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version 1.7, 2013/02/08 23:41:13 version 1.37, 2015/10/30 20:21:28
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 /*=========================================== /*===========================================
  
    The following 14 functions calculate the following spaceweather indices:    The following 14 functions calculate the following spaceweather indices:
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     MEANPOT Mean photospheric excess magnetic energy density in ergs per cubic centimeter     MEANPOT Mean photospheric excess magnetic energy density in ergs per cubic centimeter
     TOTPOT Total photospheric magnetic energy density in ergs per cubic centimeter     TOTPOT Total photospheric magnetic energy density in ergs per cubic centimeter
     MEANSHR Mean shear angle (measured using Btotal) in degrees     MEANSHR Mean shear angle (measured using Btotal) in degrees
    R_VALUE Karel Schrijver's R parameter
  
    The indices are calculated on the pixels in which the conf_disambig segment is greater than 70 and    The indices are calculated on the pixels in which the conf_disambig segment is greater than 70 and
    pixels in which the bitmap segment is greater than 30. These ranges are selected because the CCD    pixels in which the bitmap segment is greater than 30. These ranges are selected because the CCD
    coordinate bitmaps are interpolated.   coordinate bitmaps are interpolated for certain data (at the time of this CVS submit, all data
    prior to 2013.08.21_17:24:00_TAI contain interpolated bitmaps; data post-2013.08.21_17:24:00_TAI
    contain nearest-neighbor bitmaps).
  
    In the CCD coordinates, this means that we are selecting the pixels that equal 90 in conf_disambig    In the CCD coordinates, this means that we are selecting the pixels that equal 90 in conf_disambig
    and the pixels that equal 33 or 44 in bitmap. Here are the definitions of the pixel values:   and the pixels that equal 33 or 34 in bitmap. Here are the definitions of the pixel values:
  
    For conf_disambig:    For conf_disambig:
    50 : not all solutions agree (weak field method applied)    50 : not all solutions agree (weak field method applied)
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    Written by Monica Bobra 15 August 2012    Written by Monica Bobra 15 August 2012
    Potential Field code (appended) written by Keiji Hayashi    Potential Field code (appended) written by Keiji Hayashi
    Error analysis modification 21 October 2013
  
 ===========================================*/ ===========================================*/
 #include <math.h> #include <math.h>
   #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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 //  To convert G to G*cm^2, simply multiply by the number of square centimeters per pixel. //  To convert G to G*cm^2, simply multiply by the number of square centimeters per pixel.
 //  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS). //  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS).
 //  (Gauss/pix^2)(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.cm/m)^2 //  (Gauss/pix^2)(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.cm/m)^2
 //  =(Gauss/pix^2)(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2  //  =Gauss*cm^2
 //  =(1.30501e15)Gauss*cm^2  
   
 //  The disambig mask value selects only the pixels with values of 5 or 7 -- that is,  
 //  5: pixels for which the radial acute disambiguation solution was chosen  
 //  7: pixels for which the radial acute and NRWA disambiguation agree  
  
 int computeAbsFlux(float *bz, int *dims, float *absFlux,  int computeAbsFlux(float *bz_err, float *bz, int *dims, float *absFlux,
                                    float *mean_vf_ptr, int *mask,  int *bitmask,                     float *mean_vf_ptr, float *mean_vf_err_ptr, float *count_mask_ptr, int *mask,
                                    float cdelt1, double rsun_ref, double rsun_obs)                     int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
  
 { {
  
     int nx = dims[0], ny = dims[1];      int nx = dims[0];
     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;
  
   
       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++)
Line 88  int computeAbsFlux(float *bz, int *dims,
Line 93  int computeAbsFlux(float *bz, int *dims,
                   if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                   if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                   if isnan(bz[j * nx + i]) continue;                   if isnan(bz[j * nx + i]) continue;
                   sum += (fabs(bz[j * nx + i]));                   sum += (fabs(bz[j * nx + i]));
               err += bz_err[j * nx + i]*bz_err[j * nx + i];
                   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;
      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;
Line 118  int computeBh(float *bx, float *by, floa
Line 127  int computeBh(float *bx, float *by, floa
           {           {
             for (j = 0; j < ny; j++)             for (j = 0; j < ny; j++)
               {               {
                 if isnan(bx[j * nx + i]) continue;              if isnan(bx[j * nx + i])
                 if isnan(by[j * nx + i]) continue;              {
                   bh[j * nx + i] = NAN;
                   bh_err[j * nx + i] = NAN;
                   continue;
               }
               if isnan(by[j * nx + i])
               {
                   bh[j * nx + i] = NAN;
                   bh_err[j * nx + i] = NAN;
                   continue;
               }
                 bh[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] );                 bh[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] );
                 sum += bh[j * nx + i];                 sum += bh[j * nx + i];
               bh_err[j * nx + i]=sqrt( bx[j * nx + i]*bx[j * nx + i]*bx_err[j * nx + i]*bx_err[j * nx + i] + by[j * nx + i]*by[j * nx + i]*by_err[j * nx + i]*by_err[j * nx + i])/ bh[j * nx + i];
                 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)
   //
   // 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;     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 156  int computeGamma(float *bx, float *by, f
Line 180  int computeGamma(float *bx, float *by, f
                   {                   {
                     if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                     if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                     if isnan(bz[j * nx + i]) continue;                     if isnan(bz[j * nx + i]) continue;
                     sum += (atan (fabs( bz[j * nx + i] / bh[j * nx + i] ))* (180./PI));                  if isnan(bz_err[j * nx + i]) continue;
                   if isnan(bh_err[j * nx + i]) continue;
                   if 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++;                     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)/(count_mask))*(180./PI);
       //printf("MEANGAM=%f\n",*mean_gamma_ptr);
       //printf("MEANGAM_err=%f\n",*mean_gamma_err_ptr);
      return 0;      return 0;
 } }
  
Line 171  int computeGamma(float *bx, float *by, f
Line 204  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 183  int computeB_total(float *bx, float *by,
Line 219  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(bx[j * nx + i])
                 if isnan(by[j * nx + i]) continue;              {
                 if isnan(bz[j * nx + i]) continue;                  bt[j * nx + i] = NAN;
                   bt_err[j * nx + i] = NAN;
                   continue;
               }
               if isnan(by[j * nx + i])
               {
                   bt[j * nx + i] = NAN;
                   bt_err[j * nx + i] = NAN;
                   continue;
               }
               if isnan(bz[j * nx + i])
               {
                   bt[j * nx + i] = NAN;
                   bt_err[j * nx + i] = NAN;
                   continue;
               }
                 bt[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] + bz[j * nx + i]*bz[j * nx + i]);                 bt[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] + bz[j * nx + i]*bz[j * nx + i]);
               bt_err[j * nx + i]=sqrt(bx[j * nx + i]*bx[j * nx + i]*bx_err[j * nx + i]*bx_err[j * nx + i] + by[j * nx + i]*by[j * nx + i]*by_err[j * nx + i]*by_err[j * nx + i] +  bz[j * nx + i]*bz[j * nx + i]*bz_err[j * nx + i]*bz_err[j * nx + i] ) / bt[j * nx + i];
               }               }
           }           }
      return 0;      return 0;
Line 195  int computeB_total(float *bx, float *by,
Line 247  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, float *err_termAt, float *err_termBt)
 { {
  
     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 213  int computeBtotalderivative(float *bt, i
Line 267  int computeBtotalderivative(float *bt, i
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
               {               {
                 derx_bt[j * nx + i] = (bt[j * nx + i+1] - bt[j * nx + i-1])*0.5;                 derx_bt[j * nx + i] = (bt[j * nx + i+1] - bt[j * nx + i-1])*0.5;
              err_termAt[j * nx + i] = (((bt[j * nx + (i+1)]-bt[j * nx + (i-1)])*(bt[j * nx + (i+1)]-bt[j * nx + (i-1)])) * (bt_err[j * nx + (i+1)]*bt_err[j * nx + (i+1)] + bt_err[j * nx + (i-1)]*bt_err[j * nx + (i-1)])) ;
               }               }
           }           }
  
Line 222  int computeBtotalderivative(float *bt, i
Line 277  int computeBtotalderivative(float *bt, i
             for (j = 1; j <= ny-2; j++)             for (j = 1; j <= ny-2; j++)
               {               {
                 dery_bt[j * nx + i] = (bt[(j+1) * nx + i] - bt[(j-1) * nx + i])*0.5;                 dery_bt[j * nx + i] = (bt[(j+1) * nx + i] - bt[(j-1) * nx + i])*0.5;
              err_termBt[j * nx + i] = (((bt[(j+1) * nx + i]-bt[(j-1) * nx + i])*(bt[(j+1) * nx + i]-bt[(j-1) * nx + i])) * (bt_err[(j+1) * nx + i]*bt_err[(j+1) * nx + i] + bt_err[(j-1) * nx + i]*bt_err[(j-1) * nx + i])) ;
               }               }
           }           }
  
       /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
         /* consider the edges */      ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
         i=0;         i=0;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
Line 251  int computeBtotalderivative(float *bt, i
Line 308  int computeBtotalderivative(float *bt, i
              dery_bt[j * nx + i] = ( (3*bt[j * nx + i]) + (-4*bt[(j-1) * nx + i]) - (-bt[(j-2) * nx + i]) )*0.5;              dery_bt[j * nx + i] = ( (3*bt[j * nx + i]) + (-4*bt[(j-1) * nx + i]) - (-bt[(j-2) * nx + i]) )*0.5;
           }           }
  
       // Calculate the sum only
         for (i = 0; i <= nx-1; i++)      for (i = 1; i <= nx-2; i++)
           {           {
             for (j = 0; j <= ny-1; j++)          for (j = 1; j <= ny-2; j++)
             {             {
                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
               if ( (derx_bt[j * nx + i] + dery_bt[j * nx + i]) == 0) continue;
               if isnan(bt[j * nx + i])      continue;
               if isnan(bt[(j+1) * nx + i])  continue;
               if isnan(bt[(j-1) * nx + i])  continue;
               if isnan(bt[j * nx + i-1])    continue;
               if isnan(bt[j * nx + i+1])    continue;
               if isnan(bt_err[j * nx + i])  continue;
                if isnan(derx_bt[j * nx + i]) continue;                if isnan(derx_bt[j * nx + i]) continue;
                if isnan(dery_bt[j * nx + i]) continue;                if isnan(dery_bt[j * nx + i]) continue;
                sum += sqrt( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  ); /* Units of Gauss */                sum += sqrt( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  ); /* Units of Gauss */
               err += err_termBt[j * nx + i] / (16.0*( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  ))+
                      err_termAt[j * nx + i] / (16.0*( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  )) ;
                count_mask++;                count_mask++;
             }             }
           }           }
  
         *mean_derivative_btotal_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram      *mean_derivative_btotal_ptr     = (sum)/(count_mask);
         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;         return 0;
 } }
  
Line 273  int computeBtotalderivative(float *bt, i
Line 342  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, float *err_termAh, float *err_termBh)
 { {
  
         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++)
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
               {               {
                 derx_bh[j * nx + i] = (bh[j * nx + i+1] - bh[j * nx + i-1])*0.5;                 derx_bh[j * nx + i] = (bh[j * nx + i+1] - bh[j * nx + i-1])*0.5;
              err_termAh[j * nx + i] = (((bh[j * nx + (i+1)]-bh[j * nx + (i-1)])*(bh[j * nx + (i+1)]-bh[j * nx + (i-1)])) * (bh_err[j * nx + (i+1)]*bh_err[j * nx + (i+1)] + bh_err[j * nx + (i-1)]*bh_err[j * nx + (i-1)]));
               }               }
           }           }
  
Line 299  int computeBhderivative(float *bh, int *
Line 372  int computeBhderivative(float *bh, int *
             for (j = 1; j <= ny-2; j++)             for (j = 1; j <= ny-2; j++)
               {               {
                 dery_bh[j * nx + i] = (bh[(j+1) * nx + i] - bh[(j-1) * nx + i])*0.5;                 dery_bh[j * nx + i] = (bh[(j+1) * nx + i] - bh[(j-1) * nx + i])*0.5;
             err_termBh[j * nx + i] = (((bh[ (j+1) * nx + i]-bh[(j-1) * nx + i])*(bh[(j+1) * nx + i]-bh[(j-1) * nx + i])) * (bh_err[(j+1) * nx + i]*bh_err[(j+1) * nx + i] + bh_err[(j-1) * nx + i]*bh_err[(j-1) * nx + i]));
               }               }
           }           }
  
       /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
         /* consider the edges */      ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
         i=0;         i=0;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
Line 334  int computeBhderivative(float *bh, int *
Line 409  int computeBhderivative(float *bh, int *
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
             {             {
                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
               if ( (derx_bh[j * nx + i] + dery_bh[j * nx + i]) == 0) continue;
               if isnan(bh[j * nx + i])      continue;
               if isnan(bh[(j+1) * nx + i])  continue;
               if isnan(bh[(j-1) * nx + i])  continue;
               if isnan(bh[j * nx + i-1])    continue;
               if isnan(bh[j * nx + i+1])    continue;
               if isnan(bh_err[j * nx + i])  continue;
                if isnan(derx_bh[j * nx + i]) continue;                if isnan(derx_bh[j * nx + i]) continue;
                if isnan(dery_bh[j * nx + i]) continue;                if isnan(dery_bh[j * nx + i]) continue;
                sum += sqrt( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  ); /* Units of Gauss */                sum += sqrt( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  ); /* Units of Gauss */
               err += err_termBh[j * nx + i] / (16.0*( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  ))+
                      err_termAh[j * nx + i] / (16.0*( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  )) ;
                count_mask++;                count_mask++;
             }             }
           }           }
  
         *mean_derivative_bh_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram         *mean_derivative_bh_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
       *mean_derivative_bh_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
       //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, float *err_termA, float *err_termB)
 { {
  
         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;
              err_termA[j * nx + i] = (((bz[j * nx + (i+1)]-bz[j * nx + (i-1)])*(bz[j * nx + (i+1)]-bz[j * nx + (i-1)])) * (bz_err[j * nx + (i+1)]*bz_err[j * nx + (i+1)] + bz_err[j * nx + (i-1)]*bz_err[j * nx + (i-1)]));
               }               }
           }           }
  
Line 374  int computeBzderivative(float *bz, int *
Line 465  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;
              err_termB[j * nx + i] = (((bz[(j+1) * nx + i]-bz[(j-1) * nx + i])*(bz[(j+1) * nx + i]-bz[(j-1) * nx + i])) * (bz_err[(j+1) * nx + i]*bz_err[(j+1) * nx + i] + bz_err[(j-1) * nx + i]*bz_err[(j-1) * nx + i]));
               }               }
           }           }
  
       /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
         /* consider the edges */      ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
         i=0;         i=0;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
              if isnan(bz[j * nx + i]) continue;  
              derx_bz[j * nx + i] = ( (-3*bz[j * nx + i]) + (4*bz[j * nx + (i+1)]) - (bz[j * nx + (i+2)]) )*0.5;              derx_bz[j * nx + i] = ( (-3*bz[j * nx + i]) + (4*bz[j * nx + (i+1)]) - (bz[j * nx + (i+2)]) )*0.5;
           }           }
  
         i=nx-1;         i=nx-1;
         for (j = 0; j <= ny-1; j++)         for (j = 0; j <= ny-1; j++)
           {           {
              if isnan(bz[j * nx + i]) continue;  
              derx_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[j * nx + (i-1)]) - (-bz[j * nx + (i-2)]) )*0.5;              derx_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[j * nx + (i-1)]) - (-bz[j * nx + (i-2)]) )*0.5;
           }           }
  
         j=0;         j=0;
         for (i = 0; i <= nx-1; i++)         for (i = 0; i <= nx-1; i++)
           {           {
              if isnan(bz[j * nx + i]) continue;  
              dery_bz[j * nx + i] = ( (-3*bz[j*nx + i]) + (4*bz[(j+1) * nx + i]) - (bz[(j+2) * nx + i]) )*0.5;              dery_bz[j * nx + i] = ( (-3*bz[j*nx + i]) + (4*bz[(j+1) * nx + i]) - (bz[(j+2) * nx + i]) )*0.5;
           }           }
  
         j=ny-1;         j=ny-1;
         for (i = 0; i <= nx-1; i++)         for (i = 0; i <= nx-1; i++)
           {           {
              if isnan(bz[j * nx + i]) continue;  
              dery_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[(j-1) * nx + i]) - (-bz[(j-2) * nx + i]) )*0.5;              dery_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[(j-1) * nx + i]) - (-bz[(j-2) * nx + i]) )*0.5;
           }           }
  
Line 414  int computeBzderivative(float *bz, int *
Line 502  int computeBzderivative(float *bz, int *
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
             {             {
                // if ( (derx_bz[j * nx + i]-dery_bz[j * nx + i]) == 0) continue;  
                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
               if ( (derx_bz[j * nx + i] + dery_bz[j * nx + i]) == 0) continue;
                if isnan(bz[j * nx + i]) continue;                if isnan(bz[j * nx + i]) continue;
               if isnan(bz[(j+1) * nx + i])  continue;
               if isnan(bz[(j-1) * nx + i])  continue;
               if isnan(bz[j * nx + i-1])    continue;
               if isnan(bz[j * nx + i+1])    continue;
               if isnan(bz_err[j * nx + i])  continue;
                if isnan(derx_bz[j * nx + i]) continue;                if isnan(derx_bz[j * nx + i]) continue;
                if isnan(dery_bz[j * nx + i]) continue;                if isnan(dery_bz[j * nx + i]) continue;
                sum += sqrt( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  ); /* Units of Gauss */                sum += sqrt( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  ); /* Units of Gauss */
               err += err_termB[j * nx + i] / (16.0*( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  )) +
                      err_termA[j * nx + i] / (16.0*( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  )) ;
                count_mask++;                count_mask++;
             }             }
           }           }
  
         *mean_derivative_bz_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram         *mean_derivative_bz_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
       *mean_derivative_bz_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
       //printf("MEANGBZ=%f\n",*mean_derivative_bz_ptr);
       //printf("MEANGBZ_err=%f\n",*mean_derivative_bz_err_ptr);
   
         return 0;         return 0;
 } }
  
Line 445  int computeBzderivative(float *bz, int *
Line 544  int computeBzderivative(float *bz, int *
 // //
 //  To change units from Gauss/pixel to mA/m^2 (the units for Jz in Leka and Barnes, 2003), //  To change units from Gauss/pixel to mA/m^2 (the units for Jz in Leka and Barnes, 2003),
 //  one must perform the following unit conversions: //  one must perform the following unit conversions:
 //  (Gauss/pix)(pix/arcsec)(arcsec/meter)(Newton/Gauss*Ampere*meter)(Ampere^2/Newton)(milliAmpere/Ampere), or  //  (Gauss)(1/arcsec)(arcsec/meter)(Newton/Gauss*Ampere*meter)(Ampere^2/Newton)(milliAmpere/Ampere), or
 //  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(1 T / 10^4 Gauss)(1 / 4*PI*10^-7)( 10^3 milliAmpere/Ampere),  //  (Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(1 T / 10^4 Gauss)(1 / 4*PI*10^-7)( 10^3 milliAmpere/Ampere), or
   //  (Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(1000.),
 //  where a Tesla is represented as a Newton/Ampere*meter. //  where a Tesla is represented as a Newton/Ampere*meter.
 // //
 //  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS). //  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS).
Line 455  int computeBzderivative(float *bz, int *
Line 555  int computeBzderivative(float *bz, int *
 //  jz * (35.0) //  jz * (35.0)
 // //
 //  The units of total unsigned vertical current (us_i) are simply in A. In this case, we would have the following: //  The units of total unsigned vertical current (us_i) are simply in A. In this case, we would have the following:
 //  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(1000.)  //  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(CDELT1)(CDELT1)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)
 //  =(Gauss/pix)(1/0.5)(10^-4)(4*PI*10^7)(722500)(1000.)  //  = (Gauss/pix)(0.00010)(1/MUNAUGHT)(CDELT1)(RSUN_REF/RSUN_OBS)
 //  =(Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(1000.)  
  
 int computeJz(float *bx, float *by, int *dims, float *jz,  
                          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, float *err_term1, float *err_term2)
  
 {  
  
         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;
         float curl=0.0, us_i=0.0,test_perimeter=0.0,mean_curl=0.0;  
   
  
       /* Calculate the derivative*/
         /* brute force method of calculating the derivative (no consideration for edges) */         /* brute force method of calculating the derivative (no consideration for edges) */
   
         for (i = 1; i <= nx-2; i++)         for (i = 1; i <= nx-2; i++)
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
               {               {
                  if isnan(by[j * nx + i]) continue;  
                  derx[j * nx + i] = (by[j * nx + i+1] - by[j * nx + i-1])*0.5;                  derx[j * nx + i] = (by[j * nx + i+1] - by[j * nx + i-1])*0.5;
              err_term1[j * nx + i] = (by_err[j * nx + i+1])*(by_err[j * nx + i+1]) + (by_err[j * nx + i-1])*(by_err[j * nx + i-1]);
               }               }
           }           }
  
         /* 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;
              err_term2[j * nx + i] = (bx_err[(j+1) * nx + i])*(bx_err[(j+1) * nx + i]) + (bx_err[(j-1) * nx + i])*(bx_err[(j-1) * nx + i]);
               }               }
           }           }
  
       /* consider the edges for the arrays that contribute to the variable "sum" in the computation below.
       ignore the edges for the error terms as those arrays have been initialized to zero.
       this is okay because the error term will ultimately not include the edge pixels as they are selected out by the mask and bitmask arrays.*/
  
         /* 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;
           }           }
  
Line 529  int computeJz(float *bx, float *by, int
Line 631  int computeJz(float *bx, float *by, int
           {           {
             for (j = 0; j <= ny-1; j++)             for (j = 0; j <= ny-1; j++)
             {             {
                /* calculate jz at all points */              // calculate jz at all points
                jz[j * nx + i] = (derx[j * nx + i]-dery[j * nx + i]);                                              /* jz is in units of Gauss/pix */              jz[j * nx + i]            = (derx[j * nx + i]-dery[j * nx + i]);       // jz is in units of Gauss/pix
               jz_err[j * nx + i]        = 0.5*sqrt( err_term1[j * nx + i] + err_term2[j * nx + i] ) ;
               jz_err_squared[j * nx + i]= (jz_err[j * nx + i]*jz_err[j * nx + i]);
                count_mask++;                count_mask++;
             }             }
           }           }
   
         return 0;         return 0;
 } }
  
 /*===========================================*/ /*===========================================*/
  
 /* Example function 9:  Compute quantities on smoothed Jz array */  /* Example function 9:  Compute quantities on Jz array */
   // Compute mean and total current on Jz array.
  
 // All of the subsequent functions, including this one, use a smoothed Jz array. The smoothing is performed by Jesper's  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,
 // fresize routines. These routines are located at /cvs/JSOC/proj/libs/interpolate. A Gaussian with a FWHM of 4 pixels                      float *mean_jz_ptr, float *mean_jz_err_ptr, float *us_i_ptr, float *us_i_err_ptr, int *mask, int *bitmask,
 // and truncation width of 12 pixels is used to smooth the array; however, a quick analysis shows that the mean values  
 // of qualities like Jz and helicity do not change much as a result of smoothing. The smoothed array will, of course,  
 // give a lower total Jz as the stron field pixels have been smoothed out to neighboring weaker field pixels.  
   
 int computeJzsmooth(float *bx, float *by, int *dims, float *jz_smooth,  
                           float *mean_jz_ptr, float *us_i_ptr, int *mask, int *bitmask,  
                           float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)                           float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)
  
 { {
  
         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 curl = 0.0;
       double us_i = 0.0;
       double err = 0.0;
  
         if (nx <= 0 || ny <= 0) return 1;         if (nx <= 0 || ny <= 0) return 1;
  
         *mean_jz_ptr = 0.0;  
         float curl=0.0, us_i=0.0,test_perimeter=0.0,mean_curl=0.0;  
   
   
         /* At this point, use the smoothed Jz array with a Gaussian (FWHM of 4 pix and truncation width of 12 pixels) but keep the original array dimensions*/         /* At this point, use the smoothed Jz array with a Gaussian (FWHM of 4 pix and truncation width of 12 pixels) but keep the original array dimensions*/
         for (i = 0; i <= nx-1; i++)         for (i = 0; i <= nx-1; i++)
           {           {
Line 571  int computeJzsmooth(float *bx, float *by
Line 671  int computeJzsmooth(float *bx, float *by
                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                if isnan(derx[j * nx + i]) continue;                if isnan(derx[j * nx + i]) continue;
                if isnan(dery[j * nx + i]) continue;                if isnan(dery[j * nx + i]) continue;
                if isnan(jz_smooth[j * nx + i]) continue;              if isnan(jz[j * nx + i]) continue;
                //printf("%d,%d,%f\n",i,j,jz_smooth[j * nx + i]);              curl +=     (jz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.); /* curl is in units of mA / m^2 */
                curl +=     (jz_smooth[j * nx + i])*(1/cdelt1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT)*(1000.); /* curl is in units of mA / m^2 */              us_i += fabs(jz[j * nx + i])*(cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT);         /* us_i is in units of A */
                us_i += fabs(jz_smooth[j * nx + i])*(1/cdelt1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT);         /* us_i is in units of A  / m^2 */              err  += (jz_err[j * nx + i]*jz_err[j * nx + i]);
                count_mask++;                count_mask++;
             }             }
           }           }
  
         /* Calculate mean vertical current density (mean_curl) and total unsigned vertical current (us_i) using smoothed Jz array and continue conditions above */      /* Calculate mean vertical current density (mean_jz) and total unsigned vertical current (us_i) using smoothed Jz array and continue conditions above */
         mean_curl        = (curl/count_mask);  
         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)/count_mask)*((1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.)); // error in the quantity MEANJZD
   
         *us_i_ptr        = (us_i);                   /* us_i gets populated as TOTUSJZ */         *us_i_ptr        = (us_i);                   /* us_i gets populated as TOTUSJZ */
       *us_i_err_ptr    = (sqrt(err))*((cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT)); // error in the quantity TOTUSJZ
   
       //printf("MEANJZD=%f\n",*mean_jz_ptr);
       //printf("MEANJZD_err=%f\n",*mean_jz_err_ptr);
   
       //printf("TOTUSJZ=%g\n",*us_i_ptr);
       //printf("TOTUSJZ_err=%g\n",*us_i_err_ptr);
   
         return 0;         return 0;
  
 } }
Line 595  int computeJzsmooth(float *bx, float *by
Line 701  int computeJzsmooth(float *bx, float *by
 /* Example function 10:  Twist Parameter, alpha */ /* Example function 10:  Twist Parameter, alpha */
  
 // The twist parameter, alpha, is defined as alpha = Jz/Bz. In this case, the calculation // The twist parameter, alpha, is defined as alpha = Jz/Bz. In this case, the calculation
 // for alpha is calculated in the following way (different from Leka and Barnes' approach):  // for alpha is weighted by Bz (following Hagino et al., http://adsabs.harvard.edu/abs/2004PASJ...56..831H):
  
        // (sum of all positive Bz + abs(sum of all negative Bz)) = avg Bz  // numerator   = sum of all Jz*Bz
        // (abs(sum of all Jz at positive Bz) + abs(sum of all Jz at negative Bz)) = avg Jz  // denominator = sum of Bz*Bz
        // avg alpha = avg Jz / avg Bz  // alpha       = numerator/denominator
   
 // The sign is assigned as follows:  
 // If the sum of all Bz is greater than 0, then evaluate the sum of Jz at the positive Bz pixels.  
 // If this value is > 0, then alpha is > 0.  
 // If this value is < 0, then alpha is <0.  
 //  
 // If the sum of all Bz is less than 0, then evaluate the sum of Jz at the negative Bz pixels.  
 // If this value is > 0, then alpha is < 0.  
 // If this value is < 0, then alpha is > 0.  
  
 // The units of alpha are in 1/Mm // The units of alpha are in 1/Mm
 // The units of Jz are in Gauss/pix; the units of Bz are in Gauss. // The units of Jz are in Gauss/pix; the units of Bz are in Gauss.
Line 617  int computeJzsmooth(float *bx, float *by
Line 714  int computeJzsmooth(float *bx, float *by
 //                               = (Gauss/pix)(1/Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(10^6) //                               = (Gauss/pix)(1/Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(10^6)
 //                               = 1/Mm //                               = 1/Mm
  
 int computeAlpha(float *bz, int *dims, float *jz_smooth, float *mean_alpha_ptr, int *mask, int *bitmask,  int computeAlpha(float *jz_err, float *bz_err, float *bz, int *dims, float *jz, float *jz_smooth, float *mean_alpha_ptr, float *mean_alpha_err_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
                  float cdelt1, double rsun_ref, double rsun_obs)  
  
 { {
         int nx = dims[0], ny = dims[1];      int nx                     = dims[0];
         int i, j=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;
   
         *mean_alpha_ptr = 0.0;  
         float aa, bb, cc, bznew, alpha2, sum1, sum2, sum3, sum4, sum, sum5, sum6=0.0;  
   
         for (i = 1; i < nx-1; i++)         for (i = 1; i < nx-1; i++)
           {           {
             for (j = 1; j < ny-1; j++)             for (j = 1; j < ny-1; j++)
               {               {
                 if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                 if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                 if isnan(jz_smooth[j * nx + i]) continue;              if isnan(jz[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;
                 if (bz[j * nx + i] >  0) sum1 += ( bz[j * nx + i]);              A += jz[j*nx+i]*bz[j*nx+i];
                 if (bz[j * nx + i] <= 0) sum2 += ( bz[j * nx + i]);              B += bz[j*nx+i]*bz[j*nx+i];
                 if (bz[j * nx + i] >  0) sum3 += ( jz_smooth[j * nx + i]);  
                 if (bz[j * nx + i] <= 0) sum4 += ( jz_smooth[j * nx + i]);  
                 sum5 += bz[j * nx + i];  
               }               }
           }           }
  
         sum = (((fabs(sum3))+(fabs(sum4)))/((fabs(sum2))+sum1))*((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.)) ; /* the units for (jz/bz) are 1/Mm */          for (i = 1; i < nx-1; i++)
       {
               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;
               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];
           }
       }
  
         /* Determine the sign of alpha */      /* Determine the absolute value of alpha. The units for alpha are 1/Mm */
         if ((sum5 > 0) && (sum3 >  0)) sum=sum;      alpha_total              = ((A/B)*C);
         if ((sum5 > 0) && (sum3 <= 0)) sum=-sum;      *mean_alpha_ptr          = alpha_total;
         if ((sum5 < 0) && (sum4 <= 0)) sum=sum;      *mean_alpha_err_ptr      = (C/B)*(sqrt(total));
         if ((sum5 < 0) && (sum4 >  0)) sum=-sum;  
  
         *mean_alpha_ptr = sum; /* Units are 1/Mm */  
         return 0;         return 0;
 } }
  
 /*===========================================*/ /*===========================================*/
 /* Example function 11:  Helicity (mean current helicty, mean unsigned current helicity, and mean absolute current helicity) */  /* Example function 11:  Helicity (mean current helicty, total unsigned current helicity, absolute value of net current helicity) */
  
 //  The current helicity is defined as Bz*Jz and the units are G^2 / m //  The current helicity is defined as Bz*Jz and the units are G^2 / m
 //  The units of Jz are in G/pix; the units of Bz are in G. //  The units of Jz are in G/pix; the units of Bz are in G.
 //  Therefore, the units of Bz*Jz = (Gauss)*(Gauss/pix) = (Gauss^2/pix)(pix/arcsec)(arcsec/m)  //  Therefore, the units of Bz*Jz = (Gauss)*(Gauss/pix) = (Gauss^2/pix)(pix/arcsec)(arcsec/meter)
 //                                                      = (Gauss^2/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF) //                                                      = (Gauss^2/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)
 //                                                      = G^2 / m. //                                                      = G^2 / m.
  
   int computeHelicity(float *jz_err, float *jz_rms_err, float *bz_err, float *bz, int *dims, float *jz, float *mean_ih_ptr,
 int computeHelicity(float *bz, int *dims, float *jz_smooth, float *mean_ih_ptr, float *total_us_ih_ptr,                      float *mean_ih_err_ptr, float *total_us_ih_ptr, float *total_abs_ih_ptr,
                                         float *total_abs_ih_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)                      float *total_us_ih_err_ptr, float *total_abs_ih_err_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
  
 { {
  
         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;         if (nx <= 0 || ny <= 0) return 1;
  
         *mean_ih_ptr = 0.0;  
         float sum=0.0, sum2=0.0;  
   
         for (i = 0; i < nx; i++)         for (i = 0; i < nx; i++)
         {         {
                 for (j = 0; j < ny; j++)                 for (j = 0; j < ny; j++)
                 {                 {
                 if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;                 if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                 if isnan(jz_smooth[j * nx + i]) continue;              if isnan(jz[j * nx + i])     continue;
                 if isnan(bz[j * nx + i]) continue;                 if isnan(bz[j * nx + i]) continue;
               if isnan(jz_err[j * nx + i]) continue;
               if isnan(bz_err[j * nx + i]) continue;
                 if (bz[j * nx + i] == 0.0) continue;                 if (bz[j * nx + i] == 0.0) continue;
                 if (jz_smooth[j * nx + i] == 0.0) continue;              if (jz[j * nx + i] == 0.0)   continue;
                 sum  +=     (jz_smooth[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref);              sum     +=     (jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to MEANJZH and ABSNJZH
                 sum2 += fabs(jz_smooth[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref);              sum2    += fabs(jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to TOTUSJH
               err     += (jz_err[j * nx + i]*jz_err[j * nx + i]*bz[j * nx + i]*bz[j * nx + i]) + (bz_err[j * nx + i]*bz_err[j * nx + i]*jz[j * nx + i]*jz[j * nx + i]);
                 count_mask++;                 count_mask++;
                 }                 }
          }          }
  
             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(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;         return 0;
 } }
Line 708  int computeHelicity(float *bz, int *dims
Line 831  int computeHelicity(float *bz, int *dims
 /* Example function 12:  Sum of Absolute Value per polarity  */ /* Example function 12:  Sum of Absolute Value per polarity  */
  
 //  The Sum of the Absolute Value per polarity is defined as the following: //  The Sum of the Absolute Value per polarity is defined as the following:
 //  fabs(sum(jz gt 0)) + fabs(sum(jz lt 0)) and the units are in Amperes.  //  fabs(sum(jz gt 0)) + fabs(sum(jz lt 0)) and the units are in Amperes per square arcsecond.
 //  The units of jz are in G/pix. In this case, we would have the following: //  The units of jz are in G/pix. In this case, we would have the following:
 //  Jz = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(RSUN_OBS/RSUN_REF), //  Jz = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(RSUN_OBS/RSUN_REF),
 //     = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS) //     = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)
   //
   //  The error in this quantity is the same as the error in the mean vertical current (mean_jz_err).
  
 int computeSumAbsPerPolarity(float *bz, float *jz_smooth, int *dims, float *totaljzptr,  int computeSumAbsPerPolarity(float *jz_err, float *bz_err, float *bz, float *jz, int *dims, float *totaljzptr, float *totaljz_err_ptr,
                                                          int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)                                                          int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
  
 { {
         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(bz[j * nx + i]) continue;
                 if (bz[j * nx + i] >  0) sum1 += ( jz_smooth[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);              if isnan(jz[j * nx + i]) continue;
                 if (bz[j * nx + i] <= 0) sum2 += ( jz_smooth[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);              if (bz[j * nx + i] >  0) 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 */      *totaljzptr    = fabs(sum1) + fabs(sum2);  /* Units are Amperes per arcsecond */
       *totaljz_err_ptr = sqrt(err)*(1/cdelt1)*fabs((0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs));
       //printf("SAVNCPP=%g\n",*totaljzptr);
       //printf("SAVNCPP_err=%g\n",*totaljz_err_ptr);
   
         return 0;         return 0;
 } }
  
 /*===========================================*/ /*===========================================*/
 /* Example function 13:  Mean photospheric excess magnetic energy and total photospheric excess magnetic energy density */ /* Example function 13:  Mean photospheric excess magnetic energy and total photospheric excess magnetic energy density */
 // The units for magnetic energy density in cgs are ergs per cubic centimeter. The formula B^2/8*PI integrated over all space, dV // The units for magnetic energy density in cgs are ergs per cubic centimeter. The formula B^2/8*PI integrated over all space, dV
 // automatically yields erg per cubic centimeter for an input B in Gauss.  // automatically yields erg per cubic centimeter for an input B in Gauss. Note that the 8*PI can come out of the integral; thus,
   // the integral is over B^2 dV and the 8*PI is divided at the end.
 // //
 // Total magnetic energy is the magnetic energy density times dA, or the area, and the units are thus ergs/cm. To convert // Total magnetic energy is the magnetic energy density times dA, or the area, and the units are thus ergs/cm. To convert
 // ergs per centimeter cubed to ergs per centimeter, simply multiply by the area per pixel in cm: // ergs per centimeter cubed to ergs per centimeter, simply multiply by the area per pixel in cm:
 // erg/cm^3(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.)^2  //   erg/cm^3*(CDELT1^2)*(RSUN_REF/RSUN_OBS ^2)*(100.^2)
 // = erg/cm^3(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2  // = erg/cm^3*(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2
 // = erg/cm^3(1.30501e15)  // = erg/cm^3*(1.30501e15)
 // = erg/cm(1/pix^2) // = erg/cm(1/pix^2)
  
 int computeFreeEnergy(float *bx, float *by, float *bpx, float *bpy, int *dims,  int computeFreeEnergy(float *bx_err, float *by_err, float *bx, float *by, float *bpx, float *bpy, int *dims,
                                           float *meanpotptr, float *totpotptr, int *mask, int *bitmask,                        float *meanpotptr, float *meanpot_err_ptr, float *totpotptr, float *totpot_err_ptr, int *mask, int *bitmask,
                                           float cdelt1, double rsun_ref, double rsun_obs)                                           float cdelt1, double rsun_ref, double rsun_obs)
  
 { {
         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++)
           {           {
Line 773  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 ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
                  if isnan(bx[j * nx + i]) continue;                  if isnan(bx[j * nx + i]) continue;
                  if isnan(by[j * nx + i]) continue;                  if isnan(by[j * nx + i]) continue;
                  sum += ((    ((bx[j * nx + i])*(bx[j * nx + i]) + (by[j * nx + i])*(by[j * nx + i]) ) -  ((bpx[j * nx + i])*(bpx[j * nx + i]) + (bpy[j * nx + i])*(bpy[j * nx + i]))  )/8.*PI);              sum  += ( ((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++;                  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;         return 0;
 } }
  
 /*===========================================*/ /*===========================================*/
 /* Example function 14:  Mean 3D shear angle, area with shear greater than 45, mean horizontal shear angle, area with horizontal shear angle greater than 45 */ /* Example function 14:  Mean 3D shear angle, area with shear greater than 45, mean horizontal shear angle, area with horizontal shear angle greater than 45 */
  
 int computeShearAngle(float *bx, float *by, float *bz, float *bpx, float *bpy, float *bpz, int *dims,  int computeShearAngle(float *bx_err, float *by_err, float *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;         *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 812  int computeShearAngle(float *bx, float *
Line 982  int computeShearAngle(float *bx, float *
                  if isnan(bz[j * nx + i]) continue;                  if isnan(bz[j * nx + i]) continue;
                  if isnan(bx[j * nx + i]) continue;                  if isnan(bx[j * nx + i]) continue;
                  if isnan(by[j * nx + i]) continue;                  if isnan(by[j * nx + i]) continue;
                  /* For mean 3D shear angle, area with shear greater than 45*/              if isnan(bx_err[j * nx + i]) continue;
               if isnan(by_err[j * nx + i]) continue;
               if isnan(bz_err[j * nx + i]) continue;
   
               /* For mean 3D shear angle, percentage with shear greater than 45*/
                  dotproduct            = (bpx[j * nx + i])*(bx[j * nx + i]) + (bpy[j * nx + i])*(by[j * nx + i]) + (bpz[j * nx + i])*(bz[j * nx + i]);                  dotproduct            = (bpx[j * nx + i])*(bx[j * nx + i]) + (bpy[j * nx + i])*(by[j * nx + i]) + (bpz[j * nx + i])*(bz[j * nx + i]);
                  magnitude_potential   = sqrt((bpx[j * nx + i]*bpx[j * nx + i]) + (bpy[j * nx + i]*bpy[j * nx + i]) + (bpz[j * nx + i]*bpz[j * nx + i]));                  magnitude_potential   = sqrt((bpx[j * nx + i]*bpx[j * nx + i]) + (bpy[j * nx + i]*bpy[j * nx + i]) + (bpz[j * nx + i]*bpz[j * nx + i]));
                  magnitude_vector      = sqrt( (bx[j * nx + i]*bx[j * nx + i]) + (by[j * nx + i]*by[j * nx + i]) + (bz[j * nx + i]*bz[j * nx + i]) );                  magnitude_vector      = sqrt( (bx[j * nx + i]*bx[j * nx + i]) + (by[j * nx + i]*by[j * nx + i]) + (bz[j * nx + i]*bz[j * nx + i]) );
               //printf("dotproduct=%f\n",dotproduct);
               //printf("magnitude_potential=%f\n",magnitude_potential);
               //printf("magnitude_vector=%f\n",magnitude_vector);
   
                  shear_angle           = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);                  shear_angle           = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);
               sumsum                  += shear_angle;
               //printf("shear_angle=%f\n",shear_angle);
                  count ++;                  count ++;
                  sum += shear_angle ;  
                  if (shear_angle > 45) count_mask ++;                  if (shear_angle > 45) count_mask ++;
   
               // For the error analysis
   
               term1 = bx[j * nx + i]*by[j * nx + i]*bpy[j * nx + i] - by[j * nx + i]*by[j * nx + i]*bpx[j * nx + i] + bz[j * nx + i]*bx[j * nx + i]*bpz[j * nx + i] - bz[j * nx + i]*bz[j * nx + i]*bpx[j * nx + i];
               term2 = bx[j * nx + i]*bx[j * nx + i]*bpy[j * nx + i] - bx[j * nx + i]*by[j * nx + i]*bpx[j * nx + i] + bx[j * nx + i]*bz[j * nx + i]*bpy[j * nx + i] - bz[j * nx + i]*by[j * nx + i]*bpz[j * nx + i];
               term3 = bx[j * nx + i]*bx[j * nx + i]*bpz[j * nx + i] - bx[j * nx + i]*bz[j * nx + i]*bpx[j * nx + i] + by[j * nx + i]*by[j * nx + i]*bpz[j * nx + i] - by[j * nx + i]*bz[j * nx + i]*bpy[j * nx + i];
   
               part1 = bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] + bz[j * nx + i]*bz[j * nx + i];
               part2 = bpx[j * nx + i]*bpx[j * nx + i] + bpy[j * nx + i]*bpy[j * nx + i] + bpz[j * nx + i]*bpz[j * nx + i];
               part3 = bx[j * nx + i]*bpx[j * nx + i] + by[j * nx + i]*bpy[j * nx + i] + bz[j * nx + i]*bpz[j * nx + i];
   
               // denominator is squared
               denominator = part1*part1*part1*part2*(1.0-((part3*part3)/(part1*part2)));
   
               err = (term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) +
               (term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) +
               (term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) ;
   
               }               }
           }           }
   
         /* For mean 3D shear angle, area with shear greater than 45*/         /* For mean 3D shear angle, area with shear greater than 45*/
         *meanshear_angleptr = (sum)/(count);              /* Units are degrees */      *meanshear_angleptr = (sumsum)/(count);                 /* Units are degrees */
         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;         return 0;
 } }
  
   /*===========================================*/
   /* Example function 15: R parameter as defined in Schrijver, 2007 */
   //
   // Note that there is a restriction on the function fsample()
   // If the following occurs:
   //      nx_out > floor((ny_in-1)/scale + 1)
   //      ny_out > floor((ny_in-1)/scale + 1),
   // where n*_out are the dimensions of the output array and n*_in
   // are the dimensions of the input array, fsample() will usually result
   // in a segfault (though not always, depending on how the segfault was accessed.)
   
   int computeR(float *bz_err, float *los, int *dims, float *Rparam, float cdelt1,
                float *rim, float *p1p0, float *p1n0, float *p1p, float *p1n, float *p1,
                float *pmap, int nx1, int ny1,
                int scale, float *p1pad, int nxp, int nyp, float *pmapn)
   
   {
       int nx = dims[0];
       int ny = dims[1];
       int i = 0;
       int j = 0;
       int index, index1;
       double sum = 0.0;
       double err = 0.0;
       *Rparam = 0.0;
       struct fresize_struct fresboxcar, fresgauss;
       struct fint_struct fints;
       float sigma = 10.0/2.3548;
   
       // set up convolution kernels
       init_fresize_boxcar(&fresboxcar,1,1);
       init_fresize_gaussian(&fresgauss,sigma,20,1);
   
       // =============== [STEP 1] ===============
       // bin the line-of-sight magnetogram down by a factor of scale
       fsample(los, rim, nx, ny, nx, nx1, ny1, nx1, scale, 0, 0, 0.0);
   
       // =============== [STEP 2] ===============
       // identify positive and negative pixels greater than +/- 150 gauss
       // and label those pixels with a 1.0 in arrays p1p0 and p1n0
       for (i = 0; i < nx1; i++)
       {
           for (j = 0; j < ny1; j++)
           {
               index = j * nx1 + i;
               if (rim[index] > 150)
                   p1p0[index]=1.0;
               else
                   p1p0[index]=0.0;
               if (rim[index] < -150)
                   p1n0[index]=1.0;
               else
                   p1n0[index]=0.0;
           }
       }
   
       // =============== [STEP 3] ===============
       // smooth each of the negative and positive pixel bitmaps
       fresize(&fresboxcar, p1p0, p1p, nx1, ny1, nx1, nx1, ny1, nx1, 0, 0, 0.0);
       fresize(&fresboxcar, p1n0, p1n, nx1, ny1, nx1, nx1, ny1, nx1, 0, 0, 0.0);
   
       // =============== [STEP 4] ===============
       // find the pixels for which p1p and p1n are both equal to 1.
       // this defines the polarity inversion line
       for (i = 0; i < nx1; i++)
       {
           for (j = 0; j < ny1; j++)
           {
               index = j * nx1 + i;
               if ((p1p[index] > 0.0) && (p1n[index] > 0.0))
                   p1[index]=1.0;
               else
                   p1[index]=0.0;
           }
       }
   
       // pad p1 with zeroes so that the gaussian colvolution in step 5
       // does not cut off data within hwidth of the edge
   
       // step i: zero p1pad
       for (i = 0; i < nxp; i++)
       {
           for (j = 0; j < nyp; j++)
           {
               index = j * nxp + i;
               p1pad[index]=0.0;
           }
       }
   
       // step ii: place p1 at the center of p1pad
       for (i = 0; i < nx1; i++)
       {
          for (j = 0; j < ny1; j++)
          {
               index  = j * nx1 + i;
               index1 = (j+20) * nxp + (i+20);
               p1pad[index1]=p1[index];
           }
       }
   
       // =============== [STEP 5] ===============
       // convolve the polarity inversion line map with a gaussian
       // to identify the region near the plarity inversion line
       // the resultant array is called pmap
       fresize(&fresgauss, p1pad, pmap, nxp, nyp, nxp, nxp, nyp, nxp, 0, 0, 0.0);
   
   
      // select out the nx1 x ny1 non-padded array  within pmap
       for (i = 0; i < nx1; i++)
       {
          for (j = 0; j < ny1; j++)
          {
               index  = j * nx1 + i;
               index1 = (j+20) * nxp + (i+20);
               pmapn[index]=pmap[index1];
           }
       }
   
       // =============== [STEP 6] ===============
       // the R parameter is calculated
       for (i = 0; i < nx1; i++)
       {
           for (j = 0; j < ny1; j++)
           {
               index = j * nx1 + i;
               if isnan(pmapn[index]) continue;
               if isnan(rim[index]) continue;
               sum += pmapn[index]*abs(rim[index]);
           }
       }
   
       if (sum < 1.0)
           *Rparam = 0.0;
       else
           *Rparam = log10(sum);
   
       //printf("R_VALUE=%f\n",*Rparam);
   
       free_fresize(&fresboxcar);
       free_fresize(&fresgauss);
   
       return 0;
   
   }
   
   /*===========================================*/
   /* Example function 16: Lorentz force as defined in Fisher, 2012 */
   //
   // This calculation is adapted from Xudong's code
   // at /proj/cgem/lorentz/apps/lorentz.c
   
   int computeLorentz(float *bx,  float *by, float *bz, float *fx, float *fy, float *fz, int *dims,
                      float *totfx_ptr, float *totfy_ptr, float *totfz_ptr, float *totbsq_ptr,
                      float *epsx_ptr, float *epsy_ptr, float *epsz_ptr, int *mask, int *bitmask,
                      float cdelt1, double rsun_ref, double rsun_obs)
   
   {
   
       int nx = dims[0];
       int ny = dims[1];
       int nxny = nx*ny;
       int j = 0;
       int index;
       double totfx = 0, totfy = 0, totfz = 0;
       double bsq = 0, totbsq = 0;
       double epsx = 0, epsy = 0, epsz = 0;
       double area = cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;
       double k_h = -1.0 * area / (4. * PI) / 1.0e20;
       double k_z = area / (8. * PI) / 1.0e20;
   
       if (nx <= 0 || ny <= 0) return 1;
   
       for (int i = 0; i < nxny; i++)
       {
          if ( mask[i] < 70 || bitmask[i] < 30 ) continue;
          if isnan(bx[i]) continue;
          if isnan(by[i]) continue;
          if isnan(bz[i]) continue;
          fx[i]  = bx[i] * bz[i] * k_h;
          fy[i]  = by[i] * bz[i] * k_h;
          fz[i]  = (bx[i] * bx[i] + by[i] * by[i] - bz[i] * bz[i]) * k_z;
          bsq    = bx[i] * bx[i] + by[i] * by[i] + bz[i] * bz[i];
          totfx  += fx[i]; totfy += fy[i]; totfz += fz[i];
          totbsq += bsq;
       }
   
       *totfx_ptr  = totfx;
       *totfy_ptr  = totfy;
       *totfz_ptr  = totfz;
       *totbsq_ptr = totbsq;
       *epsx_ptr   = (totfx / k_h) / totbsq;
       *epsy_ptr   = (totfy / k_h) / totbsq;
       *epsz_ptr   = (totfz / k_z) / totbsq;
   
       //printf("TOTBSQ=%f\n",*totbsq_ptr);
   
       return 0;
   
   }
  
 /*==================KEIJI'S CODE =========================*/ /*==================KEIJI'S CODE =========================*/
  
Line 948  void greenpot(float *bx, float *by, floa
Line 1349  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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