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version 1.3, 2012/10/23 18:42:56 version 1.19, 2013/10/18 23:36:02
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 /*=========================================== /*===========================================
  
    The following 13 functions calculate the following spaceweather indices:     The following 14 functions calculate the following spaceweather indices:
  
     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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 ===========================================*/ ===========================================*/
 #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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 //  =(Gauss/pix^2)(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2 //  =(Gauss/pix^2)(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2
 //  =(1.30501e15)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 sum=0.0;
       double err = 0.0;
     if (nx <= 0 || ny <= 0) return 1;  
   
     *absFlux = 0.0;     *absFlux = 0.0;
     *mean_vf_ptr =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 (i = 0; i < nx; i++)
                 {                 {
                   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(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];
                   count_mask++;                   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_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;
        //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;
 } }
  
 /*===========================================*/ /*===========================================*/
 /* 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,
                           float *mean_hf_ptr, int *mask, int *bitmask)                           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;     *mean_hf_ptr =0.0;
  
     if (nx <= 0 || ny <= 0) return 1;     if (nx <= 0 || ny <= 0) return 1;
  
         for (j = 0; j < ny; j++)  
           {  
             for (i = 0; i < nx; i++)             for (i = 0; i < nx; i++)
               {               {
               for (j = 0; j < ny; j++)
                 {
                   if isnan(bx[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];
                 count_mask++;                 count_mask++;
               }               }
           }           }
  
     *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)
                                  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;     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 (i = 0; i < nx; i++)
           {           {
             for (j = 0; j < ny; j++)             for (j = 0; j < ny; j++)
Line 152  int computeGamma(float *bx, float *by, f
Line 171  int computeGamma(float *bx, float *by, f
                 if (bh[j * nx + i] > 100)                 if (bh[j * nx + i] > 100)
                   {                   {
                     if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                     if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                     sum += (atan (fabs( bz[j * nx + i] / bh[j * nx + i] ))* (180./PI));                      if isnan(bz[j * nx + i]) continue;
                       if isnan(bz_err[j * nx + i]) continue;
                       if isnan(bh_err[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 += (( 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);
                     count_mask++;                     count_mask++;
                   }                   }
               }               }
           }           }
  
      *mean_gamma_ptr = sum/count_mask;      *mean_gamma_ptr = sum/count_mask;
      printf("*mean_gamma_ptr=%f\n",*mean_gamma_ptr);       *mean_gamma_err_ptr = (sqrt(err*err))/(count_mask*100.0); // 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 167  int computeGamma(float *bx, float *by, f
Line 193  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];
     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;     if (nx <= 0 || ny <= 0) return 1;
  
Line 179  int computeB_total(float *bx, float *by,
Line 208  int computeB_total(float *bx, float *by,
           {           {
             for (j = 0; j < ny; j++)             for (j = 0; j < ny; j++)
               {               {
                   if isnan(bx[j * nx + i]) continue;
                   if isnan(by[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 188  int computeB_total(float *bx, float *by,
Line 221  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];
     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;     *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) */         /* 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 245  int computeBtotalderivative(float *bt, i
Line 280  int computeBtotalderivative(float *bt, i
           }           }
  
  
         /* 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_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 (i = 0; i <= nx-1; i++)
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; 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 ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) 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 */                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];
                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); // 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 279  int computeBtotalderivative(float *bt, i
Line 304  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];
         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;         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) */         /* 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 335  int computeBhderivative(float *bh, int *
Line 363  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 (i = 0; i <= nx-1; i++)
           {           {
             for (j = 0; j <= ny-1; j++)             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 ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) 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 */                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];
                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)
           //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];
         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;         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) */         /* 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(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;
               }               }
           }           }
Line 392  int computeBzderivative(float *bz, int *
Line 416  int computeBzderivative(float *bz, int *
           {           {
             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;
               }               }
           }           }
Line 401  int computeBzderivative(float *bz, int *
Line 426  int computeBzderivative(float *bz, int *
         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;
           }           }
  
  
         /*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 (i = 0; i <= nx-1; i++)
           {           {
             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 ( (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_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 */                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];
                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)
           //printf("MEANGBZ=%f\n",*mean_derivative_bz_ptr);
           //printf("MEANGBZ_err=%f\n",*mean_derivative_bz_err_ptr);
   
         return 0;         return 0;
 } }
  
 /*===========================================*/ /*===========================================*/
   
 /* Example function 8:  Current Jz = (dBy/dx) - (dBx/dy) */ /* Example function 8:  Current Jz = (dBy/dx) - (dBx/dy) */
  
 //  In discretized space like data pixels, //  In discretized space like data pixels,
Line 470  int computeBzderivative(float *bz, int *
Line 493  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).
 //  In that case, we would have the following: //  In that case, we would have the following:
 //  (Gauss/pix)(1/0.5)(1/722500)(10^-4)(4*PI*10^7)(10^3), or //  (Gauss/pix)(1/0.5)(1/722500)(10^-4)(4*PI*10^7)(10^3), or
 //  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 *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;         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) */         /* 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;
                  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;
                  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++)
           {           {
                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;
           }           }
  
         /* Just some print statements          for (i = 1; i <= nx-2; i++)
         for (i = 0; i < nx; i++)  
           {           {
              for (j = 0; j < ny; j++)              for (j = 1; j <= ny-2; j++)
               {               {
               printf("j=%d\n",j);                 // calculate jz at all points
               printf("i=%d\n",i);  
               printf("dery[j*nx+i]=%f\n",dery[j*nx+i]);                 jz[j * nx + i]            = (derx[j * nx + i]-dery[j * nx + i]);       // jz is in units of Gauss/pix
               printf("derx[j*nx+i]=%f\n",derx[j*nx+i]);                 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]) +
               printf("bx[j*nx+i]=%f\n",bx[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)]) ) ;
               printf("by[j*nx+i]=%f\n",by[j*nx+i]);                 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 (i = 0; i <= nx-1; i++)
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
             {             {
                // if ( (derx[j * nx + i]-dery[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;
                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(derx[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 */                 if isnan(dery[j * nx + i]) continue;
                jz[j * nx + i] = (derx[j * nx + i]-dery[j * nx + i]);                                                          /* jz is in units of Gauss/pix */                 if isnan(jz[j * nx + i]) continue;
                  curl +=     (jz[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 */
                  err  += (jz_err[j * nx + i]*jz_err[j * nx + i]);
                count_mask++;                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 */         *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 MEANJZD */  
           *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;
  
 } }
  
   
 /*===========================================*/ /*===========================================*/
 /* 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. // 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 // 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) //                               = (Gauss/pix)(1/Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(10^6)
 //                               = 1/Mm //                               = 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;         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;
                   //if (jz_err[j * nx + i] > abs(jz[j * nx + i]) ) continue;
                   //if (bz_err[j * nx + i] > abs(bz[j * nx + i]) ) 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++)         for (i = 1; i < nx-1; i++)
           {           {
Line 614  int computeAlpha(float *bz, int *dims, f
Line 704  int computeAlpha(float *bz, int *dims, 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(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 (bz[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;         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 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, 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 sum_err = 0.0;
  
         if (nx <= 0 || ny <= 0) return 1;         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 (i = 0; i < nx; i++)
                 {                 {
                   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[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[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
                     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));
                 count_mask++;                 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 */             *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*100.0)    ;  // error in the quantity MEANJZH
           *total_us_ih_err_ptr  = (sqrt(sum_err*sum_err)) / (100.0)               ;  // error in the quantity TOTUSJH
           *total_abs_ih_err_ptr = (sqrt(sum_err*sum_err)) / (100.0)               ;  // 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;
 } }
  
 /*===========================================*/ /*===========================================*/
 /* 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: //  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.
 //  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, 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)
  
 { {
         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;         if (nx <= 0 || ny <= 0) return 1;
  
         *totaljzptr=0.0;  
         float sum1=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(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]);
                   count_mask++;
               }               }
           }           }
  
         *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 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 // 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)
  
 { {
         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;         *totpotptr=0.0;
         *meanpotptr=0.0;         *meanpotptr=0.0;
         float sum=0.0;  
           if (nx <= 0 || ny <= 0) return 1;
  
         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;
                  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);                   if isnan(bx[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);
                    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])) );
                    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]);
                  count_mask++;                  count_mask++;
               }               }
           }           }
  
         *meanpotptr = (sum)/(count_mask);              /* Units are ergs per cubic centimeter */          *meanpotptr      = (sum1/(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))*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)
   
           /* 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 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 *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 *mask, int *bitmask)  
 { {
         int nx = dims[0], ny = dims[1];          int nx = dims[0];
         int i, j;          int ny = dims[1];
           int i = 0;
         if (nx <= 0 || ny <= 0) return 1;          int j = 0;
           int count_mask = 0;
           double dotproduct = 0.0;
           double magnitude_potential = 0.0;
           double magnitude_vector = 0.0;
           double shear_angle = 0.0;
           double err = 0.0;
           double sum = 0.0;
           double count = 0.0;
         *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 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++)         for (i = 0; i < nx; i++)
           {           {
Line 777  int computeShearAngle(float *bx, float *
Line 922  int computeShearAngle(float *bx, float *
                  if isnan(bpy[j * nx + i]) continue;                  if isnan(bpy[j * nx + i]) continue;
                  if isnan(bpz[j * nx + i]) continue;                  if isnan(bpz[j * nx + i]) continue;
                  if isnan(bz[j * nx + i]) continue;                  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*/                  /* For mean 3D shear angle, area 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]));
Line 784  int computeShearAngle(float *bx, float *
Line 931  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))*(100.0);/* 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;
 } }
Line 913  void greenpot(float *bx, float *by, floa
Line 1063  void greenpot(float *bx, float *by, floa
  
  
 /*===========END OF KEIJI'S CODE =========================*/ /*===========END OF KEIJI'S CODE =========================*/
   
   char *sw_functions_version() // Returns CVS version of sw_functions.c
   {
     return strdup("$Id$");
   }
   
 /* ---------------- end of this file ----------------*/ /* ---------------- end of this file ----------------*/

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