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Comparing proj/sharp/apps/sw_functions.c (file contents):
Revision 1.1 by xudong, Thu Aug 23 08:38:33 2012 UTC vs.
Revision 1.17 by mbobra, Wed Jul 24 02:35:08 2013 UTC

#	Line 1 | Line 1
1		/*===========================================
2
3	<	The following 13 functions calculate the following spaceweather indices:
3	>	The following 14 functions calculate the following spaceweather indices:
4
5		USFLUX Total unsigned flux in Maxwells
6		MEANGAM Mean inclination angle, gamma, in degrees
#	Line 18 | Line 18
18		TOTPOT Total photospheric magnetic energy density in ergs per cubic centimeter
19		MEANSHR Mean shear angle (measured using Btotal) in degrees
20
21	<	The indices are calculated on the pixels in which the disambig bitmap equals 5 or 7:
22	<	5: pixels for which the radial acute disambiguation solution was chosen
23	<	7: pixels for which the radial acute and NRWA disambiguation agree
21	>	The indices are calculated on the pixels in which the conf_disambig segment is greater than 70 and
22	>	pixels in which the bitmap segment is greater than 30. These ranges are selected because the CCD
23	>	coordinate bitmaps are interpolated.
24	>
25	>	In the CCD coordinates, this means that we are selecting the pixels that equal 90 in conf_disambig
26	>	and the pixels that equal 33 or 44 in bitmap. Here are the definitions of the pixel values:
27	>
28	>	For conf_disambig:
29	>	50 : not all solutions agree (weak field method applied)
30	>	60 : not all solutions agree (weak field + annealed)
31	>	90 : all solutions agree (strong field + annealed)
32	>	0 : not disambiguated
33	>
34	>	For bitmap:
35	>	1  : weak field outside smooth bounding curve
36	>	2  : strong field outside smooth bounding curve
37	>	33 : weak field inside smooth bounding curve
38	>	34 : strong field inside smooth bounding curve
39
40		Written by Monica Bobra 15 August 2012
41		Potential Field code (appended) written by Keiji Hayashi
42
43		===========================================*/
44		#include <math.h>
45	+	#include <mkl.h>
46
47	<	#define PI              (M_PI)
47	>	#define PI       (M_PI)
48		#define MUNAUGHT (0.0000012566370614) /* magnetic constant */
49
50		/*===========================================*/
#	Line 51 | Line 67
67		//  5: pixels for which the radial acute disambiguation solution was chosen
68		//  7: pixels for which the radial acute and NRWA disambiguation agree
69
70	<	int computeAbsFlux(float *bz, int *dims, float *absFlux,
71	<	float *mean_vf_ptr, int *mask,
72	<	float cdelt1, double rsun_ref, double rsun_obs)
70	>	int computeAbsFlux(float *bz_err, float *bz, int *dims, float *absFlux,
71	>	float *mean_vf_ptr, float *mean_vf_err_ptr, float *count_mask_ptr, int *mask,
72	>	int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
73
74		{
75
76	<	int nx = dims[0], ny = dims[1];
77	<	int i, j, count_mask=0;
78	<	double sum=0.0;
79	<
80	<	if (nx <= 0 || ny <= 0) return 1;
81	<
76	>	int nx = dims[0];
77	>	int ny = dims[1];
78	>	int i = 0;
79	>	int j = 0;
80	>	int count_mask = 0;
81	>	double sum = 0.0;
82	>	double err = 0.0;
83		*absFlux = 0.0;
84	<	*mean_vf_ptr =0.0;
84	>	*mean_vf_ptr = 0.0;
85	>
86	>
87	>	if (nx <= 0 || ny <= 0) return 1;
88
89	<	for (j = 0; j < ny; j++)
89	>	for (i = 0; i < nx; i++)
90		{
91	<	for (i = 0; i < nx; i++)
91	>	for (j = 0; j < ny; j++)
92		{
93	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
93	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
94	>	if isnan(bz[j * nx + i]) continue;
95		sum += (fabs(bz[j * nx + i]));
96	<	//sum += (fabs(bz[j * nx + i]))*inverseMu[j * nx + i]; // use this with mu function
96	>	//printf("i,j,bz[j * nx + i]=%d,%d,%f\n",i,j,bz[j * nx + i]);
97	>	err += bz_err[j * nx + i]*bz_err[j * nx + i];
98		count_mask++;
99		}
100		}
101
102	<	printf("nx=%d,ny=%d,count_mask=%d,sum=%f\n",nx,ny,count_mask,sum);
103	<	printf("cdelt1=%f,rsun_ref=%f,rsun_obs=%f\n",cdelt1,rsun_ref,rsun_obs);
104	<	*mean_vf_ptr = sum*cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;
102	>	*mean_vf_ptr     = sum*cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;
103	>	*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
104	>	*count_mask_ptr  = count_mask;
105	>	//printf("cdelt1=%f\n",cdelt1);
106	>	//printf("rsun_obs=%f\n",rsun_obs);
107	>	//printf("rsun_ref=%f\n",rsun_ref);
108	>	//printf("CMASK=%g\n",*count_mask_ptr);
109	>	//printf("USFLUX=%g\n",*mean_vf_ptr);
110	>	//printf("sum=%f\n",sum);
111	>	//printf("USFLUX_err=%g\n",*mean_vf_err_ptr);
112		return 0;
113		}
114
115		/*===========================================*/
116	<	/* Example function 2: Calculate Bh in units of Gauss */
116	>	/* Example function 2: Calculate Bh, the horizontal field, in units of Gauss */
117		// Native units of Bh are Gauss
118
119	<	int computeBh(float *bx, float *by, float *bz, float *bh, int *dims,
120	<	float *mean_hf_ptr, int *mask)
119	>	int computeBh(float *bx_err, float *by_err, float *bh_err, float *bx, float *by, float *bz, float *bh, int *dims,
120	>	float *mean_hf_ptr, int *mask, int *bitmask)
121
122		{
123
124	<	int nx = dims[0], ny = dims[1];
125	<	int i, j, count_mask=0;
126	<	float sum=0.0;
127	<	*mean_hf_ptr =0.0;
124	>	int nx = dims[0];
125	>	int ny = dims[1];
126	>	int i = 0;
127	>	int j = 0;
128	>	int count_mask = 0;
129	>	double sum = 0.0;
130	>	*mean_hf_ptr = 0.0;
131
132		if (nx <= 0 || ny <= 0) return 1;
133
134	<	for (j = 0; j < ny; j++)
134	>	for (i = 0; i < nx; i++)
135		{
136	<	for (i = 0; i < nx; i++)
136	>	for (j = 0; j < ny; j++)
137		{
138	+	if isnan(bx[j * nx + i]) continue;
139	+	if isnan(by[j * nx + i]) continue;
140		bh[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] );
141		sum += bh[j * nx + i];
142	+	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];
143		count_mask++;
144		}
145		}
146
147		*mean_hf_ptr = sum/(count_mask); // would be divided by nx*ny if shape of count_mask = shape of magnetogram
148	<	printf("*mean_hf_ptr=%f\n",*mean_hf_ptr);
148	>
149		return 0;
150		}
151
152		/*===========================================*/
153		/* Example function 3: Calculate Gamma in units of degrees */
154		// Native units of atan(x) are in radians; to convert from radians to degrees, multiply by (180./PI)
155	+	// Redo calculation in radians for error analysis (since derivatives are only true in units of radians).
156
157	<
158	<	int computeGamma(float *bx, float *by, float *bz, float *bh, int *dims,
123	<	float *mean_gamma_ptr, int *mask)
157	>	int computeGamma(float *bz_err, float *bh_err, float *bx, float *by, float *bz, float *bh, int *dims,
158	>	float *mean_gamma_ptr, float *mean_gamma_err_ptr, int *mask, int *bitmask)
159		{
160	<	int nx = dims[0], ny = dims[1];
161	<	int i, j, count_mask=0;
160	>	int nx = dims[0];
161	>	int ny = dims[1];
162	>	int i = 0;
163	>	int j = 0;
164	>	int count_mask = 0;
165	>	double sum = 0.0;
166	>	double err = 0.0;
167	>	*mean_gamma_ptr = 0.0;
168
169		if (nx <= 0 || ny <= 0) return 1;
129	–
130	–	*mean_gamma_ptr=0.0;
131	–	float sum=0.0;
132	–	int count=0;
170
171		for (i = 0; i < nx; i++)
172		{
#	Line 137 | Line 174 | int computeGamma(float *bx, float *by, f
174		{
175		if (bh[j * nx + i] > 100)
176		{
177	<	//if (mask[j * nx + i] != 90 ) continue;
178	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
179	<	sum += (atan (fabs( bz[j * nx + i] / bh[j * nx + i] ))* (180./PI));
180	<	count_mask++;
177	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
178	>	if isnan(bz[j * nx + i]) continue;
179	>	if isnan(bz_err[j * nx + i]) continue;
180	>	if isnan(bh_err[j * nx + i]) continue;
181	>	if (bz[j * nx + i] == 0) continue;
182	>	sum += (atan(fabs(bz[j * nx + i]/bh[j * nx + i] )))*(180./PI);
183	>	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);
184	>	count_mask++;
185		}
186		}
187		}
188
189		*mean_gamma_ptr = sum/count_mask;
190	<	printf("*mean_gamma_ptr=%f\n",*mean_gamma_ptr);
190	>	*mean_gamma_err_ptr = (sqrt(err*err))/(count_mask*100.0); // error in the quantity (sum)/(count_mask)
191	>	//printf("MEANGAM=%f\n",*mean_gamma_ptr);
192	>	//printf("MEANGAM_err=%f\n",*mean_gamma_err_ptr);
193		return 0;
194		}
195
#	Line 154 | Line 197 | int computeGamma(float *bx, float *by, f
197		/* Example function 4: Calculate B_Total*/
198		// Native units of B_Total are in gauss
199
200	<	int computeB_total(float *bx, float *by, float *bz, float *bt, int *dims, int *mask)
200	>	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)
201		{
202
203	<	int nx = dims[0], ny = dims[1];
204	<	int i, j, count_mask=0;
203	>	int nx = dims[0];
204	>	int ny = dims[1];
205	>	int i = 0;
206	>	int j = 0;
207	>	int count_mask = 0;
208
209		if (nx <= 0 || ny <= 0) return 1;
210
#	Line 166 | Line 212 | int computeB_total(float *bx, float *by,
212		{
213		for (j = 0; j < ny; j++)
214		{
215	+	if isnan(bx[j * nx + i]) continue;
216	+	if isnan(by[j * nx + i]) continue;
217	+	if isnan(bz[j * nx + i]) continue;
218		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]);
219	+	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];
220		}
221		}
222		return 0;
#	Line 175 | Line 225 | int computeB_total(float *bx, float *by,
225		/*===========================================*/
226		/* Example function 5:  Derivative of B_Total SQRT( (dBt/dx)^2 + (dBt/dy)^2 ) */
227
228	<	int computeBtotalderivative(float *bt, int *dims, float *mean_derivative_btotal_ptr, int *mask, float *derx_bt, float *dery_bt)
228	>	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)
229		{
230
231	<	int nx = dims[0], ny = dims[1];
232	<	int i, j, count_mask=0;
233	<
234	<	if (nx <= 0 || ny <= 0) return 1;
235	<
231	>	int nx = dims[0];
232	>	int ny = dims[1];
233	>	int i = 0;
234	>	int j = 0;
235	>	int count_mask = 0;
236	>	double sum = 0.0;
237	>	double err = 0.0;
238		*mean_derivative_btotal_ptr = 0.0;
187	–	float sum = 0.0;
239
240	+	if (nx <= 0 || ny <= 0) return 1;
241
242		/* brute force method of calculating the derivative (no consideration for edges) */
243		for (i = 1; i <= nx-2; i++)
#	Line 232 | Line 284 | int computeBtotalderivative(float *bt, i
284		}
285
286
235	–	/* Just some print statements
236	–	for (i = 0; i < nx; i++)
237	–	{
238	–	for (j = 0; j < ny; j++)
239	–	{
240	–	printf("j=%d\n",j);
241	–	printf("i=%d\n",i);
242	–	printf("dery_bt[j*nx+i]=%f\n",dery_bt[j*nx+i]);
243	–	printf("derx_bt[j*nx+i]=%f\n",derx_bt[j*nx+i]);
244	–	printf("bt[j*nx+i]=%f\n",bt[j*nx+i]);
245	–	}
246	–	}
247	–	*/
248	–
287		for (i = 0; i <= nx-1; i++)
288		{
289		for (j = 0; j <= ny-1; j++)
290		{
291	<	// if ( (derx_bt[j * nx + i]-dery_bt[j * nx + i]) == 0) continue;
292	<	//if (mask[j * nx + i] != 90 ) continue;
293	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
291	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
292	>	if isnan(derx_bt[j * nx + i]) continue;
293	>	if isnan(dery_bt[j * nx + i]) continue;
294		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 */
295	+	err += (2.0)*bt_err[j * nx + i]*bt_err[j * nx + i];
296		count_mask++;
297		}
298		}
299
300	<	*mean_derivative_btotal_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
301	<	printf("*mean_derivative_btotal_ptr=%f\n",*mean_derivative_btotal_ptr);
300	>	*mean_derivative_btotal_ptr     = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
301	>	*mean_derivative_btotal_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
302	>	//printf("MEANGBT=%f\n",*mean_derivative_btotal_ptr);
303	>	//printf("MEANGBT_err=%f\n",*mean_derivative_btotal_err_ptr);
304		return 0;
305		}
306
#	Line 267 | Line 308 | int computeBtotalderivative(float *bt, i
308		/*===========================================*/
309		/* Example function 6:  Derivative of Bh SQRT( (dBh/dx)^2 + (dBh/dy)^2 ) */
310
311	<	int computeBhderivative(float *bh, int *dims, float *mean_derivative_bh_ptr, int *mask, float *derx_bh, float *dery_bh)
311	>	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)
312		{
313
314	<	int nx = dims[0], ny = dims[1];
315	<	int i, j, count_mask=0;
314	>	int nx = dims[0];
315	>	int ny = dims[1];
316	>	int i = 0;
317	>	int j = 0;
318	>	int count_mask = 0;
319	>	double sum= 0.0;
320	>	double err =0.0;
321	>	*mean_derivative_bh_ptr = 0.0;
322
323		if (nx <= 0 || ny <= 0) return 1;
324
278	–	*mean_derivative_bh_ptr = 0.0;
279	–	float sum = 0.0;
280	–
325		/* brute force method of calculating the derivative (no consideration for edges) */
326		for (i = 1; i <= nx-2; i++)
327		{
#	Line 323 | Line 367 | int computeBhderivative(float *bh, int *
367		}
368
369
326	–	/*Just some print statements
327	–	for (i = 0; i < nx; i++)
328	–	{
329	–	for (j = 0; j < ny; j++)
330	–	{
331	–	printf("j=%d\n",j);
332	–	printf("i=%d\n",i);
333	–	printf("dery_bh[j*nx+i]=%f\n",dery_bh[j*nx+i]);
334	–	printf("derx_bh[j*nx+i]=%f\n",derx_bh[j*nx+i]);
335	–	printf("bh[j*nx+i]=%f\n",bh[j*nx+i]);
336	–	}
337	–	}
338	–	*/
339	–
370		for (i = 0; i <= nx-1; i++)
371		{
372		for (j = 0; j <= ny-1; j++)
373		{
374	<	// if ( (derx_bh[j * nx + i]-dery_bh[j * nx + i]) == 0) continue;
375	<	//if (mask[j * nx + i] != 90 ) continue;
376	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
374	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
375	>	if isnan(derx_bh[j * nx + i]) continue;
376	>	if isnan(dery_bh[j * nx + i]) continue;
377		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 */
378	+	err += (2.0)*bh_err[j * nx + i]*bh_err[j * nx + i];
379		count_mask++;
380		}
381		}
382
383	<	*mean_derivative_bh_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
383	>	*mean_derivative_bh_ptr     = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
384	>	*mean_derivative_bh_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
385	>	//printf("MEANGBH=%f\n",*mean_derivative_bh_ptr);
386	>	//printf("MEANGBH_err=%f\n",*mean_derivative_bh_err_ptr);
387	>
388		return 0;
389		}
390
391		/*===========================================*/
392		/* Example function 7:  Derivative of B_vertical SQRT( (dBz/dx)^2 + (dBz/dy)^2 ) */
393
394	<	int computeBzderivative(float *bz, int *dims, float *mean_derivative_bz_ptr, int *mask, float *derx_bz, float *dery_bz)
394	>	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)
395		{
396
397	<	int nx = dims[0], ny = dims[1];
398	<	int i, j, count_mask=0;
397	>	int nx = dims[0];
398	>	int ny = dims[1];
399	>	int i = 0;
400	>	int j = 0;
401	>	int count_mask = 0;
402	>	double sum = 0.0;
403	>	double err = 0.0;
404	>	*mean_derivative_bz_ptr = 0.0;
405
406		if (nx <= 0 || ny <= 0) return 1;
407
367	–	*mean_derivative_bz_ptr = 0.0;
368	–	float sum = 0.0;
369	–
408		/* brute force method of calculating the derivative (no consideration for edges) */
409		for (i = 1; i <= nx-2; i++)
410		{
411		for (j = 0; j <= ny-1; j++)
412		{
413	+	if isnan(bz[j * nx + i]) continue;
414		derx_bz[j * nx + i] = (bz[j * nx + i+1] - bz[j * nx + i-1])*0.5;
415		}
416		}
#	Line 381 | Line 420 | int computeBzderivative(float *bz, int *
420		{
421		for (j = 1; j <= ny-2; j++)
422		{
423	+	if isnan(bz[j * nx + i]) continue;
424		dery_bz[j * nx + i] = (bz[(j+1) * nx + i] - bz[(j-1) * nx + i])*0.5;
425		}
426		}
#	Line 390 | Line 430 | int computeBzderivative(float *bz, int *
430		i=0;
431		for (j = 0; j <= ny-1; j++)
432		{
433	+	if isnan(bz[j * nx + i]) continue;
434		derx_bz[j * nx + i] = ( (-3*bz[j * nx + i]) + (4*bz[j * nx + (i+1)]) - (bz[j * nx + (i+2)]) )*0.5;
435		}
436
437		i=nx-1;
438		for (j = 0; j <= ny-1; j++)
439		{
440	+	if isnan(bz[j * nx + i]) continue;
441		derx_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[j * nx + (i-1)]) - (-bz[j * nx + (i-2)]) )*0.5;
442		}
443
444		j=0;
445		for (i = 0; i <= nx-1; i++)
446		{
447	+	if isnan(bz[j * nx + i]) continue;
448		dery_bz[j * nx + i] = ( (-3*bz[j*nx + i]) + (4*bz[(j+1) * nx + i]) - (bz[(j+2) * nx + i]) )*0.5;
449		}
450
451		j=ny-1;
452		for (i = 0; i <= nx-1; i++)
453		{
454	+	if isnan(bz[j * nx + i]) continue;
455		dery_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[(j-1) * nx + i]) - (-bz[(j-2) * nx + i]) )*0.5;
456		}
457
458
415	–	/*Just some print statements
416	–	for (i = 0; i < nx; i++)
417	–	{
418	–	for (j = 0; j < ny; j++)
419	–	{
420	–	printf("j=%d\n",j);
421	–	printf("i=%d\n",i);
422	–	printf("dery_bz[j*nx+i]=%f\n",dery_bz[j*nx+i]);
423	–	printf("derx_bz[j*nx+i]=%f\n",derx_bz[j*nx+i]);
424	–	printf("bz[j*nx+i]=%f\n",bz[j*nx+i]);
425	–	}
426	–	}
427	–	*/
428	–
459		for (i = 0; i <= nx-1; i++)
460		{
461		for (j = 0; j <= ny-1; j++)
462		{
463		// if ( (derx_bz[j * nx + i]-dery_bz[j * nx + i]) == 0) continue;
464	<	//if (mask[j * nx + i] != 90 ) continue;
465	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
464	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
465	>	if isnan(bz[j * nx + i]) continue;
466	>	//if isnan(bz_err[j * nx + i]) continue;
467	>	if isnan(derx_bz[j * nx + i]) continue;
468	>	if isnan(dery_bz[j * nx + i]) continue;
469		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 */
470	+	err += 2.0*bz_err[j * nx + i]*bz_err[j * nx + i];
471		count_mask++;
472		}
473		}
474
475		*mean_derivative_bz_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
476	+	*mean_derivative_bz_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
477	+	//printf("MEANGBZ=%f\n",*mean_derivative_bz_ptr);
478	+	//printf("MEANGBZ_err=%f\n",*mean_derivative_bz_err_ptr);
479	+
480		return 0;
481		}
482
483		/*===========================================*/
446	–
484		/* Example function 8:  Current Jz = (dBy/dx) - (dBx/dy) */
485
486		//  In discretized space like data pixels,
#	Line 460 | Line 497 | int computeBzderivative(float *bz, int *
497		//
498		//  To change units from Gauss/pixel to mA/m^2 (the units for Jz in Leka and Barnes, 2003),
499		//  one must perform the following unit conversions:
500	<	//  (Gauss/pix)(pix/arcsec)(arcsec/meter)(Newton/Gauss*Ampere*meter)(Ampere^2/Newton)(milliAmpere/Ampere), or
501	<	//  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(1 T / 10^4 Gauss)(1 / 4*PI*10^-7)( 10^3 milliAmpere/Ampere),
500	>	//  (Gauss)(1/arcsec)(arcsec/meter)(Newton/Gauss*Ampere*meter)(Ampere^2/Newton)(milliAmpere/Ampere), or
501	>	//  (Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(1 T / 10^4 Gauss)(1 / 4*PI*10^-7)( 10^3 milliAmpere/Ampere), or
502	>	//  (Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(1000.),
503		//  where a Tesla is represented as a Newton/Ampere*meter.
504	+	//
505		//  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS).
506		//  In that case, we would have the following:
507		//  (Gauss/pix)(1/0.5)(1/722500)(10^-4)(4*PI*10^7)(10^3), or
508		//  jz * (35.0)
509		//
510		//  The units of total unsigned vertical current (us_i) are simply in A. In this case, we would have the following:
511	<	//  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(1000.)
512	<	//  =(Gauss/pix)(1/CDELT1)(0.0010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(1000.)
474	<	//  =(Gauss/pix)(1/0.5)(10^-4)(4*PI*10^7)(722500)(1000.)
475	<	//  =(Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(1000.)
511	>	//  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(CDELT1)(CDELT1)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)
512	>	//  = (Gauss/pix)(0.00010)(1/MUNAUGHT)(CDELT1)(RSUN_REF/RSUN_OBS)
513
477	–	int computeJz(float *bx, float *by, int *dims, float *jz,
478	–	float *mean_jz_ptr, float *us_i_ptr, int *mask,
479	–	float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)
514
515	+	// Comment out random number generator, which can only run on solar3
516	+	//int computeJz(float *bx_err, float *by_err, float *bx, float *by, int *dims, float *jz, float *jz_err, float *jz_err_squared,
517	+	//            int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery, float *noisebx,
518	+	//              float *noiseby, float *noisebz)
519
520	+	int computeJz(float *bx_err, float *by_err, float *bx, float *by, int *dims, float *jz, float *jz_err, float *jz_err_squared,
521	+	int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)
522
483	–	{
484	–
485	–	int nx = dims[0], ny = dims[1];
486	–	int i, j, count_mask=0;
523
524	<	if (nx <= 0 || ny <= 0) return 1;
524	>	{
525	>	int nx = dims[0];
526	>	int ny = dims[1];
527	>	int i = 0;
528	>	int j = 0;
529	>	int count_mask = 0;
530
531	<	*mean_jz_ptr = 0.0;
491	<	float curl=0.0, us_i=0.0,test_perimeter=0.0,mean_curl=0.0;
492	<
531	>	if (nx <= 0 || ny <= 0) return 1;
532
533	+	/* Calculate the derivative*/
534		/* brute force method of calculating the derivative (no consideration for edges) */
535	+
536		for (i = 1; i <= nx-2; i++)
537		{
538		for (j = 0; j <= ny-1; j++)
539		{
540	+	if isnan(by[j * nx + i]) continue;
541		derx[j * nx + i] = (by[j * nx + i+1] - by[j * nx + i-1])*0.5;
542		}
543		}
544
503	–	/* brute force method of calculating the derivative (no consideration for edges) */
545		for (i = 0; i <= nx-1; i++)
546		{
547		for (j = 1; j <= ny-2; j++)
548		{
549	+	if isnan(bx[j * nx + i]) continue;
550		dery[j * nx + i] = (bx[(j+1) * nx + i] - bx[(j-1) * nx + i])*0.5;
551		}
552		}
553
554	<
513	<	/* consider the edges */
554	>	// consider the edges
555		i=0;
556		for (j = 0; j <= ny-1; j++)
557		{
558	+	if isnan(by[j * nx + i]) continue;
559		derx[j * nx + i] = ( (-3*by[j * nx + i]) + (4*by[j * nx + (i+1)]) - (by[j * nx + (i+2)]) )*0.5;
560		}
561
562		i=nx-1;
563		for (j = 0; j <= ny-1; j++)
564		{
565	+	if isnan(by[j * nx + i]) continue;
566		derx[j * nx + i] = ( (3*by[j * nx + i]) + (-4*by[j * nx + (i-1)]) - (-by[j * nx + (i-2)]) )*0.5;
567	<	}
567	>	}
568
569		j=0;
570		for (i = 0; i <= nx-1; i++)
571		{
572	+	if isnan(bx[j * nx + i]) continue;
573		dery[j * nx + i] = ( (-3*bx[j*nx + i]) + (4*bx[(j+1) * nx + i]) - (bx[(j+2) * nx + i]) )*0.5;
574		}
575
576		j=ny-1;
577	<	for (i = 0; i <= nx-1; i++)
577	>	for (i = 0; i <= nx-1; i++)
578		{
579	+	if isnan(bx[j * nx + i]) continue;
580		dery[j * nx + i] = ( (3*bx[j * nx + i]) + (-4*bx[(j-1) * nx + i]) - (-bx[(j-2) * nx + i]) )*0.5;
581		}
582
583	<	/* Just some print statements
584	<	for (i = 0; i < nx; i++)
585	<	{
586	<	for (j = 0; j < ny; j++)
587	<	{
543	<	printf("j=%d\n",j);
544	<	printf("i=%d\n",i);
545	<	printf("dery[j*nx+i]=%f\n",dery[j*nx+i]);
546	<	printf("derx[j*nx+i]=%f\n",derx[j*nx+i]);
547	<	printf("bx[j*nx+i]=%f\n",bx[j*nx+i]);
548	<	printf("by[j*nx+i]=%f\n",by[j*nx+i]);
549	<	}
550	<	}
551	<	*/
583	>	for (i = 1; i <= nx-2; i++)
584	>	{
585	>	for (j = 1; j <= ny-2; j++)
586	>	{
587	>	// calculate jz at all points
588
589	+	jz[j * nx + i]            = (derx[j * nx + i]-dery[j * nx + i]);       // jz is in units of Gauss/pix
590
591	+	// the next 7 lines can be used with a for loop that goes from i=0;i<=nx-1 and j=0;j<=ny-1.
592	+	//int i1, j1,i2, j2;
593	+	//i1 = i + 1 ; if (i1 >nx-1){i1=nx-1;}
594	+	//j1 = j + 1 ; if (j1 >ny-1){j1=ny-1;}
595	+	//i2 = i - 1; if (i2 < 0){i2 = 0;}
596	+	//j2 = j - 1; if (j2 < 0){i2 = 0;}
597	+	//jz_err[j * nx + i]        = 0.5*sqrt( (bx_err[j1 * nx + i]*bx_err[j1 * nx + i]) + (bx_err[j2 * nx + i]*bx_err[j2 * nx + i]) +
598	+	//                                     (by_err[j * nx + i1]*by_err[j * nx + i1]) + (by_err[j * nx + i2]*by_err[j * nx + i2]) ) ;
599	+
600	+	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]) +
601	+	(by_err[j * nx + (i+1)]*by_err[j * nx + (i+1)]) + (by_err[j * nx + (i-1)]*by_err[j * nx + (i-1)]) ) ;
602	+	jz_err_squared[j * nx + i]= (jz_err[j * nx + i]*jz_err[j * nx + i]);
603	+	count_mask++;
604	+
605	+	}
606	+	}
607	+	return 0;
608	+	}
609	+
610	+	/*===========================================*/
611	+
612	+
613	+	/* Example function 9:  Compute quantities on Jz array */
614	+	// Compute mean and total current on Jz array.
615	+
616	+	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,
617	+	float *mean_jz_ptr, float *mean_jz_err_ptr, float *us_i_ptr, float *us_i_err_ptr, int *mask, int *bitmask,
618	+	float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)
619	+
620	+	{
621	+
622	+	int nx = dims[0];
623	+	int ny = dims[1];
624	+	int i = 0;
625	+	int j = 0;
626	+	int count_mask = 0;
627	+	double curl = 0.0;
628	+	double us_i = 0.0;
629	+	double err = 0.0;
630	+
631	+	if (nx <= 0 || ny <= 0) return 1;
632	+
633	+	/* 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*/
634		for (i = 0; i <= nx-1; i++)
635		{
636		for (j = 0; j <= ny-1; j++)
637		{
638	<	// if ( (derx[j * nx + i]-dery[j * nx + i]) == 0) continue;
639	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
640	<	//if (mask[j * nx + i] != 90 ) continue;
641	<	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 */
642	<	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 */
643	<	jz[j * nx + i] = (derx[j * nx + i]-dery[j * nx + i]);                                                          /* jz is in units of Gauss/pix */
644	<
638	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
639	>	if isnan(derx[j * nx + i]) continue;
640	>	if isnan(dery[j * nx + i]) continue;
641	>	if isnan(jz[j * nx + i]) continue;
642	>	curl +=     (jz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.); /* curl is in units of mA / m^2 */
643	>	us_i += fabs(jz[j * nx + i])*(cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT);         /* us_i is in units of A */
644	>	err  += (jz_err[j * nx + i]*jz_err[j * nx + i]);
645		count_mask++;
646	<	}
646	>	}
647		}
648
649	<	mean_curl        = (curl/count_mask);
570	<	printf("mean_curl=%f\n",mean_curl);
571	<	printf("cdelt1, what is it?=%f\n",cdelt1);
649	>	/* Calculate mean vertical current density (mean_jz) and total unsigned vertical current (us_i) using smoothed Jz array and continue conditions above */
650		*mean_jz_ptr     = curl/(count_mask);        /* mean_jz gets populated as MEANJZD */
651	<	printf("count_mask=%d\n",count_mask);
652	<	*us_i_ptr        = (us_i);                   /* us_i gets populated as MEANJZD */
651	>	*mean_jz_err_ptr = (sqrt(err))*fabs(((rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.))/(count_mask)); // error in the quantity MEANJZD
652	>
653	>	*us_i_ptr        = (us_i);                   /* us_i gets populated as TOTUSJZ */
654	>	*us_i_err_ptr    = (sqrt(err))*fabs((cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT)); // error in the quantity TOTUSJZ
655	>
656	>	//printf("MEANJZD=%f\n",*mean_jz_ptr);
657	>	//printf("MEANJZD_err=%f\n",*mean_jz_err_ptr);
658	>
659	>	//printf("TOTUSJZ=%g\n",*us_i_ptr);
660	>	//printf("TOTUSJZ_err=%g\n",*us_i_err_ptr);
661	>
662		return 0;
663
664		}
665
579	–
666		/*===========================================*/
581	–	/* Example function 9:  Twist Parameter, alpha */
667
668	<	// The twist parameter, alpha, is defined as alpha = Jz/Bz and the units are in 1/Mm
668	>	/* Example function 10:  Twist Parameter, alpha */
669	>
670	>	// The twist parameter, alpha, is defined as alpha = Jz/Bz. In this case, the calculation
671	>	// for alpha is calculated in the following way (different from Leka and Barnes' approach):
672	>
673	>	// (sum of all positive Bz + abs(sum of all negative Bz)) = avg Bz
674	>	// (abs(sum of all Jz at positive Bz) + abs(sum of all Jz at negative Bz)) = avg Jz
675	>	// avg alpha = avg Jz / avg Bz
676	>
677	>	// The sign is assigned as follows:
678	>	// If the sum of all Bz is greater than 0, then evaluate the sum of Jz at the positive Bz pixels.
679	>	// If this value is > 0, then alpha is > 0.
680	>	// If this value is < 0, then alpha is <0.
681	>	//
682	>	// If the sum of all Bz is less than 0, then evaluate the sum of Jz at the negative Bz pixels.
683	>	// If this value is > 0, then alpha is < 0.
684	>	// If this value is < 0, then alpha is > 0.
685	>
686	>	// The units of alpha are in 1/Mm
687		// The units of Jz are in Gauss/pix; the units of Bz are in Gauss.
688		//
689		// Therefore, the units of Jz/Bz = (Gauss/pix)(1/Gauss)(pix/arcsec)(arsec/meter)(meter/Mm), or
690		//                               = (Gauss/pix)(1/Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(10^6)
691		//                               = 1/Mm
692
693	<	int computeAlpha(float *bz, int *dims, float *jz, float *mean_alpha_ptr, int *mask,
694	<	float cdelt1, double rsun_ref, double rsun_obs)
693	>	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)
694	>
695		{
696	<	int nx = dims[0], ny = dims[1];
697	<	int i, j, count_mask=0;
696	>	int nx = dims[0];
697	>	int ny = dims[1];
698	>	int i = 0;
699	>	int j = 0;
700	>	int count_mask = 0;
701	>	double a = 0.0;
702	>	double b = 0.0;
703	>	double c = 0.0;
704	>	double d = 0.0;
705	>	double sum1 = 0.0;
706	>	double sum2 = 0.0;
707	>	double sum3 = 0.0;
708	>	double sum4 = 0.0;
709	>	double sum = 0.0;
710	>	double sum5 = 0.0;
711	>	double sum6 = 0.0;
712	>	double sum_err = 0.0;
713
714		if (nx <= 0 || ny <= 0) return 1;
715
598	–	*mean_alpha_ptr = 0.0;
599	–	float aa, bb, cc, bznew, alpha2, sum=0.0;
600	–
716		for (i = 1; i < nx-1; i++)
717		{
718		for (j = 1; j < ny-1; j++)
719		{
720	<	//if (mask[j * nx + i] != 90 ) continue;
606	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
720	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
721		if isnan(jz[j * nx + i]) continue;
722		if isnan(bz[j * nx + i]) continue;
723	<	if (bz[j * nx + i] == 0.0) continue;
724	<	sum += (jz[j * nx + i] / bz[j * nx + i])*((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.)) ; /* the units for (jz/bz) are 1/Mm */
723	>	if (jz[j * nx + i]     == 0.0) continue;
724	>	if (bz_err[j * nx + i] == 0.0) continue;
725	>	if (bz[j * nx + i]     == 0.0) continue;
726	>	if (bz[j * nx + i] >  0) sum1 += ( bz[j * nx + i] ); a++;
727	>	if (bz[j * nx + i] <= 0) sum2 += ( bz[j * nx + i] ); b++;
728	>	if (bz[j * nx + i] >  0) sum3 += ( jz[j * nx + i] ); c++;
729	>	if (bz[j * nx + i] <= 0) sum4 += ( jz[j * nx + i] ); d++;
730	>	sum5    += bz[j * nx + i];
731	>	/* sum_err is a fractional uncertainty */
732	>	sum_err += sqrt(((jz_err[j * nx + i]*jz_err[j * nx + i])/(jz[j * nx + i]*jz[j * nx + i])) + ((bz_err[j * nx + i]*bz_err[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i]))) * fabs( ( (jz[j * nx + i]) / (bz[j * nx + i]) ) *(1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.));
733		count_mask++;
734		}
735		}
736	+
737	+	sum     = (((fabs(sum3))+(fabs(sum4)))/((fabs(sum2))+sum1))*((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.)); /* the units for (jz/bz) are 1/Mm */
738	+
739	+	/* Determine the sign of alpha */
740	+	if ((sum5 > 0) && (sum3 >  0)) sum=sum;
741	+	if ((sum5 > 0) && (sum3 <= 0)) sum=-sum;
742	+	if ((sum5 < 0) && (sum4 <= 0)) sum=sum;
743	+	if ((sum5 < 0) && (sum4 >  0)) sum=-sum;
744	+
745	+	*mean_alpha_ptr = sum; /* Units are 1/Mm */
746	+	*mean_alpha_err_ptr    = (sqrt(sum_err*sum_err)) / ((a+b+c+d)*100.0); // error in the quantity (sum)/(count_mask); factor of 100 comes from converting percent
747	+
748	+	//printf("MEANALP=%f\n",*mean_alpha_ptr);
749	+	//printf("MEANALP_err=%f\n",*mean_alpha_err_ptr);
750
615	–	printf("cdelt1=%f,rsun_ref=%f,rsun_obs=%f\n",cdelt1,rsun_ref,rsun_obs);
616	–	printf("count_mask=%d\n",count_mask);
617	–	printf("sum=%f\n",sum);
618	–	*mean_alpha_ptr = sum/count_mask; /* Units are 1/Mm */
751		return 0;
752		}
753
754		/*===========================================*/
755	<	/* Example function 10:  Helicity (mean current helicty, mean unsigned current helicity, and mean absolute current helicity) */
755	>	/* Example function 11:  Helicity (mean current helicty, total unsigned current helicity, absolute value of net current helicity) */
756
757		//  The current helicity is defined as Bz*Jz and the units are G^2 / m
758		//  The units of Jz are in G/pix; the units of Bz are in G.
759	<	//  Therefore, the units of Bz*Jz = (Gauss)*(Gauss/pix) = (Gauss^2/pix)(pix/arcsec)(arcsec/m)
759	>	//  Therefore, the units of Bz*Jz = (Gauss)*(Gauss/pix) = (Gauss^2/pix)(pix/arcsec)(arcsec/meter)
760		//                                                      = (Gauss^2/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)
761	<	//                                                      = G^2 / m.
630	<
761	>	//                                                      =  G^2 / m.
762
763	<	int computeHelicity(float *bz, int *dims, float *jz, float *mean_ih_ptr, float *total_us_ih_ptr,
764	<	float *total_abs_ih_ptr, int *mask, float cdelt1, double rsun_ref, double rsun_obs)
763	>	int computeHelicity(float *jz_err, float *jz_rms_err, float *bz_err, float *bz, int *dims, float *jz, float *mean_ih_ptr,
764	>	float *mean_ih_err_ptr, float *total_us_ih_ptr, float *total_abs_ih_ptr,
765	>	float *total_us_ih_err_ptr, float *total_abs_ih_err_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
766
767		{
768
769	<	int nx = dims[0], ny = dims[1];
770	<	int i, j, count_mask=0;
769	>	int nx = dims[0];
770	>	int ny = dims[1];
771	>	int i = 0;
772	>	int j = 0;
773	>	int count_mask = 0;
774	>	double sum = 0.0;
775	>	double sum2 = 0.0;
776	>	double sum_err = 0.0;
777
778		if (nx <= 0 || ny <= 0) return 1;
779
780	<	*mean_ih_ptr = 0.0;
643	<	float sum=0.0, sum2=0.0;
644	<
645	<	for (j = 0; j < ny; j++)
780	>	for (i = 0; i < nx; i++)
781		{
782	<	for (i = 0; i < nx; i++)
782	>	for (j = 0; j < ny; j++)
783		{
784	<	//if (mask[j * nx + i] != 90 ) continue;
785	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
786	<	if isnan(jz[j * nx + i]) continue;
787	<	if isnan(bz[j * nx + i]) continue;
788	<	if (bz[j * nx + i] == 0.0) continue;
789	<	if (jz[j * nx + i] == 0.0) continue;
790	<	sum  +=     (jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref);
791	<	sum2 += fabs(jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref);
792	<	count_mask++;
784	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
785	>	if isnan(jz[j * nx + i]) continue;
786	>	if isnan(bz[j * nx + i]) continue;
787	>	if (bz[j * nx + i] == 0.0) continue;
788	>	if (jz[j * nx + i] == 0.0) continue;
789	>	sum     +=     (jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to MEANJZH and ABSNJZH
790	>	sum2    += fabs(jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to TOTUSJH
791	>	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));
792	>	count_mask++;
793		}
794		}
795
796	<	printf("sum/count_mask=%f\n",sum/count_mask);
797	<	printf("(1/cdelt1)*(rsun_obs/rsun_ref)=%f\n",(1/cdelt1)*(rsun_obs/rsun_ref));
798	<	*mean_ih_ptr     = sum/count_mask; /* Units are G^2 / m ; keyword is MEANJZH */
799	<	*total_us_ih_ptr = sum2;           /* Units are G^2 / m */
800	<	*total_abs_ih_ptr= fabs(sum);      /* Units are G^2 / m */
796	>	*mean_ih_ptr          = sum/count_mask ; /* Units are G^2 / m ; keyword is MEANJZH */
797	>	*total_us_ih_ptr      = sum2           ; /* Units are G^2 / m ; keyword is TOTUSJH */
798	>	*total_abs_ih_ptr     = fabs(sum)      ; /* Units are G^2 / m ; keyword is ABSNJZH */
799	>
800	>	*mean_ih_err_ptr      = (sqrt(sum_err*sum_err)) / (count_mask*100.0)    ;  // error in the quantity MEANJZH
801	>	*total_us_ih_err_ptr  = (sqrt(sum_err*sum_err)) / (100.0)               ;  // error in the quantity TOTUSJH
802	>	*total_abs_ih_err_ptr = (sqrt(sum_err*sum_err)) / (100.0)               ;  // error in the quantity ABSNJZH
803	>
804	>	//printf("MEANJZH=%f\n",*mean_ih_ptr);
805	>	//printf("MEANJZH_err=%f\n",*mean_ih_err_ptr);
806	>
807	>	//printf("TOTUSJH=%f\n",*total_us_ih_ptr);
808	>	//printf("TOTUSJH_err=%f\n",*total_us_ih_err_ptr);
809	>
810	>	//printf("ABSNJZH=%f\n",*total_abs_ih_ptr);
811	>	//printf("ABSNJZH_err=%f\n",*total_abs_ih_err_ptr);
812
813		return 0;
814		}
815
816		/*===========================================*/
817	<	/* Example function 11:  Sum of Absolute Value per polarity  */
817	>	/* Example function 12:  Sum of Absolute Value per polarity  */
818
819		//  The Sum of the Absolute Value per polarity is defined as the following:
820		//  fabs(sum(jz gt 0)) + fabs(sum(jz lt 0)) and the units are in Amperes.
821		//  The units of jz are in G/pix. In this case, we would have the following:
822		//  Jz = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(RSUN_OBS/RSUN_REF),
823		//     = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)
824	+	//
825	+	//  The error in this quantity is the same as the error in the mean vertical current (mean_jz_err).
826
827	<	int computeSumAbsPerPolarity(float *bz, float *jz, int *dims, float *totaljzptr,
828	<	int *mask, float cdelt1, double rsun_ref, double rsun_obs)
827	>	int computeSumAbsPerPolarity(float *jz_err, float *bz_err, float *bz, float *jz, int *dims, float *totaljzptr, float *totaljz_err_ptr,
828	>	int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
829
830		{
831	<	int nx = dims[0], ny = dims[1];
832	<	int i, j, count_mask=0;
831	>	int nx = dims[0];
832	>	int ny = dims[1];
833	>	int i=0;
834	>	int j=0;
835	>	int count_mask=0;
836	>	double sum1=0.0;
837	>	double sum2=0.0;
838	>	double err=0.0;
839	>	*totaljzptr=0.0;
840
841		if (nx <= 0 || ny <= 0) return 1;
687	–
688	–	*totaljzptr=0.0;
689	–	float sum1=0.0, sum2=0.0;
842
843		for (i = 0; i < nx; i++)
844		{
845		for (j = 0; j < ny; j++)
846		{
847	<	//if (mask[j * nx + i] != 90 ) continue;
848	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
847	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
848	>	if isnan(bz[j * nx + i]) continue;
849		if (bz[j * nx + i] >  0) sum1 += ( jz[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);
850		if (bz[j * nx + i] <= 0) sum2 += ( jz[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);
851	+	err += (jz_err[j * nx + i]*jz_err[j * nx + i]);
852	+	count_mask++;
853		}
854		}
855
856	<	*totaljzptr = fabs(sum1) + fabs(sum2);  /* Units are A */
856	>	*totaljzptr    = fabs(sum1) + fabs(sum2);  /* Units are A */
857	>	*totaljz_err_ptr = sqrt(err)*(1/cdelt1)*fabs((0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs));
858	>	//printf("SAVNCPP=%g\n",*totaljzptr);
859	>	//printf("SAVNCPP_err=%g\n",*totaljz_err_ptr);
860	>
861		return 0;
862		}
863
864		/*===========================================*/
865	<	/* Example function 12:  Mean photospheric excess magnetic energy and total photospheric excess magnetic energy density */
865	>	/* Example function 13:  Mean photospheric excess magnetic energy and total photospheric excess magnetic energy density */
866		// The units for magnetic energy density in cgs are ergs per cubic centimeter. The formula B^2/8*PI integrated over all space, dV
867	<	// automatically yields erg per cubic centimeter for an input B in Gauss.
867	>	// automatically yields erg per cubic centimeter for an input B in Gauss. Note that the 8*PI can come out of the integral; thus,
868	>	// the integral is over B^2 dV and the 8*PI is divided at the end.
869		//
870		// Total magnetic energy is the magnetic energy density times dA, or the area, and the units are thus ergs/cm. To convert
871		// ergs per centimeter cubed to ergs per centimeter, simply multiply by the area per pixel in cm:
872	<	// erg/cm^3(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.)^2
873	<	// = erg/cm^3(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2
874	<	// = erg/cm^3(1.30501e15)
872	>	//   erg/cm^3*(CDELT1^2)*(RSUN_REF/RSUN_OBS ^2)*(100.^2)
873	>	// = erg/cm^3*(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2
874	>	// = erg/cm^3*(1.30501e15)
875		// = erg/cm(1/pix^2)
876
877	<	int computeFreeEnergy(float *bx, float *by, float *bpx, float *bpy, int *dims,
878	<	float *meanpotptr, float *totpotptr, int *mask,
877	>	int computeFreeEnergy(float *bx_err, float *by_err, float *bx, float *by, float *bpx, float *bpy, int *dims,
878	>	float *meanpotptr, float *meanpot_err_ptr, float *totpotptr, float *totpot_err_ptr, int *mask, int *bitmask,
879		float cdelt1, double rsun_ref, double rsun_obs)
880
881		{
882	<	int nx = dims[0], ny = dims[1];
883	<	int i, j, count_mask=0;
884	<
882	>	int nx = dims[0];
883	>	int ny = dims[1];
884	>	int i = 0;
885	>	int j = 0;
886	>	int count_mask = 0;
887	>	double sum = 0.0;
888	>	double sum1 = 0.0;
889	>	double err = 0.0;
890	>	*totpotptr = 0.0;
891	>	*meanpotptr = 0.0;
892	>
893		if (nx <= 0 || ny <= 0) return 1;
727	–
728	–	*totpotptr=0.0;
729	–	*meanpotptr=0.0;
730	–	float sum=0.0;
894
895		for (i = 0; i < nx; i++)
896		{
897		for (j = 0; j < ny; j++)
898		{
899	<	//if (mask[j * nx + i] != 90 ) continue;
900	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
901	<	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);
899	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
900	>	if isnan(bx[j * nx + i]) continue;
901	>	if isnan(by[j * nx + i]) continue;
902	>	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);
903	>	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])) );
904	>	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]);
905		count_mask++;
906		}
907		}
908
909	<	*meanpotptr = (sum)/(count_mask);              /* Units are ergs per cubic centimeter */
910	<	*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 */
909	>	*meanpotptr      = (sum1/(8.*PI)) / (count_mask);     /* Units are ergs per cubic centimeter */
910	>	*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)
911	>
912	>	/* Units of sum are ergs/cm^3, units of factor are cm^2/pix^2; therefore, units of totpotptr are ergs per centimeter */
913	>	*totpotptr       = (sum)/(8.*PI);
914	>	*totpot_err_ptr  = (sqrt(err))*fabs(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0*(1/(8.*PI)));
915	>
916	>	//printf("MEANPOT=%g\n",*meanpotptr);
917	>	//printf("MEANPOT_err=%g\n",*meanpot_err_ptr);
918	>
919	>	//printf("TOTPOT=%g\n",*totpotptr);
920	>	//printf("TOTPOT_err=%g\n",*totpot_err_ptr);
921	>
922		return 0;
923		}
924
925		/*===========================================*/
926	<	/* 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 */
926	>	/* 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 */
927
928	<	int computeShearAngle(float *bx, float *by, float *bz, float *bpx, float *bpy, float *bpz, int *dims,
929	<	float *meanshear_angleptr, float *area_w_shear_gt_45ptr,
753	<	float *meanshear_anglehptr, float *area_w_shear_gt_45hptr,
754	<	int *mask)
928	>	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,
929	>	float *meanshear_angleptr, float *meanshear_angle_err_ptr, float *area_w_shear_gt_45ptr, int *mask, int *bitmask)
930		{
931	<	int nx = dims[0], ny = dims[1];
932	<	int i, j;
931	>	int nx = dims[0];
932	>	int ny = dims[1];
933	>	int i = 0;
934	>	int j = 0;
935	>	int count_mask = 0;
936	>	double dotproduct = 0.0;
937	>	double magnitude_potential = 0.0;
938	>	double magnitude_vector = 0.0;
939	>	double shear_angle = 0.0;
940	>	double err = 0.0;
941	>	double sum = 0.0;
942	>	double count = 0.0;
943	>	*area_w_shear_gt_45ptr = 0.0;
944	>	*meanshear_angleptr = 0.0;
945
946		if (nx <= 0 || ny <= 0) return 1;
760	–
761	–	*area_w_shear_gt_45ptr=0.0;
762	–	*meanshear_angleptr=0.0;
763	–	float dotproduct, magnitude_potential, magnitude_vector, shear_angle=0.0, sum = 0.0, count=0.0, count_mask=0.0;
764	–	float dotproducth, magnitude_potentialh, magnitude_vectorh, shear_angleh=0.0, sum1 = 0.0, counth = 0.0;
947
948		for (i = 0; i < nx; i++)
949		{
950		for (j = 0; j < ny; j++)
951		{
952	<	//if (mask[j * nx + i] != 90 ) continue;
771	<	if ( (mask[j * nx + i] != 7) && (mask[j * nx + i] != 5) ) continue;
952	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
953		if isnan(bpx[j * nx + i]) continue;
954		if isnan(bpy[j * nx + i]) continue;
955		if isnan(bpz[j * nx + i]) continue;
956		if isnan(bz[j * nx + i]) continue;
957	+	if isnan(bx[j * nx + i]) continue;
958	+	if isnan(by[j * nx + i]) continue;
959		/* For mean 3D shear angle, area with shear greater than 45*/
960		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]);
961	<	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]));
962	<	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]) );
961	>	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]));
962	>	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]) );
963		shear_angle           = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);
964		count ++;
965		sum += shear_angle ;
966	+	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])));
967		if (shear_angle > 45) count_mask ++;
968		}
969		}
970
971		/* For mean 3D shear angle, area with shear greater than 45*/
972	<	*meanshear_angleptr = (sum)/(count);              /* Units are degrees */
973	<	printf("count_mask=%f\n",count_mask);
974	<	printf("count=%f\n",count);
975	<	*area_w_shear_gt_45ptr = (count_mask/(count))*(100.);  /* The area here is a fractional area -- the % of the total area */
972	>	*meanshear_angleptr = (sum)/(count);                 /* Units are degrees */
973	>	*meanshear_angle_err_ptr = (sqrt(err*err))/(count);  // error in the quantity (sum)/(count_mask)
974	>	*area_w_shear_gt_45ptr   = (count_mask/(count))*(100.0);/* The area here is a fractional area -- the % of the total area */
975	>
976	>	//printf("MEANSHR=%f\n",*meanshear_angleptr);
977	>	//printf("MEANSHR_err=%f\n",*meanshear_angle_err_ptr);
978
979		return 0;
980		}
#	Line 909 | Line 1095 | void greenpot(float *bx, float *by, floa
1095
1096
1097		/*===========END OF KEIJI'S CODE =========================*/
1098	+
1099	+	char *sw_functions_version() // Returns CVS version of sw_functions.c
1100	+	{
1101	+	return strdup("$Id$");
1102	+	}
1103	+
1104		/* ---------------- end of this file ----------------*/

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