;
Line 135  int computeBh(float *bx_err, float *by_e
Line 133  int computeBh(float *bx_err, float *by_e
           {           {
             for (j = 0; j < ny; j++)             for (j = 0; j < ny; j++)
               {               {
                 if isnan(bx[j * nx + i]) continue;              if isnan(bx[j * nx + i])
                 if isnan(by[j * nx + i]) continue;              {
                   bh[j * nx + i] = NAN;
                   bh_err[j * nx + i] = NAN;
                   continue;
               }
               if isnan(by[j * nx + i])
               {
                   bh[j * nx + i] = NAN;
                   bh_err[j * nx + i] = NAN;
                   continue;
               }
                 bh[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] );                 bh[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] );
                 sum += bh[j * nx + i];                 sum += bh[j * nx + i];
                 bh_err[j * nx + i]=sqrt( bx[j * nx + i]*bx[j * nx + i]*bx_err[j * nx + i]*bx_err[j * nx + i] + by[j * nx + i]*by[j * nx + i]*by_err[j * nx + i]*by_err[j * nx + i])/ bh[j * nx + i];                 bh_err[j * nx + i]=sqrt( bx[j * nx + i]*bx[j * nx + i]*bx_err[j * nx + i]*bx_err[j * nx + i] + by[j * nx + i]*by[j * nx + i]*by_err[j * nx + i]*by_err[j * nx + i])/ bh[j * nx + i];
Line 152  int computeBh(float *bx_err, float *by_e
Line 160  int computeBh(float *bx_err, float *by_e
 /*===========================================*/ /*===========================================*/
 /* Example function 3: Calculate Gamma in units of degrees */ /* Example function 3: Calculate Gamma in units of degrees */
 // Native units of atan(x) are in radians; to convert from radians to degrees, multiply by (180./PI) // Native units of atan(x) are in radians; to convert from radians to degrees, multiply by (180./PI)
 // Redo calculation in radians for error analysis (since derivatives are only true in units of radians).  //
   // Error analysis calculations are done in radians (since derivatives are only true in units of radians),
   // and multiplied by (180./PI) at the end for consistency in units.
  
 int computeGamma(float *bz_err, float *bh_err, float *bx, float *by, float *bz, float *bh, int *dims, int computeGamma(float *bz_err, float *bh_err, float *bx, float *by, float *bz, float *bh, int *dims,
                  float *mean_gamma_ptr, float *mean_gamma_err_ptr, int *mask, int *bitmask)                  float *mean_gamma_ptr, float *mean_gamma_err_ptr, int *mask, int *bitmask)
Line 162  int computeGamma(float *bz_err, float *b
Line 172  int computeGamma(float *bz_err, float *b
     int i=0;     int i=0;
     int j=0;     int j=0;
     int count_mask=0;     int count_mask=0;
     float sum=0.0;      double sum = 0.0;
     float err=0.0;      double err = 0.0;
     float err_value=0.0;  
     *mean_gamma_ptr=0.0;     *mean_gamma_ptr=0.0;
  
     if (nx <= 0 || ny <= 0) return 1;     if (nx <= 0 || ny <= 0) return 1;
Line 179  int computeGamma(float *bz_err, float *b
Line 188  int computeGamma(float *bz_err, float *b
                     if isnan(bz[j * nx + i]) continue;                     if isnan(bz[j * nx + i]) continue;
                     if isnan(bz_err[j * nx + i]) continue;                     if isnan(bz_err[j * nx + i]) continue;
                     if isnan(bh_err[j * nx + i]) continue;                     if isnan(bh_err[j * nx + i]) continue;
                   if isnan(bh[j * nx + i]) continue;
                     if (bz[j * nx + i] == 0) continue;                     if (bz[j * nx + i] == 0) continue;
                     sum += (atan(fabs(bz[j * nx + i]/bh[j * nx + i] )))*(180./PI);                  sum += fabs(atan(bh[j * nx + i]/fabs(bz[j * nx + i])))*(180./PI);
                     err += (( sqrt ( ((bz_err[j * nx + i]*bz_err[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i])) + ((bh_err[j * nx + i]*bh_err[j * nx + i])/(bh[j * nx + i]*bh[j * nx + i])))  * fabs(bz[j * nx + i]/bh[j * nx + i]) ) / (1 + (bz[j * nx + i]/bh[j * nx + i])*(bz[j * nx + i]/bh[j * nx + i]))) *(180./PI);                  err += (1/(1+((bh[j * nx + i]*bh[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i]))))*(1/(1+((bh[j * nx + i]*bh[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i])))) *
                   ( ((bh_err[j * nx + i]*bh_err[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i])) +
                    ((bh[j * nx + i]*bh[j * nx + i]*bz_err[j * nx + i]*bz_err[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i]*bz[j * nx + i]*bz[j * nx + i])) );
                     count_mask++;                     count_mask++;
                   }                   }
               }               }
           }           }
  
      *mean_gamma_ptr = sum/count_mask;      *mean_gamma_ptr = sum/count_mask;
      *mean_gamma_err_ptr = (sqrt(err*err))/(count_mask*100.0); // error in the quantity (sum)/(count_mask)      *mean_gamma_err_ptr = (sqrt(err)/(count_mask))*(180./PI);
      printf("MEANGAM=%f\n",*mean_gamma_ptr);      //printf("MEANGAM=%f\n",*mean_gamma_ptr);
      printf("MEANGAM_err=%f\n",*mean_gamma_err_ptr);      //printf("MEANGAM_err=%f\n",*mean_gamma_err_ptr);
      return 0;      return 0;
 } }
  
Line 213  int computeB_total(float *bx_err, float
Line 225  int computeB_total(float *bx_err, float
           {           {
             for (j = 0; j < ny; j++)             for (j = 0; j < ny; j++)
               {               {
                 if isnan(bx[j * nx + i]) continue;              if isnan(bx[j * nx + i])
                 if isnan(by[j * nx + i]) continue;              {
                 if isnan(bz[j * nx + i]) continue;                  bt[j * nx + i] = NAN;
                   bt_err[j * nx + i] = NAN;
                   continue;
               }
               if isnan(by[j * nx + i])
               {
                   bt[j * nx + i] = NAN;
                   bt_err[j * nx + i] = NAN;
                   continue;
               }
               if isnan(bz[j * nx + i])
               {
                   bt[j * nx + i] = NAN;
                   bt_err[j * nx + i] = NAN;
                   continue;
               }
                 bt[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] + bz[j * nx + i]*bz[j * nx + i]);                 bt[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] + bz[j * nx + i]*bz[j * nx + i]);
                 bt_err[j * nx + i]=sqrt(bx[j * nx + i]*bx[j * nx + i]*bx_err[j * nx + i]*bx_err[j * nx + i] + by[j * nx + i]*by[j * nx + i]*by_err[j * nx + i]*by_err[j * nx + i] + bz[j * nx + i]*bz[j * nx + i]*bz_err[j * nx + i]*bz_err[j * nx + i] )/bt[j * nx + i];                 bt_err[j * nx + i]=sqrt(bx[j * nx + i]*bx[j * nx + i]*bx_err[j * nx + i]*bx_err[j * nx + i] + by[j * nx + i]*by[j * nx + i]*by_err[j * nx + i]*by_err[j * nx + i] + bz[j * nx + i]*bz[j * nx + i]*bz_err[j * nx + i]*bz_err[j * nx + i] )/bt[j * nx + i];
               }               }
Line 226  int computeB_total(float *bx_err, float
Line 253  int computeB_total(float *bx_err, float
 /*===========================================*/ /*===========================================*/
 /* Example function 5:  Derivative of B_Total SQRT( (dBt/dx)^2 + (dBt/dy)^2 ) */ /* Example function 5:  Derivative of B_Total SQRT( (dBt/dx)^2 + (dBt/dy)^2 ) */
  
 int computeBtotalderivative(float *bt, int *dims, float *mean_derivative_btotal_ptr, int *mask, int *bitmask, float *derx_bt, float *dery_bt, float *bt_err, float *mean_derivative_btotal_err_ptr)  int computeBtotalderivative(float *bt, int *dims, float *mean_derivative_btotal_ptr, int *mask, int *bitmask, float *derx_bt, float *dery_bt, float *bt_err, float *mean_derivative_btotal_err_ptr, float *err_termAt, float *err_termBt)
 { {
  
     int nx = dims[0];     int nx = dims[0];
Line 234  int computeBtotalderivative(float *bt, i
Line 261  int computeBtotalderivative(float *bt, i
     int i=0;     int i=0;
     int j=0;     int j=0;
     int count_mask=0;     int count_mask=0;
     float sum=0.0;      double sum = 0.0;
     float err = 0.0;      double err = 0.0;
     *mean_derivative_btotal_ptr = 0.0;     *mean_derivative_btotal_ptr = 0.0;
  
     if (nx <= 0 || ny <= 0) return 1;     if (nx <= 0 || ny <= 0) return 1;
Line 246  int computeBtotalderivative(float *bt, i
Line 273  int computeBtotalderivative(float *bt, i
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
               {               {
                 derx_bt[j * nx + i] = (bt[j * nx + i+1] - bt[j * nx + i-1])*0.5;                 derx_bt[j * nx + i] = (bt[j * nx + i+1] - bt[j * nx + i-1])*0.5;
              err_termAt[j * nx + i] = (((bt[j * nx + (i+1)]-bt[j * nx + (i-1)])*(bt[j * nx + (i+1)]-bt[j * nx + (i-1)])) * (bt_err[j * nx + (i+1)]*bt_err[j * nx + (i+1)] + bt_err[j * nx + (i-1)]*bt_err[j * nx + (i-1)])) ;
               }               }
           }           }
  
Line 255  int computeBtotalderivative(float *bt, i
Line 283  int computeBtotalderivative(float *bt, i
             for (j = 1; j <= ny-2; j++)             for (j = 1; j <= ny-2; j++)
               {               {
                 dery_bt[j * nx + i] = (bt[(j+1) * nx + i] - bt[(j-1) * nx + i])*0.5;                 dery_bt[j * nx + i] = (bt[(j+1) * nx + i] - bt[(j-1) * nx + i])*0.5;
              err_termBt[j * nx + i] = (((bt[(j+1) * nx + i]-bt[(j-1) * nx + i])*(bt[(j+1) * nx + i]-bt[(j-1) * nx + i])) * (bt_err[(j+1) * nx + i]*bt_err[(j+1) * nx + i] + bt_err[(j-1) * nx + i]*bt_err[(j-1) * nx + i])) ;
               }               }
           }           }
  
       /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
         /* consider the edges */      ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
         i=0;         i=0;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
Line 284  int computeBtotalderivative(float *bt, i
Line 314  int computeBtotalderivative(float *bt, i
              dery_bt[j * nx + i] = ( (3*bt[j * nx + i]) + (-4*bt[(j-1) * nx + i]) - (-bt[(j-2) * nx + i]) )*0.5;              dery_bt[j * nx + i] = ( (3*bt[j * nx + i]) + (-4*bt[(j-1) * nx + i]) - (-bt[(j-2) * nx + i]) )*0.5;
           }           }
  
       // Calculate the sum only
         for (i = 0; i <= nx-1; i++)      for (i = 1; i <= nx-2; i++)
           {           {
             for (j = 0; j <= ny-1; j++)          for (j = 1; j <= ny-2; j++)
             {             {
                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
               if ( (derx_bt[j * nx + i] + dery_bt[j * nx + i]) == 0) continue;
               if isnan(bt[j * nx + i])      continue;
               if isnan(bt[(j+1) * nx + i])  continue;
               if isnan(bt[(j-1) * nx + i])  continue;
               if isnan(bt[j * nx + i-1])    continue;
               if isnan(bt[j * nx + i+1])    continue;
               if isnan(bt_err[j * nx + i])  continue;
                if isnan(derx_bt[j * nx + i]) continue;                if isnan(derx_bt[j * nx + i]) continue;
                if isnan(dery_bt[j * nx + i]) continue;                if isnan(dery_bt[j * nx + i]) continue;
                sum += sqrt( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  ); /* Units of Gauss */                sum += sqrt( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  ); /* Units of Gauss */
                err += (2.0)*bt_err[j * nx + i]*bt_err[j * nx + i];              err += err_termBt[j * nx + i] / (16.0*( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  ))+
                      err_termAt[j * nx + i] / (16.0*( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  )) ;
                count_mask++;                count_mask++;
             }             }
           }           }
  
         *mean_derivative_btotal_ptr     = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram      *mean_derivative_btotal_ptr     = (sum)/(count_mask);
         *mean_derivative_btotal_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)      *mean_derivative_btotal_err_ptr = (sqrt(err))/(count_mask);
         printf("MEANGBT=%f\n",*mean_derivative_btotal_ptr);      //printf("MEANGBT=%f\n",*mean_derivative_btotal_ptr);
         printf("MEANGBT_err=%f\n",*mean_derivative_btotal_err_ptr);      //printf("MEANGBT_err=%f\n",*mean_derivative_btotal_err_ptr);
   
         return 0;         return 0;
 } }
  
Line 309  int computeBtotalderivative(float *bt, i
Line 348  int computeBtotalderivative(float *bt, i
 /*===========================================*/ /*===========================================*/
 /* Example function 6:  Derivative of Bh SQRT( (dBh/dx)^2 + (dBh/dy)^2 ) */ /* Example function 6:  Derivative of Bh SQRT( (dBh/dx)^2 + (dBh/dy)^2 ) */
  
 int computeBhderivative(float *bh, float *bh_err, int *dims, float *mean_derivative_bh_ptr, float *mean_derivative_bh_err_ptr, int *mask, int *bitmask, float *derx_bh, float *dery_bh)  int computeBhderivative(float *bh, float *bh_err, int *dims, float *mean_derivative_bh_ptr, float *mean_derivative_bh_err_ptr, int *mask, int *bitmask, float *derx_bh, float *dery_bh, float *err_termAh, float *err_termBh)
 { {
  
      int nx = dims[0];      int nx = dims[0];
Line 317  int computeBhderivative(float *bh, float
Line 356  int computeBhderivative(float *bh, float
      int i=0;      int i=0;
      int j=0;      int j=0;
      int count_mask=0;      int count_mask=0;
      float sum=0.0;      double sum= 0.0;
      float err =0.0;      double err =0.0;
      *mean_derivative_bh_ptr = 0.0;      *mean_derivative_bh_ptr = 0.0;
  
         if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;
Line 329  int computeBhderivative(float *bh, float
Line 368  int computeBhderivative(float *bh, float
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
               {               {
                 derx_bh[j * nx + i] = (bh[j * nx + i+1] - bh[j * nx + i-1])*0.5;                 derx_bh[j * nx + i] = (bh[j * nx + i+1] - bh[j * nx + i-1])*0.5;
              err_termAh[j * nx + i] = (((bh[j * nx + (i+1)]-bh[j * nx + (i-1)])*(bh[j * nx + (i+1)]-bh[j * nx + (i-1)])) * (bh_err[j * nx + (i+1)]*bh_err[j * nx + (i+1)] + bh_err[j * nx + (i-1)]*bh_err[j * nx + (i-1)]));
               }               }
           }           }
  
Line 338  int computeBhderivative(float *bh, float
Line 378  int computeBhderivative(float *bh, float
             for (j = 1; j <= ny-2; j++)             for (j = 1; j <= ny-2; j++)
               {               {
                 dery_bh[j * nx + i] = (bh[(j+1) * nx + i] - bh[(j-1) * nx + i])*0.5;                 dery_bh[j * nx + i] = (bh[(j+1) * nx + i] - bh[(j-1) * nx + i])*0.5;
             err_termBh[j * nx + i] = (((bh[ (j+1) * nx + i]-bh[(j-1) * nx + i])*(bh[(j+1) * nx + i]-bh[(j-1) * nx + i])) * (bh_err[(j+1) * nx + i]*bh_err[(j+1) * nx + i] + bh_err[(j-1) * nx + i]*bh_err[(j-1) * nx + i]));
               }               }
           }           }
  
       /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
         /* consider the edges */      ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
         i=0;         i=0;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
Line 373  int computeBhderivative(float *bh, float
Line 415  int computeBhderivative(float *bh, float
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
             {             {
                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
               if ( (derx_bh[j * nx + i] + dery_bh[j * nx + i]) == 0) continue;
               if isnan(bh[j * nx + i])      continue;
               if isnan(bh[(j+1) * nx + i])  continue;
               if isnan(bh[(j-1) * nx + i])  continue;
               if isnan(bh[j * nx + i-1])    continue;
               if isnan(bh[j * nx + i+1])    continue;
               if isnan(bh_err[j * nx + i])  continue;
                if isnan(derx_bh[j * nx + i]) continue;                if isnan(derx_bh[j * nx + i]) continue;
                if isnan(dery_bh[j * nx + i]) continue;                if isnan(dery_bh[j * nx + i]) continue;
                sum += sqrt( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  ); /* Units of Gauss */                sum += sqrt( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  ); /* Units of Gauss */
                err += (2.0)*bh_err[j * nx + i]*bh_err[j * nx + i];              err += err_termBh[j * nx + i] / (16.0*( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  ))+
                      err_termAh[j * nx + i] / (16.0*( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  )) ;
                count_mask++;                count_mask++;
             }             }
           }           }
  
         *mean_derivative_bh_ptr     = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram         *mean_derivative_bh_ptr     = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
         *mean_derivative_bh_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)         *mean_derivative_bh_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
         printf("MEANGBH=%f\n",*mean_derivative_bh_ptr);      //printf("MEANGBH=%f\n",*mean_derivative_bh_ptr);
         printf("MEANGBH_err=%f\n",*mean_derivative_bh_err_ptr);      //printf("MEANGBH_err=%f\n",*mean_derivative_bh_err_ptr);
  
         return 0;         return 0;
 } }
Line 392  int computeBhderivative(float *bh, float
Line 442  int computeBhderivative(float *bh, float
 /*===========================================*/ /*===========================================*/
 /* Example function 7:  Derivative of B_vertical SQRT( (dBz/dx)^2 + (dBz/dy)^2 ) */ /* Example function 7:  Derivative of B_vertical SQRT( (dBz/dx)^2 + (dBz/dy)^2 ) */
  
 int computeBzderivative(float *bz, float *bz_err, int *dims, float *mean_derivative_bz_ptr, float *mean_derivative_bz_err_ptr, int *mask, int *bitmask, float *derx_bz, float *dery_bz)  int computeBzderivative(float *bz, float *bz_err, int *dims, float *mean_derivative_bz_ptr, float *mean_derivative_bz_err_ptr, int *mask, int *bitmask, float *derx_bz, float *dery_bz, float *err_termA, float *err_termB)
 { {
  
         int nx = dims[0];         int nx = dims[0];
Line 400  int computeBzderivative(float *bz, float
Line 450  int computeBzderivative(float *bz, float
         int i=0;         int i=0;
         int j=0;         int j=0;
         int count_mask=0;         int count_mask=0;
         float sum = 0.0;      double sum = 0.0;
         float err = 0.0;      double err = 0.0;
         *mean_derivative_bz_ptr = 0.0;         *mean_derivative_bz_ptr = 0.0;
  
         if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;
Line 411  int computeBzderivative(float *bz, float
Line 461  int computeBzderivative(float *bz, float
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
               {               {
                 if isnan(bz[j * nx + i]) continue;  
                 derx_bz[j * nx + i] = (bz[j * nx + i+1] - bz[j * nx + i-1])*0.5;                 derx_bz[j * nx + i] = (bz[j * nx + i+1] - bz[j * nx + i-1])*0.5;
              err_termA[j * nx + i] = (((bz[j * nx + (i+1)]-bz[j * nx + (i-1)])*(bz[j * nx + (i+1)]-bz[j * nx + (i-1)])) * (bz_err[j * nx + (i+1)]*bz_err[j * nx + (i+1)] + bz_err[j * nx + (i-1)]*bz_err[j * nx + (i-1)]));
               }               }
           }           }
  
Line 421  int computeBzderivative(float *bz, float
Line 471  int computeBzderivative(float *bz, float
           {           {
             for (j = 1; j <= ny-2; j++)             for (j = 1; j <= ny-2; j++)
               {               {
                 if isnan(bz[j * nx + i]) continue;  
                 dery_bz[j * nx + i] = (bz[(j+1) * nx + i] - bz[(j-1) * nx + i])*0.5;                 dery_bz[j * nx + i] = (bz[(j+1) * nx + i] - bz[(j-1) * nx + i])*0.5;
              err_termB[j * nx + i] = (((bz[(j+1) * nx + i]-bz[(j-1) * nx + i])*(bz[(j+1) * nx + i]-bz[(j-1) * nx + i])) * (bz_err[(j+1) * nx + i]*bz_err[(j+1) * nx + i] + bz_err[(j-1) * nx + i]*bz_err[(j-1) * nx + i]));
               }               }
           }           }
  
       /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
         /* consider the edges */      ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
         i=0;         i=0;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
              if isnan(bz[j * nx + i]) continue;  
              derx_bz[j * nx + i] = ( (-3*bz[j * nx + i]) + (4*bz[j * nx + (i+1)]) - (bz[j * nx + (i+2)]) )*0.5;              derx_bz[j * nx + i] = ( (-3*bz[j * nx + i]) + (4*bz[j * nx + (i+1)]) - (bz[j * nx + (i+2)]) )*0.5;
           }           }
  
         i=nx-1;         i=nx-1;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
              if isnan(bz[j * nx + i]) continue;  
              derx_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[j * nx + (i-1)]) - (-bz[j * nx + (i-2)]) )*0.5;              derx_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[j * nx + (i-1)]) - (-bz[j * nx + (i-2)]) )*0.5;
           }           }
  
         j=0;         j=0;
         for (i = 0; i <= nx-1; i++)         for (i = 0; i <= nx-1; i++)
           {           {
              if isnan(bz[j * nx + i]) continue;  
              dery_bz[j * nx + i] = ( (-3*bz[j*nx + i]) + (4*bz[(j+1) * nx + i]) - (bz[(j+2) * nx + i]) )*0.5;              dery_bz[j * nx + i] = ( (-3*bz[j*nx + i]) + (4*bz[(j+1) * nx + i]) - (bz[(j+2) * nx + i]) )*0.5;
           }           }
  
         j=ny-1;         j=ny-1;
         for (i = 0; i <= nx-1; i++)         for (i = 0; i <= nx-1; i++)
           {           {
              if isnan(bz[j * nx + i]) continue;  
              dery_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[(j-1) * nx + i]) - (-bz[(j-2) * nx + i]) )*0.5;              dery_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[(j-1) * nx + i]) - (-bz[(j-2) * nx + i]) )*0.5;
           }           }
  
Line 461  int computeBzderivative(float *bz, float
Line 508  int computeBzderivative(float *bz, float
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
             {             {
                // if ( (derx_bz[j * nx + i]-dery_bz[j * nx + i]) == 0) continue;  
                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
               if ( (derx_bz[j * nx + i] + dery_bz[j * nx + i]) == 0) continue;
                if isnan(bz[j * nx + i]) continue;                if isnan(bz[j * nx + i]) continue;
                //if isnan(bz_err[j * nx + i]) continue;              if isnan(bz[(j+1) * nx + i])  continue;
               if isnan(bz[(j-1) * nx + i])  continue;
               if isnan(bz[j * nx + i-1])    continue;
               if isnan(bz[j * nx + i+1])    continue;
               if isnan(bz_err[j * nx + i])  continue;
                if isnan(derx_bz[j * nx + i]) continue;                if isnan(derx_bz[j * nx + i]) continue;
                if isnan(dery_bz[j * nx + i]) continue;                if isnan(dery_bz[j * nx + i]) continue;
                sum += sqrt( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  ); /* Units of Gauss */                sum += sqrt( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  ); /* Units of Gauss */
                err += 2.0*bz_err[j * nx + i]*bz_err[j * nx + i];              err += err_termB[j * nx + i] / (16.0*( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  )) +
                      err_termA[j * nx + i] / (16.0*( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  )) ;
                count_mask++;                count_mask++;
             }             }
           }           }
  
         *mean_derivative_bz_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram         *mean_derivative_bz_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
         *mean_derivative_bz_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)         *mean_derivative_bz_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
         printf("MEANGBZ=%f\n",*mean_derivative_bz_ptr);      //printf("MEANGBZ=%f\n",*mean_derivative_bz_ptr);
         printf("MEANGBZ_err=%f\n",*mean_derivative_bz_err_ptr);      //printf("MEANGBZ_err=%f\n",*mean_derivative_bz_err_ptr);
  
         return 0;         return 0;
 } }
Line 519  int computeBzderivative(float *bz, float
Line 571  int computeBzderivative(float *bz, float
 //              float *noiseby, float *noisebz) //              float *noiseby, float *noisebz)
  
 int computeJz(float *bx_err, float *by_err, float *bx, float *by, int *dims, float *jz, float *jz_err, float *jz_err_squared, int computeJz(float *bx_err, float *by_err, float *bx, float *by, int *dims, float *jz, float *jz_err, float *jz_err_squared,
               int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)                int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery, float *err_term1, float *err_term2)
  
  
 { {
Line 528  int computeJz(float *bx_err, float *by_e
Line 580  int computeJz(float *bx_err, float *by_e
         int i=0;         int i=0;
         int j=0;         int j=0;
         int count_mask=0;         int count_mask=0;
         float curl=0.0;  
         float us_i=0.0;  
         float test_perimeter=0.0;  
         float mean_curl=0.0;  
  
         if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;
  
Line 542  int computeJz(float *bx_err, float *by_e
Line 590  int computeJz(float *bx_err, float *by_e
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
               {               {
                  if isnan(by[j * nx + i]) continue;  
                  derx[j * nx + i] = (by[j * nx + i+1] - by[j * nx + i-1])*0.5;                  derx[j * nx + i] = (by[j * nx + i+1] - by[j * nx + i-1])*0.5;
              err_term1[j * nx + i] = (by_err[j * nx + i+1])*(by_err[j * nx + i+1]) + (by_err[j * nx + i-1])*(by_err[j * nx + i-1]);
               }               }
           }           }
  
Line 551  int computeJz(float *bx_err, float *by_e
Line 599  int computeJz(float *bx_err, float *by_e
           {           {
             for (j = 1; j <= ny-2; j++)             for (j = 1; j <= ny-2; j++)
               {               {
                  if isnan(bx[j * nx + i]) continue;  
                  dery[j * nx + i] = (bx[(j+1) * nx + i] - bx[(j-1) * nx + i])*0.5;                  dery[j * nx + i] = (bx[(j+1) * nx + i] - bx[(j-1) * nx + i])*0.5;
              err_term2[j * nx + i] = (bx_err[(j+1) * nx + i])*(bx_err[(j+1) * nx + i]) + (bx_err[(j-1) * nx + i])*(bx_err[(j-1) * nx + i]);
               }               }
           }           }
  
         // consider the edges      /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
       ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
   
         i=0;         i=0;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
              if isnan(by[j * nx + i]) continue;  
              derx[j * nx + i] = ( (-3*by[j * nx + i]) + (4*by[j * nx + (i+1)]) - (by[j * nx + (i+2)]) )*0.5;              derx[j * nx + i] = ( (-3*by[j * nx + i]) + (4*by[j * nx + (i+1)]) - (by[j * nx + (i+2)]) )*0.5;
           }           }
  
         i=nx-1;         i=nx-1;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
              if isnan(by[j * nx + i]) continue;  
              derx[j * nx + i] = ( (3*by[j * nx + i]) + (-4*by[j * nx + (i-1)]) - (-by[j * nx + (i-2)]) )*0.5;              derx[j * nx + i] = ( (3*by[j * nx + i]) + (-4*by[j * nx + (i-1)]) - (-by[j * nx + (i-2)]) )*0.5;
           }           }
  
         j=0;         j=0;
         for (i = 0; i <= nx-1; i++)         for (i = 0; i <= nx-1; i++)
           {           {
              if isnan(bx[j * nx + i]) continue;  
              dery[j * nx + i] = ( (-3*bx[j*nx + i]) + (4*bx[(j+1) * nx + i]) - (bx[(j+2) * nx + i]) )*0.5;              dery[j * nx + i] = ( (-3*bx[j*nx + i]) + (4*bx[(j+1) * nx + i]) - (bx[(j+2) * nx + i]) )*0.5;
           }           }
  
         j=ny-1;         j=ny-1;
         for (i = 0; i <= nx-1; i++)         for (i = 0; i <= nx-1; i++)
           {           {
              if isnan(bx[j * nx + i]) continue;  
              dery[j * nx + i] = ( (3*bx[j * nx + i]) + (-4*bx[(j-1) * nx + i]) - (-bx[(j-2) * nx + i]) )*0.5;              dery[j * nx + i] = ( (3*bx[j * nx + i]) + (-4*bx[(j-1) * nx + i]) - (-bx[(j-2) * nx + i]) )*0.5;
           }           }
  
Line 592  int computeJz(float *bx_err, float *by_e
Line 639  int computeJz(float *bx_err, float *by_e
             {             {
                // calculate jz at all points                // calculate jz at all points
                jz[j * nx + i] = (derx[j * nx + i]-dery[j * nx + i]);       // jz is in units of Gauss/pix                jz[j * nx + i] = (derx[j * nx + i]-dery[j * nx + i]);       // jz is in units of Gauss/pix
                jz_err[j * nx + i]=0.5*sqrt( (bx_err[(j+1) * nx + i]*bx_err[(j+1) * nx + i]) + (bx_err[(j-1) * nx + i]*bx_err[(j-1) * nx + i]) +              jz_err[j * nx + i]        = 0.5*sqrt( err_term1[j * nx + i] + err_term2[j * nx + i] ) ;
                                             (by_err[j * nx + (i+1)]*by_err[j * nx + (i+1)]) + (by_err[j * nx + (i-1)]*by_err[j * nx + (i-1)]) ) ;  
                jz_err_squared[j * nx + i]=(jz_err[j * nx + i]*jz_err[j * nx + i]);                jz_err_squared[j * nx + i]=(jz_err[j * nx + i]*jz_err[j * nx + i]);
                count_mask++;                count_mask++;
             }             }
           }           }
   
         return 0;         return 0;
 } }
  
 /*===========================================*/ /*===========================================*/
  
   
 /* Example function 9:  Compute quantities on Jz array */ /* Example function 9:  Compute quantities on Jz array */
 // Compute mean and total current on Jz array. // Compute mean and total current on Jz array.
  
Line 619  int computeJzsmooth(float *bx, float *by
Line 663  int computeJzsmooth(float *bx, float *by
         int i=0;         int i=0;
         int j=0;         int j=0;
         int count_mask=0;         int count_mask=0;
         float curl=0.0;          double curl = 0.0;
         float us_i=0.0;      double us_i = 0.0;
         float test_perimeter=0.0;      double err = 0.0;
         float mean_curl=0.0;  
         float err=0.0;  
  
         if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;
  
Line 643  int computeJzsmooth(float *bx, float *by
Line 685  int computeJzsmooth(float *bx, float *by
             }             }
           }           }
  
         /* Calculate mean vertical current density (mean_curl) and total unsigned vertical current (us_i) using smoothed Jz array and continue conditions above */      /* Calculate mean vertical current density (mean_jz) and total unsigned vertical current (us_i) using smoothed Jz array and continue conditions above */
         *mean_jz_ptr     = curl/(count_mask);        /* mean_jz gets populated as MEANJZD */         *mean_jz_ptr     = curl/(count_mask);        /* mean_jz gets populated as MEANJZD */
         *mean_jz_err_ptr = (sqrt(err))*fabs(((rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.))/(count_mask)); // error in the quantity MEANJZD      *mean_jz_err_ptr = (sqrt(err)/count_mask)*((1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.)); // error in the quantity MEANJZD
  
         *us_i_ptr        = (us_i);                   /* us_i gets populated as TOTUSJZ */         *us_i_ptr        = (us_i);                   /* us_i gets populated as TOTUSJZ */
         *us_i_err_ptr    = (sqrt(err))*fabs((cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT)); // error in the quantity TOTUSJZ      *us_i_err_ptr    = (sqrt(err))*((cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT)); // error in the quantity TOTUSJZ
  
         printf("MEANJZD=%f\n",*mean_jz_ptr);      //printf("MEANJZD=%f\n",*mean_jz_ptr);
         printf("MEANJZD_err=%f\n",*mean_jz_err_ptr);      //printf("MEANJZD_err=%f\n",*mean_jz_err_ptr);
  
         printf("TOTUSJZ=%g\n",*us_i_ptr);      //printf("TOTUSJZ=%g\n",*us_i_ptr);
         printf("TOTUSJZ_err=%g\n",*us_i_err_ptr);      //printf("TOTUSJZ_err=%g\n",*us_i_err_ptr);
  
         return 0;         return 0;
  
Line 665  int computeJzsmooth(float *bx, float *by
Line 707  int computeJzsmooth(float *bx, float *by
 /* Example function 10:  Twist Parameter, alpha */ /* Example function 10:  Twist Parameter, alpha */
  
 // The twist parameter, alpha, is defined as alpha = Jz/Bz. In this case, the calculation // The twist parameter, alpha, is defined as alpha = Jz/Bz. In this case, the calculation
 // for alpha is calculated in the following way (different from Leka and Barnes' approach):  // for alpha is weighted by Bz (following Hagino et al., http://adsabs.harvard.edu/abs/2004PASJ...56..831H):
  
        // (sum of all positive Bz + abs(sum of all negative Bz)) = avg Bz  // numerator   = sum of all Jz*Bz
        // (abs(sum of all Jz at positive Bz) + abs(sum of all Jz at negative Bz)) = avg Jz  // denominator = sum of Bz*Bz
        // avg alpha = avg Jz / avg Bz  // alpha       = numerator/denominator
   
 // The sign is assigned as follows:  
 // If the sum of all Bz is greater than 0, then evaluate the sum of Jz at the positive Bz pixels.  
 // If this value is > 0, then alpha is > 0.  
 // If this value is < 0, then alpha is <0.  
 //  
 // If the sum of all Bz is less than 0, then evaluate the sum of Jz at the negative Bz pixels.  
 // If this value is > 0, then alpha is < 0.  
 // If this value is < 0, then alpha is > 0.  
  
 // The units of alpha are in 1/Mm // The units of alpha are in 1/Mm
 // The units of Jz are in Gauss/pix; the units of Bz are in Gauss. // The units of Jz are in Gauss/pix; the units of Bz are in Gauss.
Line 694  int computeAlpha(float *jz_err, float *b
Line 727  int computeAlpha(float *jz_err, float *b
         int ny = dims[1];         int ny = dims[1];
         int i=0;         int i=0;
         int j=0;         int j=0;
         int count_mask=0;          double alpha_total         = 0.0;
         float a=0.0;      double C                   = ((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.));
         float b=0.0;      double total               = 0.0;
         float c=0.0;      double A                   = 0.0;
         float d=0.0;      double B                   = 0.0;
         float bznew=0.0;  
         float alpha2=0.0;  
         float sum1=0.0;  
         float sum2=0.0;  
         float sum3=0.0;  
         float sum4=0.0;  
         float sum=0.0;  
         float sum5=0.0;  
         float sum6=0.0;  
         float sum_err=0.0;  
  
         if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;
   
         for (i = 1; i < nx-1; i++)         for (i = 1; i < nx-1; i++)
           {           {
             for (j = 1; j < ny-1; j++)             for (j = 1; j < ny-1; j++)
Line 720  int computeAlpha(float *jz_err, float *b
Line 742  int computeAlpha(float *jz_err, float *b
                 if isnan(jz[j * nx + i]) continue;                 if isnan(jz[j * nx + i]) continue;
                 if isnan(bz[j * nx + i]) continue;                 if isnan(bz[j * nx + i]) continue;
                 if (jz[j * nx + i]     == 0.0) continue;                 if (jz[j * nx + i]     == 0.0) continue;
                 if (bz_err[j * nx + i] == 0.0) continue;  
                 if (bz[j * nx + i]     == 0.0) continue;                 if (bz[j * nx + i]     == 0.0) continue;
                 if (bz[j * nx + i] >  0) sum1 += ( bz[j * nx + i] ); a++;              A += jz[j*nx+i]*bz[j*nx+i];
                 if (bz[j * nx + i] <= 0) sum2 += ( bz[j * nx + i] ); b++;              B += bz[j*nx+i]*bz[j*nx+i];
                 if (bz[j * nx + i] >  0) sum3 += ( jz[j * nx + i] ); c++;  
                 if (bz[j * nx + i] <= 0) sum4 += ( jz[j * nx + i] ); d++;  
                 sum5    += bz[j * nx + i];  
                 /* sum_err is a fractional uncertainty */  
                 sum_err += sqrt(((jz_err[j * nx + i]*jz_err[j * nx + i])/(jz[j * nx + i]*jz[j * nx + i])) + ((bz_err[j * nx + i]*bz_err[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i]))) * fabs( ( (jz[j * nx + i]) / (bz[j * nx + i]) ) *(1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.));  
                 count_mask++;  
               }               }
           }           }
  
         sum     = (((fabs(sum3))+(fabs(sum4)))/((fabs(sum2))+sum1))*((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.)); /* the units for (jz/bz) are 1/Mm */          for (i = 1; i < nx-1; i++)
       {
         /* Determine the sign of alpha */              for (j = 1; j < ny-1; j++)
         if ((sum5 > 0) && (sum3 >  0)) sum=sum;          {
         if ((sum5 > 0) && (sum3 <= 0)) sum=-sum;              if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
         if ((sum5 < 0) && (sum4 <= 0)) sum=sum;              if isnan(jz[j * nx + i])   continue;
         if ((sum5 < 0) && (sum4 >  0)) sum=-sum;              if isnan(bz[j * nx + i])   continue;
               if (jz[j * nx + i] == 0.0) continue;
         *mean_alpha_ptr = sum; /* Units are 1/Mm */              if (bz[j * nx + i] == 0.0) continue;
         *mean_alpha_err_ptr    = (sqrt(sum_err*sum_err)) / ((a+b+c+d)*100.0); // error in the quantity (sum)/(count_mask); factor of 100 comes from converting percent              total += bz[j*nx+i]*bz[j*nx+i]*jz_err[j*nx+i]*jz_err[j*nx+i] + (jz[j*nx+i]-2*bz[j*nx+i]*A/B)*(jz[j*nx+i]-2*bz[j*nx+i]*A/B)*bz_err[j*nx+i]*bz_err[j*nx+i];
           }
       }
  
         printf("MEANALP=%f\n",*mean_alpha_ptr);      /* Determine the absolute value of alpha. The units for alpha are 1/Mm */
         printf("MEANALP_err=%f\n",*mean_alpha_err_ptr);      alpha_total              = ((A/B)*C);
       *mean_alpha_ptr          = alpha_total;
       *mean_alpha_err_ptr      = (C/B)*(sqrt(total));
  
         return 0;         return 0;
 } }
Line 772  int computeHelicity(float *jz_err, float
Line 789  int computeHelicity(float *jz_err, float
         int i=0;         int i=0;
         int j=0;         int j=0;
         int count_mask=0;         int count_mask=0;
         float sum=0.0;          double sum     = 0.0;
         float sum2=0.0;          double sum2    = 0.0;
         float sum_err=0.0;          double err     = 0.0;
  
         if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;
  
Line 785  int computeHelicity(float *jz_err, float
Line 802  int computeHelicity(float *jz_err, float
                   if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                   if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                   if isnan(jz[j * nx + i]) continue;                   if isnan(jz[j * nx + i]) continue;
                   if isnan(bz[j * nx + i]) continue;                   if isnan(bz[j * nx + i]) continue;
               if isnan(jz_err[j * nx + i]) continue;
               if isnan(bz_err[j * nx + i]) continue;
                   if (bz[j * nx + i] == 0.0) continue;                   if (bz[j * nx + i] == 0.0) continue;
                   if (jz[j * nx + i] == 0.0) continue;                   if (jz[j * nx + i] == 0.0) continue;
                   sum     +=     (jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to MEANJZH and ABSNJZH                   sum     +=     (jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to MEANJZH and ABSNJZH
                   sum2    += fabs(jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to TOTUSJH                   sum2    += fabs(jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to TOTUSJH
                   sum_err += sqrt(((jz_err[j * nx + i]*jz_err[j * nx + i])/(jz[j * nx + i]*jz[j * nx + i])) + ((bz_err[j * nx + i]*bz_err[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i]))) * fabs(jz[j * nx + i]*bz[j * nx + i]*(1/cdelt1)*(rsun_obs/rsun_ref));              err     += (jz_err[j * nx + i]*jz_err[j * nx + i]*bz[j * nx + i]*bz[j * nx + i]) + (bz_err[j * nx + i]*bz_err[j * nx + i]*jz[j * nx + i]*jz[j * nx + i]);
                   count_mask++;                   count_mask++;
                 }                 }
          }          }
Line 798  int computeHelicity(float *jz_err, float
Line 817  int computeHelicity(float *jz_err, float
         *total_us_ih_ptr      = sum2           ; /* Units are G^2 / m ; keyword is TOTUSJH */         *total_us_ih_ptr      = sum2           ; /* Units are G^2 / m ; keyword is TOTUSJH */
         *total_abs_ih_ptr     = fabs(sum)      ; /* Units are G^2 / m ; keyword is ABSNJZH */         *total_abs_ih_ptr     = fabs(sum)      ; /* Units are G^2 / m ; keyword is ABSNJZH */
  
         *mean_ih_err_ptr      = (sqrt(sum_err*sum_err)) / (count_mask*100.0)    ;  // error in the quantity MEANJZH      *mean_ih_err_ptr      = (sqrt(err)/count_mask)*(1/cdelt1)*(rsun_obs/rsun_ref) ; // error in the quantity MEANJZH
         *total_us_ih_err_ptr  = (sqrt(sum_err*sum_err)) / (100.0)               ;  // error in the quantity TOTUSJH      *total_us_ih_err_ptr  = (sqrt(err))*(1/cdelt1)*(rsun_obs/rsun_ref) ;            // error in the quantity TOTUSJH
         *total_abs_ih_err_ptr = (sqrt(sum_err*sum_err)) / (100.0)               ;  // error in the quantity ABSNJZH      *total_abs_ih_err_ptr = (sqrt(err))*(1/cdelt1)*(rsun_obs/rsun_ref) ;            // error in the quantity ABSNJZH
  
         printf("MEANJZH=%f\n",*mean_ih_ptr);      //printf("MEANJZH=%f\n",*mean_ih_ptr);
         printf("MEANJZH_err=%f\n",*mean_ih_err_ptr);      //printf("MEANJZH_err=%f\n",*mean_ih_err_ptr);
  
         printf("TOTUSJH=%f\n",*total_us_ih_ptr);      //printf("TOTUSJH=%f\n",*total_us_ih_ptr);
         printf("TOTUSJH_err=%f\n",*total_us_ih_err_ptr);      //printf("TOTUSJH_err=%f\n",*total_us_ih_err_ptr);
  
         printf("ABSNJZH=%f\n",*total_abs_ih_ptr);      //printf("ABSNJZH=%f\n",*total_abs_ih_ptr);
         printf("ABSNJZH_err=%f\n",*total_abs_ih_err_ptr);      //printf("ABSNJZH_err=%f\n",*total_abs_ih_err_ptr);
  
         return 0;         return 0;
 } }
Line 818  int computeHelicity(float *jz_err, float
Line 837  int computeHelicity(float *jz_err, float
 /* Example function 12:  Sum of Absolute Value per polarity  */ /* Example function 12:  Sum of Absolute Value per polarity  */
  
 //  The Sum of the Absolute Value per polarity is defined as the following: //  The Sum of the Absolute Value per polarity is defined as the following:
 //  fabs(sum(jz gt 0)) + fabs(sum(jz lt 0)) and the units are in Amperes.  //  fabs(sum(jz gt 0)) + fabs(sum(jz lt 0)) and the units are in Amperes per square arcsecond.
 //  The units of jz are in G/pix. In this case, we would have the following: //  The units of jz are in G/pix. In this case, we would have the following:
 //  Jz = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(RSUN_OBS/RSUN_REF), //  Jz = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(RSUN_OBS/RSUN_REF),
 //     = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS) //     = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)
Line 834  int computeSumAbsPerPolarity(float *jz_e
Line 853  int computeSumAbsPerPolarity(float *jz_e
         int i=0;         int i=0;
         int j=0;         int j=0;
         int count_mask=0;         int count_mask=0;
         float sum1=0.0;      double sum1=0.0;
         float sum2=0.0;      double sum2=0.0;
         float err=0.0;      double err=0.0;
         *totaljzptr=0.0;         *totaljzptr=0.0;
  
         if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;
Line 847  int computeSumAbsPerPolarity(float *jz_e
Line 866  int computeSumAbsPerPolarity(float *jz_e
               {               {
                 if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                 if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                 if isnan(bz[j * nx + i]) continue;                 if isnan(bz[j * nx + i]) continue;
               if isnan(jz[j * nx + i]) continue;
                 if (bz[j * nx + i] >  0) sum1 += ( jz[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);                 if (bz[j * nx + i] >  0) sum1 += ( jz[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);
                 if (bz[j * nx + i] <= 0) sum2 += ( jz[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);                 if (bz[j * nx + i] <= 0) sum2 += ( jz[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);
                 err += (jz_err[j * nx + i]*jz_err[j * nx + i]);                 err += (jz_err[j * nx + i]*jz_err[j * nx + i]);
Line 854  int computeSumAbsPerPolarity(float *jz_e
Line 874  int computeSumAbsPerPolarity(float *jz_e
               }               }
           }           }
  
         *totaljzptr    = fabs(sum1) + fabs(sum2);  /* Units are A */      *totaljzptr    = fabs(sum1) + fabs(sum2);  /* Units are Amperes per arcsecond */
         *totaljz_err_ptr = sqrt(err)*(1/cdelt1)*fabs((0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs));         *totaljz_err_ptr = sqrt(err)*(1/cdelt1)*fabs((0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs));
         printf("SAVNCPP=%g\n",*totaljzptr);      //printf("SAVNCPP=%g\n",*totaljzptr);
         printf("SAVNCPP_err=%g\n",*totaljz_err_ptr);      //printf("SAVNCPP_err=%g\n",*totaljz_err_ptr);
  
         return 0;         return 0;
 } }
Line 885  int computeFreeEnergy(float *bx_err, flo
Line 905  int computeFreeEnergy(float *bx_err, flo
         int i=0;         int i=0;
         int j=0;         int j=0;
         int count_mask=0;         int count_mask=0;
         float sum=0.0;      double sum = 0.0;
         float sum1=0.0;      double sum1 = 0.0;
         float err=0.0;      double err = 0.0;
         *totpotptr=0.0;         *totpotptr=0.0;
         *meanpotptr=0.0;         *meanpotptr=0.0;
  
Line 900  int computeFreeEnergy(float *bx_err, flo
Line 920  int computeFreeEnergy(float *bx_err, flo
                  if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                  if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                  if isnan(bx[j * nx + i]) continue;                  if isnan(bx[j * nx + i]) continue;
                  if isnan(by[j * nx + i]) continue;                  if isnan(by[j * nx + i]) continue;
                  sum  += ( ((bpx[j * nx + i] - bx[j * nx + i])*(bpx[j * nx + i] - bx[j * nx + i])) + ((bpy[j * nx + i] - by[j * nx + i])*(bpy[j * nx + i] - by[j * nx + i])) )*(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0);              sum  += ( ((bx[j * nx + i] - bpx[j * nx + i])*(bx[j * nx + i] - bpx[j * nx + i])) + ((by[j * nx + i] - bpy[j * nx + i])*(by[j * nx + i] - bpy[j * nx + i])) )*(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0);
                  sum1 += ( ((bpx[j * nx + i] - bx[j * nx + i])*(bpx[j * nx + i] - bx[j * nx + i])) + ((bpy[j * nx + i] - by[j * nx + i])*(bpy[j * nx + i] - by[j * nx + i])) );              sum1 += (  ((bx[j * nx + i] - bpx[j * nx + i])*(bx[j * nx + i] - bpx[j * nx + i])) + ((by[j * nx + i] - bpy[j * nx + i])*(by[j * nx + i] - bpy[j * nx + i])) );
                  err  += (4.0*bx[j * nx + i]*bx[j * nx + i]*bx_err[j * nx + i]*bx_err[j * nx + i]) + (4.0*by[j * nx + i]*by[j * nx + i]*by_err[j * nx + i]*by_err[j * nx + i]);              err  += 4.0*(bx[j * nx + i] - bpx[j * nx + i])*(bx[j * nx + i] - bpx[j * nx + i])*(bx_err[j * nx + i]*bx_err[j * nx + i]) +
               4.0*(by[j * nx + i] - bpy[j * nx + i])*(by[j * nx + i] - bpy[j * nx + i])*(by_err[j * nx + i]*by_err[j * nx + i]);
                  count_mask++;                  count_mask++;
               }               }
           }           }
  
         *meanpotptr      = (sum1/(8.*PI)) / (count_mask);     /* Units are ergs per cubic centimeter */      /* Units of meanpotptr are ergs per centimeter */
         *meanpot_err_ptr = (sqrt(err))*fabs(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0) / (count_mask*8.*PI); // error in the quantity (sum)/(count_mask)          *meanpotptr      = (sum1) / (count_mask*8.*PI) ;     /* Units are ergs per cubic centimeter */
       *meanpot_err_ptr = (sqrt(err)) / (count_mask*8.*PI); // error in the quantity (sum)/(count_mask)
  
         /* Units of sum are ergs/cm^3, units of factor are cm^2/pix^2; therefore, units of totpotptr are ergs per centimeter */         /* Units of sum are ergs/cm^3, units of factor are cm^2/pix^2; therefore, units of totpotptr are ergs per centimeter */
         *totpotptr       = (sum)/(8.*PI);         *totpotptr       = (sum)/(8.*PI);
         *totpot_err_ptr  = (sqrt(err))*fabs(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0*(1/(8.*PI)));         *totpot_err_ptr  = (sqrt(err))*fabs(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0*(1/(8.*PI)));
  
         printf("MEANPOT=%g\n",*meanpotptr);      //printf("MEANPOT=%g\n",*meanpotptr);
         printf("MEANPOT_err=%g\n",*meanpot_err_ptr);      //printf("MEANPOT_err=%g\n",*meanpot_err_ptr);
  
         printf("TOTPOT=%g\n",*totpotptr);      //printf("TOTPOT=%g\n",*totpotptr);
         printf("TOTPOT_err=%g\n",*totpot_err_ptr);      //printf("TOTPOT_err=%g\n",*totpot_err_ptr);
  
         return 0;         return 0;
 } }
Line 926  int computeFreeEnergy(float *bx_err, flo
Line 948  int computeFreeEnergy(float *bx_err, flo
 /*===========================================*/ /*===========================================*/
 /* Example function 14:  Mean 3D shear angle, area with shear greater than 45, mean horizontal shear angle, area with horizontal shear angle greater than 45 */ /* Example function 14:  Mean 3D shear angle, area with shear greater than 45, mean horizontal shear angle, area with horizontal shear angle greater than 45 */
  
 int computeShearAngle(float *bx_err, float *by_err, float *bh_err, float *bx, float *by, float *bz, float *bpx, float *bpy, float *bpz, int *dims,  int computeShearAngle(float *bx_err, float *by_err, float *bz_err, float *bx, float *by, float *bz, float *bpx, float *bpy, float *bpz, int *dims,
                       float *meanshear_angleptr, float *meanshear_angle_err_ptr, float *area_w_shear_gt_45ptr, int *mask, int *bitmask)                       float *meanshear_angleptr, float *meanshear_angle_err_ptr, float *area_w_shear_gt_45ptr, int *mask, int *bitmask)
   
   
 { {
         int nx = dims[0];         int nx = dims[0];
         int ny = dims[1];         int ny = dims[1];
         int i=0;         int i=0;
         int j=0;         int j=0;
         int count_mask=0;      float count_mask = 0;
         float dotproduct = 0.0;      float count = 0;
         float magnitude_potential = 0.0;      double dotproduct = 0.0;
         float magnitude_vector=0.0;      double magnitude_potential = 0.0;
         float shear_angle=0.0;      double magnitude_vector = 0.0;
         float err=0.0;      double shear_angle = 0.0;
         float sum = 0.0;      double denominator = 0.0;
         float count=0.0;      double term1 = 0.0;
       double term2 = 0.0;
       double term3 = 0.0;
       double sumsum = 0.0;
       double err = 0.0;
       double part1 = 0.0;
       double part2 = 0.0;
       double part3 = 0.0;
         *area_w_shear_gt_45ptr=0.0;         *area_w_shear_gt_45ptr=0.0;
         *meanshear_angleptr=0.0;         *meanshear_angleptr=0.0;
  
Line 957  int computeShearAngle(float *bx_err, flo
Line 988  int computeShearAngle(float *bx_err, flo
                  if isnan(bz[j * nx + i]) continue;                  if isnan(bz[j * nx + i]) continue;
                  if isnan(bx[j * nx + i]) continue;                  if isnan(bx[j * nx + i]) continue;
                  if isnan(by[j * nx + i]) continue;                  if isnan(by[j * nx + i]) continue;
                  /* For mean 3D shear angle, area with shear greater than 45*/              if isnan(bx_err[j * nx + i]) continue;
               if isnan(by_err[j * nx + i]) continue;
               if isnan(bz_err[j * nx + i]) continue;
   
               /* For mean 3D shear angle, percentage with shear greater than 45*/
                  dotproduct            = (bpx[j * nx + i])*(bx[j * nx + i]) + (bpy[j * nx + i])*(by[j * nx + i]) + (bpz[j * nx + i])*(bz[j * nx + i]);                  dotproduct            = (bpx[j * nx + i])*(bx[j * nx + i]) + (bpy[j * nx + i])*(by[j * nx + i]) + (bpz[j * nx + i])*(bz[j * nx + i]);
                  magnitude_potential   = sqrt( (bpx[j * nx + i]*bpx[j * nx + i]) + (bpy[j * nx + i]*bpy[j * nx + i]) + (bpz[j * nx + i]*bpz[j * nx + i]));                  magnitude_potential   = sqrt( (bpx[j * nx + i]*bpx[j * nx + i]) + (bpy[j * nx + i]*bpy[j * nx + i]) + (bpz[j * nx + i]*bpz[j * nx + i]));
                  magnitude_vector      = sqrt( (bx[j * nx + i]*bx[j * nx + i])   + (by[j * nx + i]*by[j * nx + i])   + (bz[j * nx + i]*bz[j * nx + i]) );                  magnitude_vector      = sqrt( (bx[j * nx + i]*bx[j * nx + i])   + (by[j * nx + i]*by[j * nx + i])   + (bz[j * nx + i]*bz[j * nx + i]) );
               //printf("dotproduct=%f\n",dotproduct);
               //printf("magnitude_potential=%f\n",magnitude_potential);
               //printf("magnitude_vector=%f\n",magnitude_vector);
   
                  shear_angle           = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);                  shear_angle           = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);
               sumsum                  += shear_angle;
               //printf("shear_angle=%f\n",shear_angle);
                  count ++;                  count ++;
                  sum += shear_angle ;  
                  err += -(1./(1.- sqrt(bx_err[j * nx + i]*bx_err[j * nx + i]+by_err[j * nx + i]*by_err[j * nx + i]+bh_err[j * nx + i]*bh_err[j * nx + i])));  
                  if (shear_angle > 45) count_mask ++;                  if (shear_angle > 45) count_mask ++;
   
               // For the error analysis
   
               term1 = bx[j * nx + i]*by[j * nx + i]*bpy[j * nx + i] - by[j * nx + i]*by[j * nx + i]*bpx[j * nx + i] + bz[j * nx + i]*bx[j * nx + i]*bpz[j * nx + i] - bz[j * nx + i]*bz[j * nx + i]*bpx[j * nx + i];
               term2 = bx[j * nx + i]*bx[j * nx + i]*bpy[j * nx + i] - bx[j * nx + i]*by[j * nx + i]*bpx[j * nx + i] + bx[j * nx + i]*bz[j * nx + i]*bpy[j * nx + i] - bz[j * nx + i]*by[j * nx + i]*bpz[j * nx + i];
               term3 = bx[j * nx + i]*bx[j * nx + i]*bpz[j * nx + i] - bx[j * nx + i]*bz[j * nx + i]*bpx[j * nx + i] + by[j * nx + i]*by[j * nx + i]*bpz[j * nx + i] - by[j * nx + i]*bz[j * nx + i]*bpy[j * nx + i];
   
               part1 = bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] + bz[j * nx + i]*bz[j * nx + i];
               part2 = bpx[j * nx + i]*bpx[j * nx + i] + bpy[j * nx + i]*bpy[j * nx + i] + bpz[j * nx + i]*bpz[j * nx + i];
               part3 = bx[j * nx + i]*bpx[j * nx + i] + by[j * nx + i]*bpy[j * nx + i] + bz[j * nx + i]*bpz[j * nx + i];
   
               // denominator is squared
               denominator = part1*part1*part1*part2*(1.0-((part3*part3)/(part1*part2)));
   
               err = (term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) +
               (term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) +
               (term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) ;
   
               }               }
           }           }
   
         /* For mean 3D shear angle, area with shear greater than 45*/         /* For mean 3D shear angle, area with shear greater than 45*/
         *meanshear_angleptr = (sum)/(count);                 /* Units are degrees */      *meanshear_angleptr = (sumsum)/(count);                 /* Units are degrees */
         *meanshear_angle_err_ptr = (sqrt(err*err))/(count);  // error in the quantity (sum)/(count_mask)  
         *area_w_shear_gt_45ptr   = (count_mask/(count))*(100.0);/* The area here is a fractional area -- the % of the total area */  
  
         printf("MEANSHR=%f\n",*meanshear_angleptr);      // For the error in the mean 3D shear angle:
         printf("MEANSHR_err=%f\n",*meanshear_angle_err_ptr);      // If count_mask is 0, then we run into a divide by zero error. In this case, set *meanshear_angle_err_ptr to NAN
       // If count_mask is greater than zero, then compute the error.
       if (count_mask == 0)
           *meanshear_angle_err_ptr = NAN;
       else
           *meanshear_angle_err_ptr = (sqrt(err)/count_mask)*(180./PI);
   
       /* The area here is a fractional area -- the % of the total area. This has no error associated with it. */
       *area_w_shear_gt_45ptr   = (count_mask/(count))*(100.0);
  
       //printf("MEANSHR=%f\n",*meanshear_angleptr);
       //printf("ERRMSHA=%f\n",*meanshear_angle_err_ptr);
       //printf("SHRGT45=%f\n",*area_w_shear_gt_45ptr);
         return 0;         return 0;
 } }
  
   /*===========================================*/
   /* Example function 15: R parameter as defined in Schrijver, 2007 */
   //
   // Note that there is a restriction on the function fsample()
   // If the following occurs:
   //      nx_out > floor((ny_in-1)/scale + 1)
   //      ny_out > floor((ny_in-1)/scale + 1),
   // where n*_out are the dimensions of the output array and n*_in
   // are the dimensions of the input array, fsample() will usually result
   // in a segfault (though not always, depending on how the segfault was accessed.)
   
   int computeR(float *bz_err, float *los, int *dims, float *Rparam, float cdelt1,
                float *rim, float *p1p0, float *p1n0, float *p1p, float *p1n, float *p1,
                float *pmap, int nx1, int ny1,
                int scale, float *p1pad, int nxp, int nyp, float *pmapn)
   
   {
       int nx = dims[0];
       int ny = dims[1];
       int i = 0;
       int j = 0;
       int index, index1;
       double sum = 0.0;
       double err = 0.0;
       *Rparam = 0.0;
       struct fresize_struct fresboxcar, fresgauss;
       struct fint_struct fints;
       float sigma = 10.0/2.3548;
   
       // set up convolution kernels
       init_fresize_boxcar(&fresboxcar,1,1);
       init_fresize_gaussian(&fresgauss,sigma,20,1);
   
       // =============== [STEP 1] ===============
       // bin the line-of-sight magnetogram down by a factor of scale
       fsample(los, rim, nx, ny, nx, nx1, ny1, nx1, scale, 0, 0, 0.0);
   
       // =============== [STEP 2] ===============
       // identify positive and negative pixels greater than +/- 150 gauss
       // and label those pixels with a 1.0 in arrays p1p0 and p1n0
       for (i = 0; i < nx1; i++)
       {
           for (j = 0; j < ny1; j++)
           {
               index = j * nx1 + i;
               if (rim[index] > 150)
                   p1p0[index]=1.0;
               else
                   p1p0[index]=0.0;
               if (rim[index] < -150)
                   p1n0[index]=1.0;
               else
                   p1n0[index]=0.0;
           }
       }
   
       // =============== [STEP 3] ===============
       // smooth each of the negative and positive pixel bitmaps
       fresize(&fresboxcar, p1p0, p1p, nx1, ny1, nx1, nx1, ny1, nx1, 0, 0, 0.0);
       fresize(&fresboxcar, p1n0, p1n, nx1, ny1, nx1, nx1, ny1, nx1, 0, 0, 0.0);
   
       // =============== [STEP 4] ===============
       // find the pixels for which p1p and p1n are both equal to 1.
       // this defines the polarity inversion line
       for (i = 0; i < nx1; i++)
       {
           for (j = 0; j < ny1; j++)
           {
               index = j * nx1 + i;
               if ((p1p[index] > 0.0) && (p1n[index] > 0.0))
                   p1[index]=1.0;
               else
                   p1[index]=0.0;
           }
       }
   
       // pad p1 with zeroes so that the gaussian colvolution in step 5
       // does not cut off data within hwidth of the edge
   
       // step i: zero p1pad
       for (i = 0; i < nxp; i++)
       {
           for (j = 0; j < nyp; j++)
           {
               index = j * nxp + i;
               p1pad[index]=0.0;
           }
       }
   
       // step ii: place p1 at the center of p1pad
       for (i = 0; i < nx1; i++)
       {
          for (j = 0; j < ny1; j++)
          {
               index  = j * nx1 + i;
               index1 = (j+20) * nxp + (i+20);
               p1pad[index1]=p1[index];
           }
       }
   
       // =============== [STEP 5] ===============
       // convolve the polarity inversion line map with a gaussian
       // to identify the region near the plarity inversion line
       // the resultant array is called pmap
       fresize(&fresgauss, p1pad, pmap, nxp, nyp, nxp, nxp, nyp, nxp, 0, 0, 0.0);
   
   
      // select out the nx1 x ny1 non-padded array  within pmap
       for (i = 0; i < nx1; i++)
       {
          for (j = 0; j < ny1; j++)
          {
               index  = j * nx1 + i;
               index1 = (j+20) * nxp + (i+20);
               pmapn[index]=pmap[index1];
           }
       }
   
       // =============== [STEP 6] ===============
       // the R parameter is calculated
       for (i = 0; i < nx1; i++)
       {
           for (j = 0; j < ny1; j++)
           {
               index = j * nx1 + i;
               if isnan(pmapn[index]) continue;
               if isnan(rim[index]) continue;
               sum += pmapn[index]*abs(rim[index]);
           }
       }
   
       if (sum < 1.0)
           *Rparam = 0.0;
       else
           *Rparam = log10(sum);
   
       //printf("R_VALUE=%f\n",*Rparam);
   
       free_fresize(&fresboxcar);
       free_fresize(&fresgauss);
   
       return 0;
   
   }
   
   /*===========================================*/
   /* Example function 16: Lorentz force as defined in Fisher, 2012 */
   //
   // This calculation is adapted from Xudong's code
   // at /proj/cgem/lorentz/apps/lorentz.c
   
   int computeLorentz(float *bx,  float *by, float *bz, float *fx, float *fy, float *fz, int *dims,
                      float *totfx_ptr, float *totfy_ptr, float *totfz_ptr, float *totbsq_ptr,
                      float *epsx_ptr, float *epsy_ptr, float *epsz_ptr, int *mask, int *bitmask,
                      float cdelt1, double rsun_ref, double rsun_obs)
   
   {
   
       int nx = dims[0];
       int ny = dims[1];
       int nxny = nx*ny;
       int j = 0;
       int index;
       double totfx = 0, totfy = 0, totfz = 0;
       double bsq = 0, totbsq = 0;
       double epsx = 0, epsy = 0, epsz = 0;
       double area = cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;
       double k_h = -1.0 * area / (4. * PI) / 1.0e20;
       double k_z = area / (8. * PI) / 1.0e20;
   
       if (nx <= 0 || ny <= 0) return 1;
   
       for (int i = 0; i < nxny; i++)
       {
          if ( mask[i] < 70 || bitmask[i] < 30 ) continue;
          if isnan(bx[i]) continue;
          if isnan(by[i]) continue;
          if isnan(bz[i]) continue;
          fx[i]  = bx[i] * bz[i] * k_h;
          fy[i]  = by[i] * bz[i] * k_h;
          fz[i]  = (bx[i] * bx[i] + by[i] * by[i] - bz[i] * bz[i]) * k_z;
          bsq    = bx[i] * bx[i] + by[i] * by[i] + bz[i] * bz[i];
          totfx  += fx[i]; totfy += fy[i]; totfz += fz[i];
          totbsq += bsq;
       }
   
       *totfx_ptr  = totfx;
       *totfy_ptr  = totfy;
       *totfz_ptr  = totfz;
       *totbsq_ptr = totbsq;
       *epsx_ptr   = (totfx / k_h) / totbsq;
       *epsy_ptr   = (totfy / k_h) / totbsq;
       *epsz_ptr   = (totfz / k_z) / totbsq;
   
       //printf("TOTBSQ=%f\n",*totbsq_ptr);
   
       return 0;
   
   }
   
   /*===========================================*/
   
   /* Example function 17: Compute total unsigned flux in units of G/cm^2 on the LOS field */
   
   //  To compute the unsigned flux, we simply calculate
   //  flux = surface integral [(vector LOS) dot (normal vector)],
   //       = surface integral [(magnitude LOS)*(magnitude normal)*(cos theta)].
   //  However, since the field is radial, we will assume cos theta = 1.
   //  Therefore the pixels only need to be corrected for the projection.
   
   //  To convert G to G*cm^2, simply multiply by the number of square centimeters per pixel.
   //  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS).
   //  (Gauss/pix^2)(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.cm/m)^2
   //  =Gauss*cm^2
   
   int computeAbsFlux_los(float *los, int *dims, float *absFlux_los,
                          float *mean_vf_los_ptr, float *count_mask_los_ptr,
                          int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
   
   {
   
       int nx = dims[0];
       int ny = dims[1];
       int i = 0;
       int j = 0;
       int count_mask_los = 0;
       double sum = 0.0;
       *absFlux_los = 0.0;
       *mean_vf_los_ptr = 0.0;
   
   
       if (nx <= 0 || ny <= 0) return 1;
   
           for (i = 0; i < nx; i++)
           {
              for (j = 0; j < ny; j++)
              {
               if ( bitmask[j * nx + i] < 30 ) continue;
               if isnan(los[j * nx + i]) continue;
               sum += (fabs(los[j * nx + i]));
               count_mask_los++;
              }
           }
   
       *mean_vf_los_ptr     = sum*cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;
       *count_mask_los_ptr  = count_mask_los;
   
       //printf("USFLUXL=%f\n",*mean_vf_los_ptr);
       //printf("CMASKL=%f\n",*count_mask_los_ptr);
   
       return 0;
   }
   
   /*===========================================*/
   /* Example function 18:  Derivative of B_LOS (approximately B_vertical) = SQRT( ( dLOS/dx )^2 + ( dLOS/dy )^2 ) */
   
   int computeLOSderivative(float *los, int *dims, float *mean_derivative_los_ptr, int *bitmask, float *derx_los, float *dery_los)
   {
   
       int nx = dims[0];
       int ny = dims[1];
       int i = 0;
       int j = 0;
       int count_mask = 0;
       double sum = 0.0;
       *mean_derivative_los_ptr = 0.0;
   
       if (nx <= 0 || ny <= 0) return 1;
   
       /* brute force method of calculating the derivative (no consideration for edges) */
       for (i = 1; i <= nx-2; i++)
       {
           for (j = 0; j <= ny-1; j++)
           {
              derx_los[j * nx + i] = (los[j * nx + i+1] - los[j * nx + i-1])*0.5;
           }
       }
   
       /* brute force method of calculating the derivative (no consideration for edges) */
       for (i = 0; i <= nx-1; i++)
       {
           for (j = 1; j <= ny-2; j++)
           {
              dery_los[j * nx + i] = (los[(j+1) * nx + i] - los[(j-1) * nx + i])*0.5;
           }
       }
   
       /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
       ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
       i=0;
       for (j = 0; j <= ny-1; j++)
       {
           derx_los[j * nx + i] = ( (-3*los[j * nx + i]) + (4*los[j * nx + (i+1)]) - (los[j * nx + (i+2)]) )*0.5;
       }
   
       i=nx-1;
       for (j = 0; j <= ny-1; j++)
       {
           derx_los[j * nx + i] = ( (3*los[j * nx + i]) + (-4*los[j * nx + (i-1)]) - (-los[j * nx + (i-2)]) )*0.5;
       }
   
       j=0;
       for (i = 0; i <= nx-1; i++)
       {
           dery_los[j * nx + i] = ( (-3*los[j*nx + i]) + (4*los[(j+1) * nx + i]) - (los[(j+2) * nx + i]) )*0.5;
       }
   
       j=ny-1;
       for (i = 0; i <= nx-1; i++)
       {
           dery_los[j * nx + i] = ( (3*los[j * nx + i]) + (-4*los[(j-1) * nx + i]) - (-los[(j-2) * nx + i]) )*0.5;
       }
   
   
       for (i = 0; i <= nx-1; i++)
       {
           for (j = 0; j <= ny-1; j++)
           {
               if ( bitmask[j * nx + i] < 30 ) continue;
               if isnan(los[j * nx + i])      continue;
               if isnan(los[(j+1) * nx + i])  continue;
               if isnan(los[(j-1) * nx + i])  continue;
               if isnan(los[j * nx + i-1])    continue;
               if isnan(los[j * nx + i+1])    continue;
               if isnan(derx_los[j * nx + i]) continue;
               if isnan(dery_los[j * nx + i]) continue;
               sum += sqrt( derx_los[j * nx + i]*derx_los[j * nx + i]  + dery_los[j * nx + i]*dery_los[j * nx + i] ); /* Units of Gauss */
               count_mask++;
           }
       }
   
       *mean_derivative_los_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
   
       //printf("MEANGBL=%f\n",*mean_derivative_los_ptr);
   
           return 0;
   }
  
 /*==================KEIJI'S CODE =========================*/ /*==================KEIJI'S CODE =========================*/
  
Line 1099  void greenpot(float *bx, float *by, floa
Line 1503  void greenpot(float *bx, float *by, floa
  
 char *sw_functions_version() // Returns CVS version of sw_functions.c char *sw_functions_version() // Returns CVS version of sw_functions.c
 { {
   return strdup("$Id$");      return strdup("$Id");
 } }
  
 /* ---------------- end of this file ----------------*/ /* ---------------- end of this file ----------------*/


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