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version 1.5, 2013/01/14 18:27:45 version 1.11, 2013/05/30 23:26:02
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===========================================*/ ===========================================*/
#include <math.h> #include <math.h>
#include <mkl.h>

#define PI              (M_PI) #define PI              (M_PI)
#define MUNAUGHT (0.0000012566370614) /* magnetic constant */ #define MUNAUGHT (0.0000012566370614) /* magnetic constant */
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//  5: pixels for which the radial acute disambiguation solution was chosen //  5: pixels for which the radial acute disambiguation solution was chosen
//  7: pixels for which the radial acute and NRWA disambiguation agree //  7: pixels for which the radial acute and NRWA disambiguation agree

int computeAbsFlux(float *bz, int *dims, float *absFlux,  int computeAbsFlux(float *bz_err, float *bz, int *dims, float *absFlux,
float *mean_vf_ptr, int *mask,  int *bitmask,                     float *mean_vf_ptr, float *mean_vf_err_ptr, float *count_mask_ptr, int *mask,
float cdelt1, double rsun_ref, double rsun_obs)                     int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)

{ {

int nx = dims[0], ny = dims[1];     int nx = dims[0], ny = dims[1];
int i, j, count_mask=0;     int i, j, count_mask=0;
double sum=0.0;      double sum,err=0.0;

if (nx <= 0 || ny <= 0) return 1;     if (nx <= 0 || ny <= 0) return 1;

 Line 88  int computeAbsFlux(float *bz, int *dims,
 Line 89  int computeAbsFlux(float *bz, int *dims,
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]));
err += bz_err[j * nx + i]*bz_err[j * nx + i];
}                 }
}         }

printf("cdelt1=%f,rsun_ref=%f,rsun_obs=%f\n",cdelt1,rsun_ref,rsun_obs);
*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
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;
} }

/*===========================================*/ /*===========================================*/
/* Example function 2: Calculate Bh in units of Gauss */  /* Example function 2: Calculate Bh, the horizontal field, in units of Gauss */
// Native units of Bh are Gauss // Native units of Bh are Gauss

int computeBh(float *bx, float *by, float *bz, float *bh, int *dims,  int computeBh(float *bx_err, float *by_err, float *bh_err, float *bx, float *by, float *bz, float *bh, int *dims,

{ {
 Line 122  int computeBh(float *bx, float *by, floa
 Line 128  int computeBh(float *bx, float *by, floa
if isnan(by[j * nx + i]) continue;                 if isnan(by[j * nx + i]) 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];
}               }
}           }

*mean_hf_ptr = sum/(count_mask); // would be divided by nx*ny if shape of count_mask = shape of magnetogram     *mean_hf_ptr = sum/(count_mask); // would be divided by nx*ny if shape of count_mask = shape of magnetogram
printf("*mean_hf_ptr=%f\n",*mean_hf_ptr);
return 0;     return 0;
} }

/*===========================================*/ /*===========================================*/
/* 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).

int computeGamma(float *bz_err, float *bh_err, float *bx, float *by, float *bz, float *bh, int *dims,
int computeGamma(float *bx, float *by, float *bz, float *bh, int *dims,                   float *mean_gamma_ptr, float *mean_gamma_err_ptr, int *mask, int *bitmask)
{ {
int nx = dims[0], ny = dims[1];     int nx = dims[0], ny = dims[1];
int i, j, count_mask=0;     int i, j, count_mask=0;
 Line 145  int computeGamma(float *bx, float *by, f
 Line 152  int computeGamma(float *bx, float *by, f
if (nx <= 0 || ny <= 0) return 1;     if (nx <= 0 || ny <= 0) return 1;

*mean_gamma_ptr=0.0;     *mean_gamma_ptr=0.0;
float sum=0.0;      float sum,err,err_value=0.0;
int count=0;

for (i = 0; i < nx; i++)         for (i = 0; i < nx; i++)
{           {
 Line 156  int computeGamma(float *bx, float *by, f
 Line 163  int computeGamma(float *bx, float *by, f
{                   {
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 += (atan (fabs( bz[j * nx + i] / bh[j * nx + i] ))* (180./PI));                      if isnan(bz_err[j * nx + i]) continue;
if isnan(bh_err[j * nx + i]) continue;
if (bz[j * nx + i] == 0) continue;
sum += (atan(fabs(bz[j * nx + i]/bh[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);
}                   }
}               }
}           }

printf("*mean_gamma_ptr=%f\n",*mean_gamma_ptr);       *mean_gamma_err_ptr = (sqrt(err*err))/(count_mask*100.); // error in the quantity (sum)/(count_mask)
printf("MEANGAM=%f\n",*mean_gamma_ptr);
printf("MEANGAM_err=%f\n",*mean_gamma_err_ptr);
return 0;      return 0;
} }

 Line 171  int computeGamma(float *bx, float *by, f
 Line 184  int computeGamma(float *bx, float *by, f
/* Example function 4: Calculate B_Total*/ /* Example function 4: Calculate B_Total*/
// Native units of B_Total are in gauss // Native units of B_Total are in gauss

int computeB_total(float *bx, float *by, float *bz, float *bt, int *dims, int *mask, int *bitmask)  int computeB_total(float *bx_err, float *by_err, float *bz_err, float *bt_err, float *bx, float *by, float *bz, float *bt, int *dims, int *mask, int *bitmask)
{ {

int nx = dims[0], ny = dims[1];     int nx = dims[0], ny = dims[1];
 Line 187  int computeB_total(float *bx, float *by,
 Line 200  int computeB_total(float *bx, float *by,
if isnan(by[j * nx + i]) continue;                 if isnan(by[j * nx + i]) continue;
if isnan(bz[j * nx + i]) continue;                 if isnan(bz[j * nx + i]) 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];
}               }
}           }
return 0;      return 0;
 Line 195  int computeB_total(float *bx, float *by,
 Line 209  int computeB_total(float *bx, float *by,
/*===========================================*/ /*===========================================*/
/* 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)  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 nx = dims[0], ny = dims[1];     int nx = dims[0], ny = dims[1];
 Line 204  int computeBtotalderivative(float *bt, i
 Line 218  int computeBtotalderivative(float *bt, i
if (nx <= 0 || ny <= 0) return 1;     if (nx <= 0 || ny <= 0) return 1;

*mean_derivative_btotal_ptr = 0.0;     *mean_derivative_btotal_ptr = 0.0;
float sum = 0.0;      float sum, err = 0.0;

/* brute force method of calculating the derivative (no consideration for edges) */         /* brute force method of calculating the derivative (no consideration for edges) */
 Line 260  int computeBtotalderivative(float *bt, i
 Line 274  int computeBtotalderivative(float *bt, i
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];
}             }
}           }

*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); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
printf("*mean_derivative_btotal_ptr=%f\n",*mean_derivative_btotal_ptr);          *mean_derivative_btotal_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
printf("MEANGBT=%f\n",*mean_derivative_btotal_ptr);
printf("MEANGBT_err=%f\n",*mean_derivative_btotal_err_ptr);
return 0;         return 0;
} }

 Line 273  int computeBtotalderivative(float *bt, i
 Line 290  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, int *dims, float *mean_derivative_bh_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)
{ {

int nx = dims[0], ny = dims[1];         int nx = dims[0], ny = dims[1];
 Line 282  int computeBhderivative(float *bh, int *
 Line 299  int computeBhderivative(float *bh, int *
if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;

*mean_derivative_bh_ptr = 0.0;         *mean_derivative_bh_ptr = 0.0;
float sum = 0.0;          float sum,err = 0.0;

/* brute force method of calculating the derivative (no consideration for edges) */         /* brute force method of calculating the derivative (no consideration for edges) */
for (i = 1; i <= nx-2; i++)         for (i = 1; i <= nx-2; i++)
 Line 337  int computeBhderivative(float *bh, int *
 Line 354  int computeBhderivative(float *bh, int *
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];
}             }
}           }

*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)
printf("MEANGBH=%f\n",*mean_derivative_bh_ptr);
printf("MEANGBH_err=%f\n",*mean_derivative_bh_err_ptr);

return 0;         return 0;
} }

/*===========================================*/ /*===========================================*/
/* 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, int *dims, float *mean_derivative_bz_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)
{ {

int nx = dims[0], ny = dims[1];         int nx = dims[0], ny = dims[1];
 Line 357  int computeBzderivative(float *bz, int *
 Line 379  int computeBzderivative(float *bz, int *
if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;

*mean_derivative_bz_ptr = 0.0;         *mean_derivative_bz_ptr = 0.0;
float sum = 0.0;          float sum,err = 0.0;

/* brute force method of calculating the derivative (no consideration for edges) */         /* brute force method of calculating the derivative (no consideration for edges) */
for (i = 1; i <= nx-2; i++)         for (i = 1; i <= nx-2; i++)
 Line 417  int computeBzderivative(float *bz, int *
 Line 439  int computeBzderivative(float *bz, int *
// if ( (derx_bz[j * nx + i]-dery_bz[j * nx + i]) == 0) continue;                // 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 isnan(bz[j * nx + i]) continue;                if isnan(bz[j * nx + i]) 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];
}             }
}           }

*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)
printf("MEANGBZ=%f\n",*mean_derivative_bz_ptr);
printf("MEANGBZ_err=%f\n",*mean_derivative_bz_err_ptr);

return 0;         return 0;
} }

 Line 445  int computeBzderivative(float *bz, int *
 Line 473  int computeBzderivative(float *bz, int *
// //
//  To change units from Gauss/pixel to mA/m^2 (the units for Jz in Leka and Barnes, 2003), //  To change units from Gauss/pixel to mA/m^2 (the units for Jz in Leka and Barnes, 2003),
//  one must perform the following unit conversions: //  one must perform the following unit conversions:
//  (Gauss/pix)(pix/arcsec)(arcsec/meter)(Newton/Gauss*Ampere*meter)(Ampere^2/Newton)(milliAmpere/Ampere), or  //  (Gauss)(1/arcsec)(arcsec/meter)(Newton/Gauss*Ampere*meter)(Ampere^2/Newton)(milliAmpere/Ampere), or
//  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(1 T / 10^4 Gauss)(1 / 4*PI*10^-7)( 10^3 milliAmpere/Ampere),  //  (Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(1 T / 10^4 Gauss)(1 / 4*PI*10^-7)( 10^3 milliAmpere/Ampere), or
//  (Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(1000.),
//  where a Tesla is represented as a Newton/Ampere*meter. //  where a Tesla is represented as a Newton/Ampere*meter.
// //
//  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).
 Line 455  int computeBzderivative(float *bz, int *
 Line 484  int computeBzderivative(float *bz, int *
//  jz * (35.0) //  jz * (35.0)
// //
//  The units of total unsigned vertical current (us_i) are simply in A. In this case, we would have the following: //  The units of total unsigned vertical current (us_i) are simply in A. In this case, we would have the following:
//  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(1000.)  //  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(CDELT1)(CDELT1)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)
//  =(Gauss/pix)(1/CDELT1)(0.0010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(1000.)  //  = (Gauss/pix)(0.00010)(1/MUNAUGHT)(CDELT1)(RSUN_REF/RSUN_OBS)
//  =(Gauss/pix)(1/0.5)(10^-4)(4*PI*10^7)(722500)(1000.)
//  =(Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(1000.)

int computeJz(float *bx, float *by, int *dims, float *jz,
float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)

// Comment out random number generator, which can only run on solar3
//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, float *noisebx,
//              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 *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)

{

{
int nx = dims[0], ny = dims[1];         int nx = dims[0], ny = dims[1];
int i, j, count_mask=0;         int i, j, count_mask=0;

 Line 475  int computeJz(float *bx, float *by, int
 Line 505  int computeJz(float *bx, float *by, int
float curl=0.0, us_i=0.0,test_perimeter=0.0,mean_curl=0.0;         float curl=0.0, us_i=0.0,test_perimeter=0.0,mean_curl=0.0;

/* Calculate the derivative*/
/* brute force method of calculating the derivative (no consideration for edges) */         /* brute force method of calculating the derivative (no consideration for edges) */

for (i = 1; i <= nx-2; i++)         for (i = 1; i <= nx-2; i++)
{           {
for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
{               {
if isnan(by[j * nx + i]) continue;                   //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;
}               }
}           }

/* brute force method of calculating the derivative (no consideration for edges) */
for (i = 0; i <= nx-1; i++)         for (i = 0; i <= nx-1; i++)
{           {
for (j = 1; j <= ny-2; j++)             for (j = 1; j <= ny-2; j++)
{               {
if isnan(bx[j * nx + i]) continue;                   //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;
}               }
}           }

// consider the edges
/* consider the edges */
i=0;         i=0;
for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
{           {
 Line 530  int computeJz(float *bx, float *by, int
 Line 561  int computeJz(float *bx, float *by, int
{           {
for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
{             {
/* 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

//printf("jz[j * nx + i]=%f,i=%d,j=%d\n,",jz[j * nx + i],i,j); // tmp.txt
//printf("i=%d,j=%d,jz[j * nx + i]=%f\n,",i,j,jz[j * nx + i]); // tmp1.txt

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]) +
(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]);
}             }
}           }
 Line 541  int computeJz(float *bx, float *by, int
 Line 580  int computeJz(float *bx, float *by, int

/*===========================================*/ /*===========================================*/

/* Example function 9:  Compute quantities on smoothed Jz array */

int computeJzsmooth(float *bx, float *by, int *dims, float *jz_smooth,  /* Example function 9:  Compute quantities on Jz array */
float *mean_jz_ptr, float *us_i_ptr, int *mask, int *bitmask,  // Compute mean and total current on Jz array.

int computeJzsmooth(float *bx, float *by, int *dims, float *jz, float *jz_smooth, float *jz_err, float *jz_rms_err, float *jz_err_squared_smooth,
float *mean_jz_ptr, float *mean_jz_err_ptr, float *us_i_ptr, float *us_i_err_ptr, int *mask, int *bitmask,
float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)                           float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)

{ {
 Line 554  int computeJzsmooth(float *bx, float *by
 Line 595  int computeJzsmooth(float *bx, float *by

if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;

*mean_jz_ptr = 0.0;          float curl,us_i,test_perimeter,mean_curl,err=0.0;
float curl=0.0, us_i=0.0,test_perimeter=0.0,mean_curl=0.0;

/* At this point, use the smoothed Jz array with a Gaussian (FWHM of 4 pix and truncation width of 12 pixels) but keep the original array dimensions*/         /* At this point, use the smoothed Jz array with a Gaussian (FWHM of 4 pix and truncation width of 12 pixels) but keep the original array dimensions*/
 Line 566  int computeJzsmooth(float *bx, float *by
 Line 606  int computeJzsmooth(float *bx, float *by
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(derx[j * nx + i]) continue;                if isnan(derx[j * nx + i]) continue;
if isnan(dery[j * nx + i]) continue;                if isnan(dery[j * nx + i]) continue;
if isnan(jz_smooth[j * nx + i]) continue;                 if isnan(jz[j * nx + i]) continue;
//printf("%d,%d,%f\n",i,j,jz_smooth[j * nx + i]);                 curl +=     (jz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.); /* curl is in units of mA / m^2 */
curl +=     (jz_smooth[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.); /* curl is in units of mA / m^2 */                 us_i += fabs(jz[j * nx + i])*(cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT);         /* us_i is in units of A */
us_i += fabs(jz_smooth[j * nx + i])*(1/cdelt1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT);         /* us_i is in units of A  / m^2 */                 err  += (jz_err[j * nx + i]*jz_err[j * nx + i]);
}             }
}           }

/* 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_curl) and total unsigned vertical current (us_i) using smoothed Jz array and continue conditions above */
printf("mean_curl=%f\n",mean_curl);
printf("cdelt1, what is it?=%f\n",cdelt1);
*mean_jz_ptr     = curl/(count_mask);        /* mean_jz gets populated as MEANJZD */         *mean_jz_ptr     = curl/(count_mask);        /* mean_jz gets populated as MEANJZD */
printf("count_mask=%d\n",count_mask);          *mean_jz_err_ptr = (sqrt(err))*fabs(((rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.))/(count_mask)); // 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

printf("MEANJZD=%f\n",*mean_jz_ptr);
printf("MEANJZD_err=%f\n",*mean_jz_err_ptr);

printf("TOTUSJZ=%g\n",*us_i_ptr);
printf("TOTUSJZ_err=%g\n",*us_i_err_ptr);

return 0;         return 0;

} }
 Line 596  int computeJzsmooth(float *bx, float *by
 Line 642  int computeJzsmooth(float *bx, float *by
// (abs(sum of all Jz at positive Bz) + abs(sum of all Jz at negative Bz)) = avg Jz        // (abs(sum of all Jz at positive Bz) + abs(sum of all Jz at negative Bz)) = avg Jz
// avg alpha = avg Jz / avg Bz        // avg alpha = avg Jz / avg Bz

// 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 603  int computeJzsmooth(float *bx, float *by
 Line 658  int computeJzsmooth(float *bx, float *by
//                               = (Gauss/pix)(1/Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(10^6) //                               = (Gauss/pix)(1/Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(10^6)
//                               = 1/Mm //                               = 1/Mm

int computeAlpha(float *bz, int *dims, float *jz_smooth, float *mean_alpha_ptr, int *mask, int *bitmask,  int computeAlpha(float *jz_err, float *bz_err, float *bz, int *dims, float *jz, float *jz_smooth, float *mean_alpha_ptr, float *mean_alpha_err_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
float cdelt1, double rsun_ref, double rsun_obs)

{ {
int nx = dims[0], ny = dims[1];         int nx = dims[0], ny = dims[1];
int i, j=0;          int i, j, count_mask, a,b,c,d=0;

if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;

*mean_alpha_ptr = 0.0;          float aa, bb, cc, bznew, alpha2, sum1, sum2, sum3, sum4, sum, sum5, sum6, sum_err=0.0;
float aa, bb, cc, bznew, alpha2, sum1, sum2, sum3, sum4, sum, sum5, sum6=0.0;

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++)
{               {
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_smooth[j * nx + i]) continue;                  //if isnan(jz_smooth[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_smooth[j * nx + i] == 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]);                  if (bz[j * nx + i] >  0) sum1 += ( bz[j * nx + i] ); a++;
if (bz[j * nx + i] <= 0) sum2 += ( bz[j * nx + i]);                  if (bz[j * nx + i] <= 0) sum2 += ( bz[j * nx + i] ); b++;
if (bz[j * nx + i] >  0) sum3 += ( jz_smooth[j * nx + i]);                  //if (bz[j * nx + i] >  0) sum3 += ( jz_smooth[j * nx + i]);
if (bz[j * nx + i] <= 0) sum4 += ( jz_smooth[j * nx + i]);                  //if (bz[j * nx + i] <= 0) sum4 += ( jz_smooth[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];                 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.));
}               }
}           }

 Line 640  int computeAlpha(float *bz, int *dims, f
 Line 702  int computeAlpha(float *bz, int *dims, f
if ((sum5 < 0) && (sum4 >  0)) sum=-sum;         if ((sum5 < 0) && (sum4 >  0)) sum=-sum;

*mean_alpha_ptr = sum; /* Units are 1/Mm */         *mean_alpha_ptr = sum; /* Units are 1/Mm */
*mean_alpha_err_ptr    = (sqrt(sum_err*sum_err)) / ((a+b+c+d)*100.); // error in the quantity (sum)/(count_mask); factor of 100 comes from converting percent

printf("a=%d\n",a);
printf("b=%d\n",b);
printf("d=%d\n",d);
printf("c=%d\n",c);

printf("MEANALP=%f\n",*mean_alpha_ptr);
printf("MEANALP_err=%f\n",*mean_alpha_err_ptr);

return 0;         return 0;
} }

/*===========================================*/ /*===========================================*/
/* Example function 11:  Helicity (mean current helicty, mean unsigned current helicity, and mean absolute current helicity) */  /* Example function 11:  Helicity (mean current helicty, total unsigned current helicity, absolute value of net current helicity) */

//  The current helicity is defined as Bz*Jz and the units are G^2 / m //  The current helicity is defined as Bz*Jz and the units are G^2 / m
//  The units of Jz are in G/pix; the units of Bz are in G. //  The units of Jz are in G/pix; the units of Bz are in G.
//  Therefore, the units of Bz*Jz = (Gauss)*(Gauss/pix) = (Gauss^2/pix)(pix/arcsec)(arcsec/m)  //  Therefore, the units of Bz*Jz = (Gauss)*(Gauss/pix) = (Gauss^2/pix)(pix/arcsec)(arcsec/meter)
//                                                      = (Gauss^2/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF) //                                                      = (Gauss^2/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)
//                                                      = G^2 / m. //                                                      = G^2 / m.

int computeHelicity(float *jz_err, float *jz_rms_err, float *bz_err, float *bz, int *dims, float *jz, float *mean_ih_ptr,
int computeHelicity(float *bz, int *dims, float *jz_smooth, float *mean_ih_ptr, float *total_us_ih_ptr,                      float *mean_ih_err_ptr, float *total_us_ih_ptr, float *total_abs_ih_ptr,
float *total_abs_ih_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)                      float *total_us_ih_err_ptr, float *total_abs_ih_err_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)

{ {

 Line 663  int computeHelicity(float *bz, int *dims
 Line 735  int computeHelicity(float *bz, int *dims

if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;

*mean_ih_ptr = 0.0;          float sum,sum2,sum_err=0.0;
float sum=0.0, sum2=0.0;

for (i = 0; i < nx; i++)         for (i = 0; i < nx; i++)
{         {
for (j = 0; j < ny; j++)                 for (j = 0; j < ny; 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 isnan(jz_smooth[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 (bz[j * nx + i] == 0.0) continue;                 if (bz[j * nx + i] == 0.0) continue;
if (jz_smooth[j * nx + i] == 0.0) continue;                    if (jz[j * nx + i] == 0.0) continue;
sum  +=     (jz_smooth[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref);                    sum     +=     (jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to MEANJZH and ABSNJZH
sum2 += fabs(jz_smooth[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref);                    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));
}                 }
}          }

printf("(1/cdelt1)*(rsun_obs/rsun_ref)=%f\n",(1/cdelt1)*(rsun_obs/rsun_ref));
*mean_ih_ptr     = sum/count_mask; /* Units are G^2 / m ; keyword is MEANJZH */             *mean_ih_ptr     = sum/count_mask; /* Units are G^2 / m ; keyword is MEANJZH */
*total_us_ih_ptr = sum2;           /* Units are G^2 / m */          *total_us_ih_ptr      = sum2           ; /* Units are G^2 / m ; keyword is TOTUSJH */
*total_abs_ih_ptr= fabs(sum);      /* Units are G^2 / m */          *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.)    ;  // error in the quantity MEANJZH
*total_us_ih_err_ptr  = (sqrt(sum_err*sum_err)) / (100.)               ;  // error in the quantity TOTUSJH
*total_abs_ih_err_ptr = (sqrt(sum_err*sum_err)) / (100.)               ;  // error in the quantity ABSNJZH

printf("MEANJZH=%f\n",*mean_ih_ptr);
printf("MEANJZH_err=%f\n",*mean_ih_err_ptr);

printf("TOTUSJH=%f\n",*total_us_ih_ptr);
printf("TOTUSJH_err=%f\n",*total_us_ih_err_ptr);

printf("ABSNJZH=%f\n",*total_abs_ih_ptr);
printf("ABSNJZH_err=%f\n",*total_abs_ih_err_ptr);

return 0;         return 0;
} }
 Line 698  int computeHelicity(float *bz, int *dims
 Line 781  int computeHelicity(float *bz, int *dims
//  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)
//
//  The error in this quantity is the same as the error in the mean vertical current (mean_jz_err).

int computeSumAbsPerPolarity(float *bz, float *jz_smooth, int *dims, float *totaljzptr,  int computeSumAbsPerPolarity(float *jz_err, float *bz_err, float *bz, float *jz, int *dims, float *totaljzptr, float *totaljz_err_ptr,
int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)                                                          int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)

{ {
 Line 709  int computeSumAbsPerPolarity(float *bz,
 Line 794  int computeSumAbsPerPolarity(float *bz,
if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;

*totaljzptr=0.0;         *totaljzptr=0.0;
float sum1=0.0, sum2=0.0;          float sum1,sum2,err=0.0;

for (i = 0; i < nx; i++)         for (i = 0; i < nx; i++)
{           {
 Line 717  int computeSumAbsPerPolarity(float *bz,
 Line 802  int computeSumAbsPerPolarity(float *bz,
{               {
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 (bz[j * nx + i] >  0) sum1 += ( jz_smooth[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_smooth[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]);
}               }
}           }

*totaljzptr = fabs(sum1) + fabs(sum2);  /* Units are A */         *totaljzptr = fabs(sum1) + fabs(sum2);  /* Units are A */
*totaljz_err_ptr = sqrt(err)*(1/cdelt1)*fabs((0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs));
printf("SAVNCPP=%g\n",*totaljzptr);
printf("SAVNCPP_err=%g\n",*totaljz_err_ptr);

return 0;         return 0;
} }

/*===========================================*/ /*===========================================*/
/* Example function 13:  Mean photospheric excess magnetic energy and total photospheric excess magnetic energy density */ /* Example function 13:  Mean photospheric excess magnetic energy and total photospheric excess magnetic energy density */
// The units for magnetic energy density in cgs are ergs per cubic centimeter. The formula B^2/8*PI integrated over all space, dV // The units for magnetic energy density in cgs are ergs per cubic centimeter. The formula B^2/8*PI integrated over all space, dV
// automatically yields erg per cubic centimeter for an input B in Gauss.  // automatically yields erg per cubic centimeter for an input B in Gauss. Note that the 8*PI can come out of the integral; thus,
// the integral is over B^2 dV and the 8*PI is divided at the end.
// //
// Total magnetic energy is the magnetic energy density times dA, or the area, and the units are thus ergs/cm. To convert // Total magnetic energy is the magnetic energy density times dA, or the area, and the units are thus ergs/cm. To convert
// ergs per centimeter cubed to ergs per centimeter, simply multiply by the area per pixel in cm: // ergs per centimeter cubed to ergs per centimeter, simply multiply by the area per pixel in cm:
// erg/cm^3(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.)^2  //   erg/cm^3*(CDELT1^2)*(RSUN_REF/RSUN_OBS ^2)*(100.^2)
// = erg/cm^3(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2  // = erg/cm^3*(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2
// = erg/cm^3(1.30501e15)  // = erg/cm^3*(1.30501e15)
// = erg/cm(1/pix^2) // = erg/cm(1/pix^2)

int computeFreeEnergy(float *bx, float *by, float *bpx, float *bpy, int *dims,  int computeFreeEnergy(float *bx_err, float *by_err, float *bx, float *by, float *bpx, float *bpy, int *dims,
float *meanpotptr, float *totpotptr, int *mask, int *bitmask,                        float *meanpotptr, float *meanpot_err_ptr, float *totpotptr, float *totpot_err_ptr, int *mask, int *bitmask,
float cdelt1, double rsun_ref, double rsun_obs)                                           float cdelt1, double rsun_ref, double rsun_obs)

{ {
 Line 750  int computeFreeEnergy(float *bx, float *
 Line 842  int computeFreeEnergy(float *bx, float *

*totpotptr=0.0;         *totpotptr=0.0;
*meanpotptr=0.0;         *meanpotptr=0.0;
float sum=0.0;          float sum,err=0.0;

for (i = 0; i < nx; i++)         for (i = 0; i < nx; i++)
{           {
 Line 759  int computeFreeEnergy(float *bx, float *
 Line 851  int computeFreeEnergy(float *bx, 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(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 += ((    ((bx[j * nx + i])*(bx[j * nx + i]) + (by[j * nx + i])*(by[j * nx + i]) ) -  ((bpx[j * nx + i])*(bpx[j * nx + i]) + (bpy[j * nx + i])*(bpy[j * nx + i]))  )/8.*PI);                   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);
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]);
}               }
}           }

*meanpotptr = (sum)/(count_mask);              /* Units are ergs per cubic centimeter */          *meanpotptr      = (sum/(8.*PI)) / (count_mask);     /* Units are ergs per cubic centimeter */
*totpotptr  = sum*(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0)*(count_mask);   /* Units of sum are ergs/cm^3, units of factor are cm^2/pix^2, units of count_mask are pix^2; therefore, units of totpotptr are ergs per 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 */
*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)));

printf("MEANPOT=%g\n",*meanpotptr);
printf("MEANPOT_err=%g\n",*meanpot_err_ptr);

printf("TOTPOT=%g\n",*totpotptr);
printf("TOTPOT_err=%g\n",*totpot_err_ptr);

return 0;         return 0;
} }

/*===========================================*/ /*===========================================*/
/* 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, float *by, float *bz, float *bpx, float *bpy, float *bpz, int *dims,  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,
float *meanshear_angleptr, float *area_w_shear_gt_45ptr,                        float *meanshear_angleptr, float *meanshear_angle_err_ptr, float *area_w_shear_gt_45ptr, int *mask, int *bitmask)
float *meanshear_anglehptr, float *area_w_shear_gt_45hptr,
{ {
int nx = dims[0], ny = dims[1];         int nx = dims[0], ny = dims[1];
int i, j;         int i, j;

if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;

*area_w_shear_gt_45ptr=0.0;          //*area_w_shear_gt_45ptr=0.0;
*meanshear_angleptr=0.0;          //*meanshear_angleptr=0.0;
float dotproduct, magnitude_potential, magnitude_vector, shear_angle=0.0, sum = 0.0, count=0.0, count_mask=0.0;          float dotproduct, magnitude_potential, magnitude_vector, shear_angle,err=0.0, sum = 0.0, count=0.0, count_mask=0.0;
float dotproducth, magnitude_potentialh, magnitude_vectorh, shear_angleh=0.0, sum1 = 0.0, counth = 0.0;

for (i = 0; i < nx; i++)         for (i = 0; i < nx; i++)
{           {
 Line 805  int computeShearAngle(float *bx, float *
 Line 906  int computeShearAngle(float *bx, float *
shear_angle           = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);                  shear_angle           = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);
count ++;                  count ++;
sum += shear_angle ;                  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 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 = (sum)/(count);              /* Units are degrees */
printf("count_mask=%f\n",count_mask);          *meanshear_angle_err_ptr = (sqrt(err*err))/(count);  // error in the quantity (sum)/(count_mask)
printf("count=%f\n",count);
*area_w_shear_gt_45ptr = (count_mask/(count))*(100.);  /* The area here is a fractional area -- the % of the total area */         *area_w_shear_gt_45ptr = (count_mask/(count))*(100.);  /* The area here is a fractional area -- the % of the total area */

printf("MEANSHR=%f\n",*meanshear_angleptr);
printf("MEANSHR_err=%f\n",*meanshear_angle_err_ptr);

return 0;         return 0;
} }

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 Removed from v.1.5 changed lines Added in v.1.11