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Diff for /JSOC/proj/sharp/apps/sw_functions.c between version 1.4 and 1.27

version 1.4, 2012/12/18 23:05:10

version 1.27, 2014/03/05 19:51:19

Line 1

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

The following 13 functions calculate the following spaceweather indices:

The following 14 functions calculate the following spaceweather indices:

USFLUX Total unsigned flux in Maxwells

MEANGAM Mean inclination angle, gamma, in degrees

Line 20

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

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

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:

50 : not all solutions agree (weak field method applied)

Line 39

Line 41

Written by Monica Bobra 15 August 2012

Potential Field code (appended) written by Keiji Hayashi

Error analysis modification 21 October 2013

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

#include <math.h>

#include <mkl.h>

#define PI (M_PI)

#define MUNAUGHT (0.0000012566370614) /* magnetic constant */

Line 59

Line 63

// 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/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,

int computeAbsFlux(float *bz_err, float *bz, int *dims, float *absFlux,

// 5: pixels for which the radial acute disambiguation solution was chosen

float *mean_vf_ptr, float *mean_vf_err_ptr, float *count_mask_ptr, int *mask,

// 7: pixels for which the radial acute and NRWA disambiguation agree

int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)

int computeAbsFlux(float *bz, int *dims, float *absFlux,

float *mean_vf_ptr, int *mask, int *bitmask,

float cdelt1, double rsun_ref, double rsun_obs)

{

int nx = dims[0], ny = dims[1];

int nx = dims[0];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

int j = 0;

int count_mask = 0;

double sum=0.0;

double err = 0.0;

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

*absFlux = 0.0;

*mean_vf_ptr =0.0;

for (j = 0; j < ny; j++)

{

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

for (i = 0; i < nx; i++)

{

for (j = 0; j < ny; j++)

{

if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;

if isnan(bz[j * nx + i]) continue;

//printf("bz[j * nx + i]=%f\n",bz[j * nx + i]);

sum += (fabs(bz[j * nx + i]));

err += bz_err[j * nx + i]*bz_err[j * nx + i];

count_mask++;

}

printf("nx=%d,ny=%d,count_mask=%d,sum=%f\n",nx,ny,count_mask,sum);

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_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;

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

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,

float *mean_hf_ptr, int *mask, int *bitmask)

{

int nx = dims[0], ny = dims[1];

int nx = dims[0];

int i, j, count_mask=0;

int ny = dims[1];

float sum=0.0;

int i = 0;

int j = 0;

int count_mask = 0;

double sum = 0.0;

*mean_hf_ptr =0.0;

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

for (i = 0; i < nx; i++)

{

for (j = 0; j < ny; j++)

{

for (i = 0; i < nx; i++)

if isnan(bx[j * nx + i])

{

if isnan(bx[j * nx + i]) continue;

bh[j * nx + i] = NAN;

if isnan(by[j * nx + i]) continue;

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] );

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];

count_mask++;

}

*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;

}

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

/* 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)

// 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 *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, int *mask, int *bitmask)

{

int nx = dims[0], ny = dims[1];

int nx = dims[0];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

int j = 0;

int count_mask = 0;

double sum = 0.0;

double err = 0.0;

*mean_gamma_ptr = 0.0;

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

*mean_gamma_ptr=0.0;

float sum=0.0;

int count=0;

for (i = 0; i < nx; i++)

{

for (j = 0; j < ny; j++)

Line 157 int computeGamma(float *bx, float *by, f

Line 178 int computeGamma(float *bx, float *by, f

{

if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) 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 isnan(bh[j * nx + i]) continue;

if (bz[j * nx + i] == 0) continue;

sum += fabs(atan(bh[j * nx + i]/fabs(bz[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++;

}

*mean_gamma_ptr = sum/count_mask;

printf("*mean_gamma_ptr=%f\n",*mean_gamma_ptr);

*mean_gamma_err_ptr = (sqrt(err)/(count_mask))*(180./PI);

//printf("MEANGAM=%f\n",*mean_gamma_ptr);

//printf("MEANGAM_err=%f\n",*mean_gamma_err_ptr);

return 0;

}

Line 172 int computeGamma(float *bx, float *by, f

Line 202 int computeGamma(float *bx, float *by, f

/* Example function 4: Calculate B_Total*/

// 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];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

int j = 0;

int count_mask = 0;

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

Line 184 int computeB_total(float *bx, float *by,

Line 217 int computeB_total(float *bx, float *by,

{

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_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;

Line 196 int computeB_total(float *bx, float *by,

Line 245 int computeB_total(float *bx, float *by,

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

/* 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];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

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

int j = 0;

int count_mask = 0;

double sum = 0.0;

double err = 0.0;

*mean_derivative_btotal_ptr = 0.0;

float sum = 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++)

Line 253 int computeBtotalderivative(float *bt, i

Line 304 int computeBtotalderivative(float *bt, i

}

/* Just some print statements

for (i = 1; i <= nx-2; i++)

for (i = 0; i < nx; i++)

{

for (j = 0; j < ny; j++)

{

printf("j=%d\n",j);

printf("i=%d\n",i);

printf("dery_bt[j*nx+i]=%f\n",dery_bt[j*nx+i]);

printf("derx_bt[j*nx+i]=%f\n",derx_bt[j*nx+i]);

printf("bt[j*nx+i]=%f\n",bt[j*nx+i]);

}

for (i = 0; i <= nx-1; i++)

{

for (j = 0; j <= ny-1; j++)

for (j = 1; j <= ny-2; j++)

{

// if ( (derx_bt[j * nx + i]-dery_bt[j * nx + i]) == 0) 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(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 */

err += (((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])) / (16.0*( derx_bt[j * nx + i]*derx_bt[j * nx + i] + dery_bt[j * nx + i]*dery_bt[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)])) / (16.0*( derx_bt[j * nx + i]*derx_bt[j * nx + i] + dery_bt[j * nx + i]*dery_bt[j * nx + i] )) ;

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);

printf("*mean_derivative_btotal_ptr=%f\n",*mean_derivative_btotal_ptr);

*mean_derivative_btotal_err_ptr = (sqrt(err))/(count_mask);

//printf("MEANGBT=%f\n",*mean_derivative_btotal_ptr);

//printf("MEANGBT_err=%f\n",*mean_derivative_btotal_err_ptr);

return 0;

}

Line 287 int computeBtotalderivative(float *bt, i

Line 337 int computeBtotalderivative(float *bt, i

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

/* 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];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

int j = 0;

int count_mask = 0;

double sum= 0.0;

double err =0.0;

*mean_derivative_bh_ptr = 0.0;

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

*mean_derivative_bh_ptr = 0.0;

float sum = 0.0;

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

for (i = 1; i <= nx-2; i++)

{

Line 343 int computeBhderivative(float *bh, int *

Line 396 int computeBhderivative(float *bh, int *

}

/*Just some print statements

for (i = 0; i < nx; i++)

{

for (j = 0; j < ny; j++)

{

printf("j=%d\n",j);

printf("i=%d\n",i);

printf("dery_bh[j*nx+i]=%f\n",dery_bh[j*nx+i]);

printf("derx_bh[j*nx+i]=%f\n",derx_bh[j*nx+i]);

printf("bh[j*nx+i]=%f\n",bh[j*nx+i]);

}

for (i = 0; i <= nx-1; i++)

{

for (j = 0; j <= ny-1; j++)

{

// if ( (derx_bh[j * nx + i]-dery_bh[j * nx + i]) == 0) 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(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 */

err += (((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])) / (16.0*( derx_bh[j * nx + i]*derx_bh[j * nx + i] + dery_bh[j * nx + i]*dery_bh[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)])) / (16.0*( derx_bh[j * nx + i]*derx_bh[j * nx + i] + dery_bh[j * nx + i]*dery_bh[j * nx + i] )) ;

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_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;

}

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

/* 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];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

int j = 0;

int count_mask = 0;

double sum = 0.0;

double err = 0.0;

*mean_derivative_bz_ptr = 0.0;

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

*mean_derivative_bz_ptr = 0.0;

float sum = 0.0;

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

for (i = 1; i <= nx-2; i++)

{

Line 437 int computeBzderivative(float *bz, int *

Line 493 int computeBzderivative(float *bz, int *

}

/*Just some print statements

for (i = 0; i < nx; i++)

{

for (j = 0; j < ny; j++)

{

printf("j=%d\n",j);

printf("i=%d\n",i);

printf("dery_bz[j*nx+i]=%f\n",dery_bz[j*nx+i]);

printf("derx_bz[j*nx+i]=%f\n",derx_bz[j*nx+i]);

printf("bz[j*nx+i]=%f\n",bz[j*nx+i]);

}

for (i = 0; i <= nx-1; i++)

{

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 ( (derx_bz[j * nx + i] + dery_bz[j * nx + i]) == 0) continue;

if isnan(bz[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(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 */

err += (((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])) /

(16.0*( derx_bz[j * nx + i]*derx_bz[j * nx + i] + dery_bz[j * nx + i]*dery_bz[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)])) /

(16.0*( derx_bz[j * nx + i]*derx_bz[j * nx + i] + dery_bz[j * nx + i]*dery_bz[j * nx + i] )) ;

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_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;

}

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

/* Example function 8: Current Jz = (dBy/dx) - (dBx/dy) */

// In discretized space like data pixels,

Line 487 int computeBzderivative(float *bz, int *

Line 541 int computeBzderivative(float *bz, int *

// 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:

// (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.

// As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS).

Line 497 int computeBzderivative(float *bz, int *

Line 552 int computeBzderivative(float *bz, int *

// jz * (35.0)

// 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 *mean_jz_ptr, float *us_i_ptr, int *mask, int *bitmask,

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 i, j, count_mask=0;

int nx = dims[0];

int ny = dims[1];

int i = 0;

int j = 0;

int count_mask = 0;

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

*mean_jz_ptr = 0.0;

/* Calculate the derivative*/

float curl=0.0, us_i=0.0,test_perimeter=0.0,mean_curl=0.0;

/* 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++)

Line 529 int computeJz(float *bx, float *by, int

Line 586 int computeJz(float *bx, float *by, int

}

/* 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++)

Line 539 int computeJz(float *bx, float *by, int

Line 595 int computeJz(float *bx, float *by, int

}

// consider the edges

/* consider the edges */

i=0;

for (j = 0; j <= ny-1; j++)

{

Line 569 int computeJz(float *bx, float *by, int

Line 624 int computeJz(float *bx, float *by, int

dery[j * nx + i] = ( (3*bx[j * nx + i]) + (-4*bx[(j-1) * nx + i]) - (-bx[(j-2) * nx + i]) )*0.5;

}

for (i = 1; i <= nx-2; i++)

{

for (j = 1; j <= ny-2; j++)

{

// 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_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]);

count_mask++;

}

return 0;

}

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

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

// 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)

{

int nx = dims[0];

int ny = dims[1];

int i = 0;

int j = 0;

int count_mask = 0;

double curl = 0.0;

double us_i = 0.0;

double err = 0.0;

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

/* 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*/

for (i = 0; i <= nx-1; i++)

{

for (j = 0; j <= ny-1; j++)

Line 577 int computeJz(float *bx, float *by, int

Line 671 int computeJz(float *bx, float *by, int

if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;

if isnan(derx[j * nx + i]) continue;

if isnan(dery[j * nx + i]) continue;

curl += (derx[j * nx + i]-dery[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.); /* curl is in units of mA / m^2 */

if isnan(jz[j * nx + i]) continue;

us_i += fabs(derx[j * nx + i]-dery[j * nx + i])*(1/cdelt1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT); /* us_i is in units of A / m^2 */

curl += (jz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.); /* curl is in units of mA / m^2 */

jz[j * nx + i] = (derx[j * nx + i]-dery[j * nx + i]); /* jz is in units of Gauss/pix */

us_i += fabs(jz[j * nx + i])*(cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT); /* us_i is in units of A */

err += (jz_err[j * nx + i]*jz_err[j * nx + i]);

count_mask++;

}

mean_curl = (curl/count_mask);

/* Calculate mean vertical current density (mean_jz) 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 */

printf("count_mask=%d\n",count_mask);

*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_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_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;

}

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

/* Example function 9: Twist Parameter, alpha */

// The twist parameter, alpha, is defined as alpha = Jz/Bz and the units are in 1/Mm

/* Example function 10: Twist Parameter, alpha */

// The twist parameter, alpha, is defined as alpha = Jz/Bz. In this case, the calculation

// for alpha is weighted by Bz (following Hagino et al., http://adsabs.harvard.edu/abs/2004PASJ...56..831H):

// numerator = sum of all Jz*Bz

// denominator = sum of Bz*Bz

// alpha = numerator/denominator

// The units of alpha are in 1/Mm

// The units of Jz are in Gauss/pix; the units of Bz are in Gauss.

// Therefore, the units of Jz/Bz = (Gauss/pix)(1/Gauss)(pix/arcsec)(arsec/meter)(meter/Mm), or

// = (Gauss/pix)(1/Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(10^6)

// = 1/Mm

int computeAlpha(float *bz, int *dims, float *jz, 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];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

int j = 0;

double alpha_total = 0.0;

double C = ((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.));

double total = 0.0;

double A = 0.0;

double B = 0.0;

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

for (i = 1; i < nx-1; i++)

*mean_alpha_ptr = 0.0;

{

float aa, bb, cc, bznew, alpha2, sum=0.0;

for (j = 1; j < ny-1; j++)

{

if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;

if isnan(jz[j * nx + i]) continue;

if isnan(bz[j * nx + i]) continue;

if (jz[j * nx + i] == 0.0) continue;

if (bz[j * nx + i] == 0.0) continue;

A += jz[j*nx+i]*bz[j*nx+i];

B += bz[j*nx+i]*bz[j*nx+i];

}

for (i = 1; i < nx-1; i++)

{

Line 623 int computeAlpha(float *bz, int *dims, f

Line 749 int computeAlpha(float *bz, int *dims, f

if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;

if isnan(jz[j * nx + i]) continue;

if isnan(bz[j * nx + i]) continue;

if (jz[j * nx + i] == 0.0) continue;

if (bz[j * nx + i] == 0.0) continue;

sum += (jz[j * nx + i] / bz[j * nx + i])*((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.)) ; /* the units for (jz/bz) are 1/Mm */

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];

count_mask++;

}

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

/* Determine the absolute value of alpha. The units for alpha are 1/Mm */

printf("count_mask=%d\n",count_mask);

alpha_total = ((A/B)*C);

printf("sum=%f\n",sum);

*mean_alpha_ptr = alpha_total;

*mean_alpha_ptr = sum/count_mask; /* Units are 1/Mm */

*mean_alpha_err_ptr = (C/B)*(sqrt(total));

return 0;

}

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

/* Example function 10: 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 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)

// = 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, 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)

{

int nx = dims[0], ny = dims[1];

int nx = dims[0];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

int j = 0;

int count_mask = 0;

double sum = 0.0;

double sum2 = 0.0;

double err = 0.0;

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

*mean_ih_ptr = 0.0;

float sum=0.0, sum2=0.0;

for (j = 0; j < ny; j++)

{

for (i = 0; i < nx; i++)

{

for (j = 0; j < ny; j++)

{

if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;

if isnan(jz[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 (jz[j * nx + i] == 0.0) continue;

sum += (jz[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[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

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++;

}

printf("sum/count_mask=%f\n",sum/count_mask);

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 */

*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(err)/count_mask)*(1/cdelt1)*(rsun_obs/rsun_ref) ; // error in the quantity MEANJZH

*total_us_ih_err_ptr = (sqrt(err))*(1/cdelt1)*(rsun_obs/rsun_ref) ; // error in the quantity TOTUSJH

*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_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;

}

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

/* Example function 11: 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:

// fabs(sum(jz gt 0)) + fabs(sum(jz lt 0)) and the units are in Amperes.

// 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),

// = (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, 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 nx = dims[0], ny = dims[1];

int nx = dims[0];

int i, j, count_mask=0;

int ny = dims[1];

int i=0;

int j=0;

int count_mask=0;

double sum1=0.0;

double sum2=0.0;

double err=0.0;

*totaljzptr=0.0;

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

*totaljzptr=0.0;

float sum1=0.0, sum2=0.0;

for (i = 0; i < nx; i++)

{

for (j = 0; j < ny; j++)

{

if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) 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) 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]);

count_mask++;

}

*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;

}

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

/* Example function 12: 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

// 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

// 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)

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)

{

int nx = dims[0], ny = dims[1];

int nx = dims[0];

int i, j, count_mask=0;

int ny = dims[1];

int i = 0;

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

int j = 0;

int count_mask = 0;

double sum = 0.0;

double sum1 = 0.0;

double err = 0.0;

*totpotptr=0.0;

*meanpotptr=0.0;

float sum=0.0;

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

for (i = 0; i < nx; i++)

{

Line 752 int computeFreeEnergy(float *bx, float *

Line 914 int computeFreeEnergy(float *bx, float *

if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;

if isnan(bx[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 += ( ((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 += ( ((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] - 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++;

}

*meanpotptr = (sum)/(count_mask); /* Units are ergs per cubic centimeter */

/* Units of meanpotptr are ergs per 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 */

*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 */

*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;

}

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

/* Example function 13: 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 *bz_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 *mask, int *bitmask)

{

int nx = dims[0], ny = dims[1];

int i, j;

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

{

int nx = dims[0];

int ny = dims[1];

int i = 0;

int j = 0;

float count_mask = 0;

float count = 0;

double dotproduct = 0.0;

double magnitude_potential = 0.0;

double magnitude_vector = 0.0;

double shear_angle = 0.0;

double denominator = 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;

*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 dotproducth, magnitude_potentialh, magnitude_vectorh, shear_angleh=0.0, sum1 = 0.0, counth = 0.0;

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

for (i = 0; i < nx; i++)

{

Line 791 int computeShearAngle(float *bx, float *

Line 982 int computeShearAngle(float *bx, float *

if isnan(bz[j * nx + i]) continue;

if isnan(bx[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]);

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]) );

//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);

sumsum += shear_angle;

//printf("shear_angle=%f\n",shear_angle);

count ++;

sum += shear_angle ;

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*/

*meanshear_angleptr = (sum)/(count); /* Units are degrees */

*meanshear_angleptr = (sumsum)/(count); /* Units are degrees */

printf("count_mask=%f\n",count_mask);

*meanshear_angle_err_ptr = (sqrt(err)/count_mask)*(180./PI);

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 */

/* 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("MEANSHR_err=%f\n",*meanshear_angle_err_ptr);

//printf("SHRGT45=%f\n",*area_w_shear_gt_45ptr);

return 0;

}

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

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 nx = dims[0];

int ny = dims[1];

int i = 0;

int j = 0;

int index;

double sum = 0.0;

double err = 0.0;

*Rparam = 0.0;

struct fresize_struct fresboxcar, fresgauss;

int scale = round(2.0/cdelt1);

float sigma = 10.0/2.3548;

init_fresize_boxcar(&fresboxcar,1,1);

// set up convolution kernel

init_fresize_gaussian(&fresgauss,sigma,20,1);

// make sure convolution kernel is smaller than or equal to array size

if ( (nx < 41.) || (ny < 41.) ) return -1;

fsample(los, rim, nx, ny, nx, nx1, ny1, nx1, scale, 0, 0, 0.0);

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;

}

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);

for (i = 0; i < nx1; i++)

{

for (j = 0; j < ny1; j++)

{

index = j * nx1 + i;

if (p1p[index] > 0 && p1n[index] > 0)

p1[index]=1.0;

else

p1[index]=0.0;

}

fresize(&fresgauss, p1, pmap, nx1, ny1, nx1, nx1, ny1, nx1, 0, 0, 0.0);

for (i = 0; i < nx1; i++)

{

for (j = 0; j < ny1; j++)

{

index = j * nx1 + i;

sum += pmap[index]*abs(rim[index]);

}

if (sum < 1.0)

*Rparam = 0.0;

else

*Rparam = log10(sum);

free_fresize(&fresboxcar);

free_fresize(&fresgauss);

return 0;

}

Line 927 void greenpot(float *bx, float *by, floa

Line 1230 void greenpot(float *bx, float *by, floa

/*===========END OF KEIJI'S CODE =========================*/

char *sw_functions_version() // Returns CVS version of sw_functions.c

{

return strdup("$Id");

}

/* ---------------- end of this file ----------------*/

Legend:

Removed from v.1.4
changed lines
	Added in v.1.27

Karen Tian