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root/JSOC/proj/sharp/apps/sw_functions.c

Comparing proj/sharp/apps/sw_functions.c (file contents):
Revision 1.3 by mbobra, Tue Oct 23 18:42:56 2012 UTC vs.
Revision 1.21 by mbobra, Mon Nov 11 23:18:40 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 20 | Line 20
20
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.
23	>	coordinate bitmaps are interpolated for certain data (at the time of this CVS submit, all data
24	>	prior to 2013.08.21_17:24:00_TAI contain interpolated bitmaps; data post-2013.08.21_17:24:00_TAI
25	>	contain nearest-neighbor bitmaps).
26
27		In the CCD coordinates, this means that we are selecting the pixels that equal 90 in conf_disambig
28	<	and the pixels that equal 33 or 44 in bitmap. Here are the definitions of the pixel values:
28	>	and the pixels that equal 33 or 34 in bitmap. Here are the definitions of the pixel values:
29
30		For conf_disambig:
31		50 : not all solutions agree (weak field method applied)
#	Line 37 | Line 39
39		33 : weak field inside smooth bounding curve
40		34 : strong field inside smooth bounding curve
41
42	<	Written by Monica Bobra 15 August 2012
42	>	Written by Monica Bobra 15 August 2012
43		Potential Field code (appended) written by Keiji Hayashi
44	+	Error analysis modification 21 October 2013
45
46		===========================================*/
47		#include <math.h>
48	+	#include <mkl.h>
49
50	<	#define PI              (M_PI)
50	>	#define PI       (M_PI)
51		#define MUNAUGHT (0.0000012566370614) /* magnetic constant */
52
53		/*===========================================*/
#	Line 59 | Line 63
63		//  To convert G to G*cm^2, simply multiply by the number of square centimeters per pixel.
64		//  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS).
65		//  (Gauss/pix^2)(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.cm/m)^2
66	<	//  =(Gauss/pix^2)(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2
63	<	//  =(1.30501e15)Gauss*cm^2
66	>	//  =Gauss*cm^2
67
68	<	//  The disambig mask value selects only the pixels with values of 5 or 7 -- that is,
69	<	//  5: pixels for which the radial acute disambiguation solution was chosen
70	<	//  7: pixels for which the radial acute and NRWA disambiguation agree
68	<
69	<	int computeAbsFlux(float *bz, int *dims, float *absFlux,
70	<	float *mean_vf_ptr, int *mask,  int *bitmask,
71	<	float cdelt1, double rsun_ref, double rsun_obs)
68	>	int computeAbsFlux(float *bz_err, float *bz, int *dims, float *absFlux,
69	>	float *mean_vf_ptr, float *mean_vf_err_ptr, float *count_mask_ptr, int *mask,
70	>	int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
71
72		{
73
74	<	int nx = dims[0], ny = dims[1];
75	<	int i, j, count_mask=0;
76	<	double sum=0.0;
77	<
78	<	if (nx <= 0 || ny <= 0) return 1;
79	<
74	>	int nx = dims[0];
75	>	int ny = dims[1];
76	>	int i = 0;
77	>	int j = 0;
78	>	int count_mask = 0;
79	>	double sum = 0.0;
80	>	double err = 0.0;
81		*absFlux = 0.0;
82	<	*mean_vf_ptr =0.0;
82	>	*mean_vf_ptr = 0.0;
83	>
84	>
85	>	if (nx <= 0 || ny <= 0) return 1;
86
87	<	for (j = 0; j < ny; j++)
87	>	for (i = 0; i < nx; i++)
88		{
89	<	for (i = 0; i < nx; i++)
89	>	for (j = 0; j < ny; j++)
90		{
91		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
92	+	if isnan(bz[j * nx + i]) continue;
93		sum += (fabs(bz[j * nx + i]));
94	+	err += bz_err[j * nx + i]*bz_err[j * nx + i];
95		count_mask++;
96		}
97		}
98
99	<	printf("nx=%d,ny=%d,count_mask=%d,sum=%f\n",nx,ny,count_mask,sum);
100	<	printf("cdelt1=%f,rsun_ref=%f,rsun_obs=%f\n",cdelt1,rsun_ref,rsun_obs);
101	<	*mean_vf_ptr = sum*cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;
99	>	*mean_vf_ptr     = sum*cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0;
100	>	*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
101	>	*count_mask_ptr  = count_mask;
102		return 0;
103		}
104
105		/*===========================================*/
106	<	/* Example function 2: Calculate Bh in units of Gauss */
106	>	/* Example function 2: Calculate Bh, the horizontal field, in units of Gauss */
107		// Native units of Bh are Gauss
108
109	<	int computeBh(float *bx, float *by, float *bz, float *bh, int *dims,
109	>	int computeBh(float *bx_err, float *by_err, float *bh_err, float *bx, float *by, float *bz, float *bh, int *dims,
110		float *mean_hf_ptr, int *mask, int *bitmask)
111
112		{
113
114	<	int nx = dims[0], ny = dims[1];
115	<	int i, j, count_mask=0;
116	<	float sum=0.0;
117	<	*mean_hf_ptr =0.0;
114	>	int nx = dims[0];
115	>	int ny = dims[1];
116	>	int i = 0;
117	>	int j = 0;
118	>	int count_mask = 0;
119	>	double sum = 0.0;
120	>	*mean_hf_ptr = 0.0;
121
122		if (nx <= 0 || ny <= 0) return 1;
123
124	<	for (j = 0; j < ny; j++)
124	>	for (i = 0; i < nx; i++)
125		{
126	<	for (i = 0; i < nx; i++)
127	<	{
128	<	bh[j * nx + i] = sqrt( bx[j * nx + i]*bx[j * nx + i] + by[j * nx + i]*by[j * nx + i] );
129	<	sum += bh[j * nx + i];
130	<	count_mask++;
126	>	for (j = 0; j < ny; j++)
127	>	{
128	>	if isnan(bx[j * nx + i])
129	>	{
130	>	bh[j * nx + i] = NAN;
131	>	bh_err[j * nx + i] = NAN;
132	>	continue;
133	>	}
134	>	if isnan(by[j * nx + i])
135	>	{
136	>	bh[j * nx + i] = NAN;
137	>	bh_err[j * nx + i] = NAN;
138	>	continue;
139	>	}
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	+	//
156	+	// Error analysis calculations are done in radians (since derivatives are only true in units of radians),
157	+	// and multiplied by (180./PI) at the end for consistency in units.
158
159	<
160	<	int computeGamma(float *bx, float *by, float *bz, float *bh, int *dims,
137	<	float *mean_gamma_ptr, int *mask, int *bitmask)
159	>	int computeGamma(float *bz_err, float *bh_err, float *bx, float *by, float *bz, float *bh, int *dims,
160	>	float *mean_gamma_ptr, float *mean_gamma_err_ptr, int *mask, int *bitmask)
161		{
162	<	int nx = dims[0], ny = dims[1];
163	<	int i, j, count_mask=0;
162	>	int nx = dims[0];
163	>	int ny = dims[1];
164	>	int i = 0;
165	>	int j = 0;
166	>	int count_mask = 0;
167	>	double sum = 0.0;
168	>	double err = 0.0;
169	>	*mean_gamma_ptr = 0.0;
170
171		if (nx <= 0 || ny <= 0) return 1;
143	–
144	–	*mean_gamma_ptr=0.0;
145	–	float sum=0.0;
146	–	int count=0;
172
173		for (i = 0; i < nx; i++)
174		{
#	Line 152 | Line 177 | int computeGamma(float *bx, float *by, f
177		if (bh[j * nx + i] > 100)
178		{
179		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
180	<	sum += (atan (fabs( bz[j * nx + i] / bh[j * nx + i] ))* (180./PI));
181	<	count_mask++;
180	>	if isnan(bz[j * nx + i]) continue;
181	>	if isnan(bz_err[j * nx + i]) continue;
182	>	if isnan(bh_err[j * nx + i]) continue;
183	>	if isnan(bh[j * nx + i]) continue;
184	>	if (bz[j * nx + i] == 0) continue;
185	>	sum += fabs(atan(bh[j * nx + i]/fabs(bz[j * nx + i])))*(180./PI);
186	>	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])))) *
187	>	( ((bh_err[j * nx + i]*bh_err[j * nx + i])/(bz[j * nx + i]*bz[j * nx + i])) +
188	>	((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])) );
189	>	count_mask++;
190		}
191		}
192		}
193
194		*mean_gamma_ptr = sum/count_mask;
195	<	printf("*mean_gamma_ptr=%f\n",*mean_gamma_ptr);
195	>	*mean_gamma_err_ptr = (sqrt(err)/(count_mask))*(180./PI);
196	>	//printf("MEANGAM=%f\n",*mean_gamma_ptr);
197	>	//printf("MEANGAM_err=%f\n",*mean_gamma_err_ptr);
198		return 0;
199		}
200
#	Line 167 | Line 202 | int computeGamma(float *bx, float *by, f
202		/* Example function 4: Calculate B_Total*/
203		// Native units of B_Total are in gauss
204
205	<	int computeB_total(float *bx, float *by, float *bz, float *bt, int *dims, int *mask, int *bitmask)
205	>	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)
206		{
207
208	<	int nx = dims[0], ny = dims[1];
209	<	int i, j, count_mask=0;
208	>	int nx = dims[0];
209	>	int ny = dims[1];
210	>	int i = 0;
211	>	int j = 0;
212	>	int count_mask = 0;
213
214		if (nx <= 0 || ny <= 0) return 1;
215
#	Line 179 | Line 217 | int computeB_total(float *bx, float *by,
217		{
218		for (j = 0; j < ny; j++)
219		{
220	<	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]);
220	>	if isnan(bx[j * nx + i])
221	>	{
222	>	bt[j * nx + i] = NAN;
223	>	bt_err[j * nx + i] = NAN;
224	>	continue;
225	>	}
226	>	if isnan(by[j * nx + i])
227	>	{
228	>	bt[j * nx + i] = NAN;
229	>	bt_err[j * nx + i] = NAN;
230	>	continue;
231	>	}
232	>	if isnan(bz[j * nx + i])
233	>	{
234	>	bt[j * nx + i] = NAN;
235	>	bt_err[j * nx + i] = NAN;
236	>	continue;
237	>	}
238	>	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]);
239	>	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];
240		}
241		}
242		return 0;
#	Line 188 | Line 245 | int computeB_total(float *bx, float *by,
245		/*===========================================*/
246		/* Example function 5:  Derivative of B_Total SQRT( (dBt/dx)^2 + (dBt/dy)^2 ) */
247
248	<	int computeBtotalderivative(float *bt, int *dims, float *mean_derivative_btotal_ptr, int *mask, int *bitmask, float *derx_bt, float *dery_bt)
248	>	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)
249		{
250
251	<	int nx = dims[0], ny = dims[1];
252	<	int i, j, count_mask=0;
253	<
254	<	if (nx <= 0 || ny <= 0) return 1;
255	<
251	>	int nx = dims[0];
252	>	int ny = dims[1];
253	>	int i = 0;
254	>	int j = 0;
255	>	int count_mask = 0;
256	>	double sum = 0.0;
257	>	double err = 0.0;
258		*mean_derivative_btotal_ptr = 0.0;
200	–	float sum = 0.0;
259
260	+	if (nx <= 0 || ny <= 0) return 1;
261
262		/* brute force method of calculating the derivative (no consideration for edges) */
263		for (i = 1; i <= nx-2; i++)
#	Line 245 | Line 304 | int computeBtotalderivative(float *bt, i
304		}
305
306
307	<	/* Just some print statements
249	<	for (i = 0; i < nx; i++)
250	<	{
251	<	for (j = 0; j < ny; j++)
252	<	{
253	<	printf("j=%d\n",j);
254	<	printf("i=%d\n",i);
255	<	printf("dery_bt[j*nx+i]=%f\n",dery_bt[j*nx+i]);
256	<	printf("derx_bt[j*nx+i]=%f\n",derx_bt[j*nx+i]);
257	<	printf("bt[j*nx+i]=%f\n",bt[j*nx+i]);
258	<	}
259	<	}
260	<	*/
261	<
262	<	for (i = 0; i <= nx-1; i++)
307	>	for (i = 1; i <= nx-2; i++)
308		{
309	<	for (j = 0; j <= ny-1; j++)
309	>	for (j = 1; j <= ny-2; j++)
310		{
266	–	// if ( (derx_bt[j * nx + i]-dery_bt[j * nx + i]) == 0) continue;
311		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
312	+	if ( (derx_bt[j * nx + i] + dery_bt[j * nx + i]) == 0) continue;
313	+	if isnan(bt[j * nx + i])      continue;
314	+	if isnan(bt[(j+1) * nx + i])  continue;
315	+	if isnan(bt[(j-1) * nx + i])  continue;
316	+	if isnan(bt[j * nx + i-1])    continue;
317	+	if isnan(bt[j * nx + i+1])    continue;
318	+	if isnan(bt_err[j * nx + i])  continue;
319	+	if isnan(derx_bt[j * nx + i]) continue;
320	+	if isnan(dery_bt[j * nx + i]) continue;
321		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 */
322	+	err += (((bt[(j+1) * nx + i]-bt[(j-1) * nx + i])*(bt[(j+1) * nx + i]-bt[(j-1) * nx + i])) * (bt_err[(j+1) * nx + i]*bt_err[(j+1) * nx + i] + bt_err[(j-1) * nx + i]*bt_err[(j-1) * nx + i])) / (16.0*( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  ))+
323	+	(((bt[j * nx + (i+1)]-bt[j * nx + (i-1)])*(bt[j * nx + (i+1)]-bt[j * nx + (i-1)])) * (bt_err[j * nx + (i+1)]*bt_err[j * nx + (i+1)] + bt_err[j * nx + (i-1)]*bt_err[j * nx + (i-1)])) / (16.0*( derx_bt[j * nx + i]*derx_bt[j * nx + i]  + dery_bt[j * nx + i]*dery_bt[j * nx + i]  )) ;
324		count_mask++;
325		}
326		}
327
328	<	*mean_derivative_btotal_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
329	<	printf("*mean_derivative_btotal_ptr=%f\n",*mean_derivative_btotal_ptr);
328	>	*mean_derivative_btotal_ptr     = (sum)/(count_mask);
329	>	*mean_derivative_btotal_err_ptr = (sqrt(err))/(count_mask);
330	>	//printf("MEANGBT=%f\n",*mean_derivative_btotal_ptr);
331	>	//printf("MEANGBT_err=%f\n",*mean_derivative_btotal_err_ptr);
332	>
333		return 0;
334		}
335
#	Line 279 | Line 337 | int computeBtotalderivative(float *bt, i
337		/*===========================================*/
338		/* Example function 6:  Derivative of Bh SQRT( (dBh/dx)^2 + (dBh/dy)^2 ) */
339
340	<	int computeBhderivative(float *bh, int *dims, float *mean_derivative_bh_ptr, int *mask, int *bitmask, float *derx_bh, float *dery_bh)
340	>	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)
341		{
342
343	<	int nx = dims[0], ny = dims[1];
344	<	int i, j, count_mask=0;
343	>	int nx = dims[0];
344	>	int ny = dims[1];
345	>	int i = 0;
346	>	int j = 0;
347	>	int count_mask = 0;
348	>	double sum= 0.0;
349	>	double err =0.0;
350	>	*mean_derivative_bh_ptr = 0.0;
351
352		if (nx <= 0 || ny <= 0) return 1;
353
290	–	*mean_derivative_bh_ptr = 0.0;
291	–	float sum = 0.0;
292	–
354		/* brute force method of calculating the derivative (no consideration for edges) */
355		for (i = 1; i <= nx-2; i++)
356		{
#	Line 335 | Line 396 | int computeBhderivative(float *bh, int *
396		}
397
398
338	–	/*Just some print statements
339	–	for (i = 0; i < nx; i++)
340	–	{
341	–	for (j = 0; j < ny; j++)
342	–	{
343	–	printf("j=%d\n",j);
344	–	printf("i=%d\n",i);
345	–	printf("dery_bh[j*nx+i]=%f\n",dery_bh[j*nx+i]);
346	–	printf("derx_bh[j*nx+i]=%f\n",derx_bh[j*nx+i]);
347	–	printf("bh[j*nx+i]=%f\n",bh[j*nx+i]);
348	–	}
349	–	}
350	–	*/
351	–
399		for (i = 0; i <= nx-1; i++)
400		{
401		for (j = 0; j <= ny-1; j++)
402		{
356	–	// if ( (derx_bh[j * nx + i]-dery_bh[j * nx + i]) == 0) continue;
403		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
404	+	if ( (derx_bh[j * nx + i] + dery_bh[j * nx + i]) == 0) continue;
405	+	if isnan(bh[j * nx + i])      continue;
406	+	if isnan(bh[(j+1) * nx + i])  continue;
407	+	if isnan(bh[(j-1) * nx + i])  continue;
408	+	if isnan(bh[j * nx + i-1])    continue;
409	+	if isnan(bh[j * nx + i+1])    continue;
410	+	if isnan(bh_err[j * nx + i])  continue;
411	+	if isnan(derx_bh[j * nx + i]) continue;
412	+	if isnan(dery_bh[j * nx + i]) continue;
413		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 */
414	+	err += (((bh[(j+1) * nx + i]-bh[(j-1) * nx + i])*(bh[(j+1) * nx + i]-bh[(j-1) * nx + i])) * (bh_err[(j+1) * nx + i]*bh_err[(j+1) * nx + i] + bh_err[(j-1) * nx + i]*bh_err[(j-1) * nx + i])) / (16.0*( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  ))+
415	+	(((bh[j * nx + (i+1)]-bh[j * nx + (i-1)])*(bh[j * nx + (i+1)]-bh[j * nx + (i-1)])) * (bh_err[j * nx + (i+1)]*bh_err[j * nx + (i+1)] + bh_err[j * nx + (i-1)]*bh_err[j * nx + (i-1)])) / (16.0*( derx_bh[j * nx + i]*derx_bh[j * nx + i]  + dery_bh[j * nx + i]*dery_bh[j * nx + i]  )) ;
416		count_mask++;
417		}
418		}
419
420	<	*mean_derivative_bh_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
420	>	*mean_derivative_bh_ptr     = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
421	>	*mean_derivative_bh_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
422	>	//printf("MEANGBH=%f\n",*mean_derivative_bh_ptr);
423	>	//printf("MEANGBH_err=%f\n",*mean_derivative_bh_err_ptr);
424	>
425		return 0;
426		}
427
428		/*===========================================*/
429		/* Example function 7:  Derivative of B_vertical SQRT( (dBz/dx)^2 + (dBz/dy)^2 ) */
430
431	<	int computeBzderivative(float *bz, int *dims, float *mean_derivative_bz_ptr, int *mask, int *bitmask, float *derx_bz, float *dery_bz)
431	>	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)
432		{
433
434	<	int nx = dims[0], ny = dims[1];
435	<	int i, j, count_mask=0;
434	>	int nx = dims[0];
435	>	int ny = dims[1];
436	>	int i = 0;
437	>	int j = 0;
438	>	int count_mask = 0;
439	>	double sum = 0.0;
440	>	double err = 0.0;
441	>	*mean_derivative_bz_ptr = 0.0;
442
443		if (nx <= 0 || ny <= 0) return 1;
444
378	–	*mean_derivative_bz_ptr = 0.0;
379	–	float sum = 0.0;
380	–
445		/* brute force method of calculating the derivative (no consideration for edges) */
446		for (i = 1; i <= nx-2; i++)
447		{
448		for (j = 0; j <= ny-1; j++)
449		{
450	+	if isnan(bz[j * nx + i]) continue;
451		derx_bz[j * nx + i] = (bz[j * nx + i+1] - bz[j * nx + i-1])*0.5;
452		}
453		}
#	Line 392 | Line 457 | int computeBzderivative(float *bz, int *
457		{
458		for (j = 1; j <= ny-2; j++)
459		{
460	+	if isnan(bz[j * nx + i]) continue;
461		dery_bz[j * nx + i] = (bz[(j+1) * nx + i] - bz[(j-1) * nx + i])*0.5;
462		}
463		}
#	Line 401 | Line 467 | int computeBzderivative(float *bz, int *
467		i=0;
468		for (j = 0; j <= ny-1; j++)
469		{
470	+	if isnan(bz[j * nx + i]) continue;
471		derx_bz[j * nx + i] = ( (-3*bz[j * nx + i]) + (4*bz[j * nx + (i+1)]) - (bz[j * nx + (i+2)]) )*0.5;
472		}
473
474		i=nx-1;
475		for (j = 0; j <= ny-1; j++)
476		{
477	+	if isnan(bz[j * nx + i]) continue;
478		derx_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[j * nx + (i-1)]) - (-bz[j * nx + (i-2)]) )*0.5;
479		}
480
481		j=0;
482		for (i = 0; i <= nx-1; i++)
483		{
484	+	if isnan(bz[j * nx + i]) continue;
485		dery_bz[j * nx + i] = ( (-3*bz[j*nx + i]) + (4*bz[(j+1) * nx + i]) - (bz[(j+2) * nx + i]) )*0.5;
486		}
487
488		j=ny-1;
489		for (i = 0; i <= nx-1; i++)
490		{
491	+	if isnan(bz[j * nx + i]) continue;
492		dery_bz[j * nx + i] = ( (3*bz[j * nx + i]) + (-4*bz[(j-1) * nx + i]) - (-bz[(j-2) * nx + i]) )*0.5;
493		}
494
495
426	–	/*Just some print statements
427	–	for (i = 0; i < nx; i++)
428	–	{
429	–	for (j = 0; j < ny; j++)
430	–	{
431	–	printf("j=%d\n",j);
432	–	printf("i=%d\n",i);
433	–	printf("dery_bz[j*nx+i]=%f\n",dery_bz[j*nx+i]);
434	–	printf("derx_bz[j*nx+i]=%f\n",derx_bz[j*nx+i]);
435	–	printf("bz[j*nx+i]=%f\n",bz[j*nx+i]);
436	–	}
437	–	}
438	–	*/
439	–
496		for (i = 0; i <= nx-1; i++)
497		{
498		for (j = 0; j <= ny-1; j++)
499		{
444	–	// if ( (derx_bz[j * nx + i]-dery_bz[j * nx + i]) == 0) continue;
500		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
501	+	if ( (derx_bz[j * nx + i] + dery_bz[j * nx + i]) == 0) continue;
502	+	if isnan(bz[j * nx + i])      continue;
503	+	if isnan(bz[(j+1) * nx + i])  continue;
504	+	if isnan(bz[(j-1) * nx + i])  continue;
505	+	if isnan(bz[j * nx + i-1])    continue;
506	+	if isnan(bz[j * nx + i+1])    continue;
507	+	if isnan(bz_err[j * nx + i])  continue;
508	+	if isnan(derx_bz[j * nx + i]) continue;
509	+	if isnan(dery_bz[j * nx + i]) continue;
510		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 */
511	+	err += (((bz[(j+1) * nx + i]-bz[(j-1) * nx + i])*(bz[(j+1) * nx + i]-bz[(j-1) * nx + i])) * (bz_err[(j+1) * nx + i]*bz_err[(j+1) * nx + i] + bz_err[(j-1) * nx + i]*bz_err[(j-1) * nx + i])) /
512	+	(16.0*( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  )) +
513	+	(((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)])) /
514	+	(16.0*( derx_bz[j * nx + i]*derx_bz[j * nx + i]  + dery_bz[j * nx + i]*dery_bz[j * nx + i]  )) ;
515		count_mask++;
516		}
517		}
518
519		*mean_derivative_bz_ptr = (sum)/(count_mask); // would be divided by ((nx-2)*(ny-2)) if shape of count_mask = shape of magnetogram
520	+	*mean_derivative_bz_err_ptr = (sqrt(err))/(count_mask); // error in the quantity (sum)/(count_mask)
521	+	//printf("MEANGBZ=%f\n",*mean_derivative_bz_ptr);
522	+	//printf("MEANGBZ_err=%f\n",*mean_derivative_bz_err_ptr);
523	+
524		return 0;
525		}
526
527		/*===========================================*/
456	–
528		/* Example function 8:  Current Jz = (dBy/dx) - (dBx/dy) */
529
530		//  In discretized space like data pixels,
#	Line 470 | Line 541 | int computeBzderivative(float *bz, int *
541		//
542		//  To change units from Gauss/pixel to mA/m^2 (the units for Jz in Leka and Barnes, 2003),
543		//  one must perform the following unit conversions:
544	<	//  (Gauss/pix)(pix/arcsec)(arcsec/meter)(Newton/Gauss*Ampere*meter)(Ampere^2/Newton)(milliAmpere/Ampere), or
545	<	//  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(1 T / 10^4 Gauss)(1 / 4*PI*10^-7)( 10^3 milliAmpere/Ampere),
544	>	//  (Gauss)(1/arcsec)(arcsec/meter)(Newton/Gauss*Ampere*meter)(Ampere^2/Newton)(milliAmpere/Ampere), or
545	>	//  (Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(1 T / 10^4 Gauss)(1 / 4*PI*10^-7)( 10^3 milliAmpere/Ampere), or
546	>	//  (Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(1000.),
547		//  where a Tesla is represented as a Newton/Ampere*meter.
548	+	//
549		//  As an order of magnitude estimate, we can assign 0.5 to CDELT1 and 722500m/arcsec to (RSUN_REF/RSUN_OBS).
550		//  In that case, we would have the following:
551		//  (Gauss/pix)(1/0.5)(1/722500)(10^-4)(4*PI*10^7)(10^3), or
552		//  jz * (35.0)
553		//
554		//  The units of total unsigned vertical current (us_i) are simply in A. In this case, we would have the following:
555	<	//  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(1000.)
556	<	//  =(Gauss/pix)(1/CDELT1)(0.0010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(1000.)
484	<	//  =(Gauss/pix)(1/0.5)(10^-4)(4*PI*10^7)(722500)(1000.)
485	<	//  =(Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(1000.)
555	>	//  (Gauss/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)(0.00010)(1/MUNAUGHT)(CDELT1)(CDELT1)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)
556	>	//  = (Gauss/pix)(0.00010)(1/MUNAUGHT)(CDELT1)(RSUN_REF/RSUN_OBS)
557
487	–	int computeJz(float *bx, float *by, int *dims, float *jz,
488	–	float *mean_jz_ptr, float *us_i_ptr, int *mask, int *bitmask,
489	–	float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)
558
559	+	// Comment out random number generator, which can only run on solar3
560	+	//int computeJz(float *bx_err, float *by_err, float *bx, float *by, int *dims, float *jz, float *jz_err, float *jz_err_squared,
561	+	//            int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery, float *noisebx,
562	+	//              float *noiseby, float *noisebz)
563
564	+	int computeJz(float *bx_err, float *by_err, float *bx, float *by, int *dims, float *jz, float *jz_err, float *jz_err_squared,
565	+	int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)
566
493	–	{
567
568	<	int nx = dims[0], ny = dims[1];
569	<	int i, j, count_mask=0;
568	>	{
569	>	int nx = dims[0];
570	>	int ny = dims[1];
571	>	int i = 0;
572	>	int j = 0;
573	>	int count_mask = 0;
574
575	<	if (nx <= 0 || ny <= 0) return 1;
499	<
500	<	*mean_jz_ptr = 0.0;
501	<	float curl=0.0, us_i=0.0,test_perimeter=0.0,mean_curl=0.0;
502	<
575	>	if (nx <= 0 || ny <= 0) return 1;
576
577	+	/* Calculate the derivative*/
578		/* brute force method of calculating the derivative (no consideration for edges) */
579	+
580		for (i = 1; i <= nx-2; i++)
581		{
582		for (j = 0; j <= ny-1; j++)
583		{
584	+	if isnan(by[j * nx + i]) continue;
585		derx[j * nx + i] = (by[j * nx + i+1] - by[j * nx + i-1])*0.5;
586		}
587		}
588
513	–	/* brute force method of calculating the derivative (no consideration for edges) */
589		for (i = 0; i <= nx-1; i++)
590		{
591		for (j = 1; j <= ny-2; j++)
592		{
593	+	if isnan(bx[j * nx + i]) continue;
594		dery[j * nx + i] = (bx[(j+1) * nx + i] - bx[(j-1) * nx + i])*0.5;
595		}
596		}
597
598	<
523	<	/* consider the edges */
598	>	// consider the edges
599		i=0;
600		for (j = 0; j <= ny-1; j++)
601		{
602	+	if isnan(by[j * nx + i]) continue;
603		derx[j * nx + i] = ( (-3*by[j * nx + i]) + (4*by[j * nx + (i+1)]) - (by[j * nx + (i+2)]) )*0.5;
604		}
605
606		i=nx-1;
607		for (j = 0; j <= ny-1; j++)
608		{
609	+	if isnan(by[j * nx + i]) continue;
610		derx[j * nx + i] = ( (3*by[j * nx + i]) + (-4*by[j * nx + (i-1)]) - (-by[j * nx + (i-2)]) )*0.5;
611	<	}
611	>	}
612
613		j=0;
614		for (i = 0; i <= nx-1; i++)
615		{
616	+	if isnan(bx[j * nx + i]) continue;
617		dery[j * nx + i] = ( (-3*bx[j*nx + i]) + (4*bx[(j+1) * nx + i]) - (bx[(j+2) * nx + i]) )*0.5;
618		}
619
620		j=ny-1;
621	<	for (i = 0; i <= nx-1; i++)
621	>	for (i = 0; i <= nx-1; i++)
622		{
623	+	if isnan(bx[j * nx + i]) continue;
624		dery[j * nx + i] = ( (3*bx[j * nx + i]) + (-4*bx[(j-1) * nx + i]) - (-bx[(j-2) * nx + i]) )*0.5;
625		}
626
627	<	/* Just some print statements
628	<	for (i = 0; i < nx; i++)
629	<	{
630	<	for (j = 0; j < ny; j++)
631	<	{
632	<	printf("j=%d\n",j);
633	<	printf("i=%d\n",i);
634	<	printf("dery[j*nx+i]=%f\n",dery[j*nx+i]);
635	<	printf("derx[j*nx+i]=%f\n",derx[j*nx+i]);
636	<	printf("bx[j*nx+i]=%f\n",bx[j*nx+i]);
637	<	printf("by[j*nx+i]=%f\n",by[j*nx+i]);
638	<	}
639	<	}
640	<	*/
627	>	for (i = 1; i <= nx-2; i++)
628	>	{
629	>	for (j = 1; j <= ny-2; j++)
630	>	{
631	>	// calculate jz at all points
632	>
633	>	jz[j * nx + i]            = (derx[j * nx + i]-dery[j * nx + i]);       // jz is in units of Gauss/pix
634	>	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]) +
635	>	(by_err[j * nx + (i+1)]*by_err[j * nx + (i+1)]) + (by_err[j * nx + (i-1)]*by_err[j * nx + (i-1)]) ) ;
636	>	jz_err_squared[j * nx + i]= (jz_err[j * nx + i]*jz_err[j * nx + i]);
637	>	count_mask++;
638	>
639	>	}
640	>	}
641	>	return 0;
642	>	}
643	>
644	>	/*===========================================*/
645	>
646	>	/* Example function 9:  Compute quantities on Jz array */
647	>	// Compute mean and total current on Jz array.
648	>
649	>	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,
650	>	float *mean_jz_ptr, float *mean_jz_err_ptr, float *us_i_ptr, float *us_i_err_ptr, int *mask, int *bitmask,
651	>	float cdelt1, double rsun_ref, double rsun_obs,float *derx, float *dery)
652	>
653	>	{
654
655	+	int nx = dims[0];
656	+	int ny = dims[1];
657	+	int i = 0;
658	+	int j = 0;
659	+	int count_mask = 0;
660	+	double curl = 0.0;
661	+	double us_i = 0.0;
662	+	double err = 0.0;
663
664	+	if (nx <= 0 || ny <= 0) return 1;
665	+
666	+	/* 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*/
667		for (i = 0; i <= nx-1; i++)
668		{
669		for (j = 0; j <= ny-1; j++)
670		{
568	–	// if ( (derx[j * nx + i]-dery[j * nx + i]) == 0) continue;
671		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
672	<	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 */
673	<	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 */
674	<	jz[j * nx + i] = (derx[j * nx + i]-dery[j * nx + i]);                                                          /* jz is in units of Gauss/pix */
675	<
672	>	if isnan(derx[j * nx + i]) continue;
673	>	if isnan(dery[j * nx + i]) continue;
674	>	if isnan(jz[j * nx + i]) continue;
675	>	curl +=     (jz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.); /* curl is in units of mA / m^2 */
676	>	us_i += fabs(jz[j * nx + i])*(cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT);         /* us_i is in units of A */
677	>	err  += (jz_err[j * nx + i]*jz_err[j * nx + i]);
678		count_mask++;
679	<	}
679	>	}
680		}
681
682	<	mean_curl        = (curl/count_mask);
579	<	printf("mean_curl=%f\n",mean_curl);
580	<	printf("cdelt1, what is it?=%f\n",cdelt1);
682	>	/* Calculate mean vertical current density (mean_jz) and total unsigned vertical current (us_i) using smoothed Jz array and continue conditions above */
683		*mean_jz_ptr     = curl/(count_mask);        /* mean_jz gets populated as MEANJZD */
684	<	printf("count_mask=%d\n",count_mask);
685	<	*us_i_ptr        = (us_i);                   /* us_i gets populated as MEANJZD */
684	>	*mean_jz_err_ptr = (sqrt(err)/count_mask)*((1/cdelt1)*(rsun_obs/rsun_ref)*(0.00010)*(1/MUNAUGHT)*(1000.)); // error in the quantity MEANJZD
685	>
686	>	*us_i_ptr        = (us_i);                   /* us_i gets populated as TOTUSJZ */
687	>	*us_i_err_ptr    = (sqrt(err))*((cdelt1/1)*(rsun_ref/rsun_obs)*(0.00010)*(1/MUNAUGHT)); // error in the quantity TOTUSJZ
688	>
689	>	//printf("MEANJZD=%f\n",*mean_jz_ptr);
690	>	//printf("MEANJZD_err=%f\n",*mean_jz_err_ptr);
691	>
692	>	//printf("TOTUSJZ=%g\n",*us_i_ptr);
693	>	//printf("TOTUSJZ_err=%g\n",*us_i_err_ptr);
694	>
695		return 0;
696
697		}
698
588	–
699		/*===========================================*/
590	–	/* Example function 9:  Twist Parameter, alpha */
700
701	<	// The twist parameter, alpha, is defined as alpha = Jz/Bz and the units are in 1/Mm
701	>	/* Example function 10:  Twist Parameter, alpha */
702	>
703	>	// The twist parameter, alpha, is defined as alpha = Jz/Bz. In this case, the calculation
704	>	// for alpha is weighted by Bz (following Hagino et al., http://adsabs.harvard.edu/abs/2004PASJ...56..831H):
705	>
706	>	// numerator   = sum of all Jz*Bz
707	>	// denominator = sum of Bz*Bz
708	>	// alpha       = numerator/denominator
709	>
710	>	// The units of alpha are in 1/Mm
711		// The units of Jz are in Gauss/pix; the units of Bz are in Gauss.
712		//
713		// Therefore, the units of Jz/Bz = (Gauss/pix)(1/Gauss)(pix/arcsec)(arsec/meter)(meter/Mm), or
714		//                               = (Gauss/pix)(1/Gauss)(1/CDELT1)(RSUN_OBS/RSUN_REF)(10^6)
715		//                               = 1/Mm
716
717	<	int computeAlpha(float *bz, int *dims, float *jz, float *mean_alpha_ptr, int *mask, int *bitmask,
718	<	float cdelt1, double rsun_ref, double rsun_obs)
717	>	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)
718	>
719		{
720	<	int nx = dims[0], ny = dims[1];
721	<	int i, j, count_mask=0;
720	>	int nx                     = dims[0];
721	>	int ny                     = dims[1];
722	>	int i                      = 0;
723	>	int j                      = 0;
724	>	double alpha_total         = 0.0;
725	>	double C                   = ((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.));
726	>	double total               = 0.0;
727	>	double A                   = 0.0;
728	>	double B                   = 0.0;
729
730		if (nx <= 0 || ny <= 0) return 1;
731	<
732	<	*mean_alpha_ptr = 0.0;
733	<	float aa, bb, cc, bznew, alpha2, sum=0.0;
731	>	for (i = 1; i < nx-1; i++)
732	>	{
733	>	for (j = 1; j < ny-1; j++)
734	>	{
735	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
736	>	if isnan(jz[j * nx + i])   continue;
737	>	if isnan(bz[j * nx + i])   continue;
738	>	if (jz[j * nx + i] == 0.0) continue;
739	>	if (bz[j * nx + i] == 0.0) continue;
740	>	A += jz[j*nx+i]*bz[j*nx+i];
741	>	B += bz[j*nx+i]*bz[j*nx+i];
742	>	}
743	>	}
744
745		for (i = 1; i < nx-1; i++)
746		{
747		for (j = 1; j < ny-1; j++)
748		{
749		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
750	<	if isnan(jz[j * nx + i]) continue;
751	<	if isnan(bz[j * nx + i]) continue;
750	>	if isnan(jz[j * nx + i])   continue;
751	>	if isnan(bz[j * nx + i])   continue;
752	>	if (jz[j * nx + i] == 0.0) continue;
753		if (bz[j * nx + i] == 0.0) continue;
754	<	sum += (jz[j * nx + i] / bz[j * nx + i])*((1/cdelt1)*(rsun_obs/rsun_ref)*(1000000.)) ; /* the units for (jz/bz) are 1/Mm */
755	<	count_mask++;
620	<	}
754	>	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];
755	>	}
756		}
757
758	<	printf("cdelt1=%f,rsun_ref=%f,rsun_obs=%f\n",cdelt1,rsun_ref,rsun_obs);
759	<	printf("count_mask=%d\n",count_mask);
760	<	printf("sum=%f\n",sum);
761	<	*mean_alpha_ptr = sum/count_mask; /* Units are 1/Mm */
758	>	/* Determine the absolute value of alpha. The units for alpha are 1/Mm */
759	>	alpha_total              = ((A/B)*C);
760	>	*mean_alpha_ptr          = alpha_total;
761	>	*mean_alpha_err_ptr      = (C/B)*(sqrt(total));
762	>
763		return 0;
764		}
765
766		/*===========================================*/
767	<	/* Example function 10:  Helicity (mean current helicty, mean unsigned current helicity, and mean absolute current helicity) */
767	>	/* Example function 11:  Helicity (mean current helicty, total unsigned current helicity, absolute value of net current helicity) */
768
769		//  The current helicity is defined as Bz*Jz and the units are G^2 / m
770		//  The units of Jz are in G/pix; the units of Bz are in G.
771	<	//  Therefore, the units of Bz*Jz = (Gauss)*(Gauss/pix) = (Gauss^2/pix)(pix/arcsec)(arcsec/m)
771	>	//  Therefore, the units of Bz*Jz = (Gauss)*(Gauss/pix) = (Gauss^2/pix)(pix/arcsec)(arcsec/meter)
772		//                                                      = (Gauss^2/pix)(1/CDELT1)(RSUN_OBS/RSUN_REF)
773	<	//                                                      = G^2 / m.
773	>	//                                                      =  G^2 / m.
774
775	<
776	<	int computeHelicity(float *bz, int *dims, float *jz, float *mean_ih_ptr, float *total_us_ih_ptr,
777	<	float *total_abs_ih_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
775	>	int computeHelicity(float *jz_err, float *jz_rms_err, float *bz_err, float *bz, int *dims, float *jz, float *mean_ih_ptr,
776	>	float *mean_ih_err_ptr, float *total_us_ih_ptr, float *total_abs_ih_ptr,
777	>	float *total_us_ih_err_ptr, float *total_abs_ih_err_ptr, int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
778
779		{
780
781	<	int nx = dims[0], ny = dims[1];
782	<	int i, j, count_mask=0;
781	>	int nx         = dims[0];
782	>	int ny         = dims[1];
783	>	int i          = 0;
784	>	int j          = 0;
785	>	int count_mask = 0;
786	>	double sum     = 0.0;
787	>	double sum2    = 0.0;
788	>	double err     = 0.0;
789
790		if (nx <= 0 || ny <= 0) return 1;
791
792	<	*mean_ih_ptr = 0.0;
651	<	float sum=0.0, sum2=0.0;
652	<
653	<	for (j = 0; j < ny; j++)
792	>	for (i = 0; i < nx; i++)
793		{
794	<	for (i = 0; i < nx; i++)
794	>	for (j = 0; j < ny; j++)
795		{
796	<	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
797	<	if isnan(jz[j * nx + i]) continue;
798	<	if isnan(bz[j * nx + i]) continue;
799	<	if (bz[j * nx + i] == 0.0) continue;
800	<	if (jz[j * nx + i] == 0.0) continue;
801	<	sum  +=     (jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref);
802	<	sum2 += fabs(jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref);
803	<	count_mask++;
796	>	if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
797	>	if isnan(jz[j * nx + i])     continue;
798	>	if isnan(bz[j * nx + i])     continue;
799	>	if isnan(jz_err[j * nx + i]) continue;
800	>	if isnan(bz_err[j * nx + i]) continue;
801	>	if (bz[j * nx + i] == 0.0)   continue;
802	>	if (jz[j * nx + i] == 0.0)   continue;
803	>	sum     +=     (jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to MEANJZH and ABSNJZH
804	>	sum2    += fabs(jz[j * nx + i]*bz[j * nx + i])*(1/cdelt1)*(rsun_obs/rsun_ref); // contributes to TOTUSJH
805	>	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]);
806	>	count_mask++;
807		}
808		}
809
810	<	printf("sum/count_mask=%f\n",sum/count_mask);
811	<	printf("(1/cdelt1)*(rsun_obs/rsun_ref)=%f\n",(1/cdelt1)*(rsun_obs/rsun_ref));
812	<	*mean_ih_ptr     = sum/count_mask; /* Units are G^2 / m ; keyword is MEANJZH */
813	<	*total_us_ih_ptr = sum2;           /* Units are G^2 / m */
814	<	*total_abs_ih_ptr= fabs(sum);      /* Units are G^2 / m */
810	>	*mean_ih_ptr          = sum/count_mask ; /* Units are G^2 / m ; keyword is MEANJZH */
811	>	*total_us_ih_ptr      = sum2           ; /* Units are G^2 / m ; keyword is TOTUSJH */
812	>	*total_abs_ih_ptr     = fabs(sum)      ; /* Units are G^2 / m ; keyword is ABSNJZH */
813	>
814	>	*mean_ih_err_ptr      = (sqrt(err)/count_mask)*(1/cdelt1)*(rsun_obs/rsun_ref) ; // error in the quantity MEANJZH
815	>	*total_us_ih_err_ptr  = (sqrt(err))*(1/cdelt1)*(rsun_obs/rsun_ref) ;            // error in the quantity TOTUSJH
816	>	*total_abs_ih_err_ptr = (sqrt(err))*(1/cdelt1)*(rsun_obs/rsun_ref) ;            // error in the quantity ABSNJZH
817	>
818	>	//printf("MEANJZH=%f\n",*mean_ih_ptr);
819	>	//printf("MEANJZH_err=%f\n",*mean_ih_err_ptr);
820	>
821	>	//printf("TOTUSJH=%f\n",*total_us_ih_ptr);
822	>	//printf("TOTUSJH_err=%f\n",*total_us_ih_err_ptr);
823	>
824	>	//printf("ABSNJZH=%f\n",*total_abs_ih_ptr);
825	>	//printf("ABSNJZH_err=%f\n",*total_abs_ih_err_ptr);
826
827		return 0;
828		}
829
830		/*===========================================*/
831	<	/* Example function 11:  Sum of Absolute Value per polarity  */
831	>	/* Example function 12:  Sum of Absolute Value per polarity  */
832
833		//  The Sum of the Absolute Value per polarity is defined as the following:
834		//  fabs(sum(jz gt 0)) + fabs(sum(jz lt 0)) and the units are in Amperes.
835		//  The units of jz are in G/pix. In this case, we would have the following:
836		//  Jz = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)(RSUN_REF/RSUN_OBS)(RSUN_OBS/RSUN_REF),
837		//     = (Gauss/pix)(1/CDELT1)(0.00010)(1/MUNAUGHT)(RSUN_REF/RSUN_OBS)
838	+	//
839	+	//  The error in this quantity is the same as the error in the mean vertical current (mean_jz_err).
840
841	<	int computeSumAbsPerPolarity(float *bz, float *jz, int *dims, float *totaljzptr,
841	>	int computeSumAbsPerPolarity(float *jz_err, float *bz_err, float *bz, float *jz, int *dims, float *totaljzptr, float *totaljz_err_ptr,
842		int *mask, int *bitmask, float cdelt1, double rsun_ref, double rsun_obs)
843
844		{
845	<	int nx = dims[0], ny = dims[1];
846	<	int i, j, count_mask=0;
845	>	int nx = dims[0];
846	>	int ny = dims[1];
847	>	int i=0;
848	>	int j=0;
849	>	int count_mask=0;
850	>	double sum1=0.0;
851	>	double sum2=0.0;
852	>	double err=0.0;
853	>	*totaljzptr=0.0;
854
855		if (nx <= 0 || ny <= 0) return 1;
694	–
695	–	*totaljzptr=0.0;
696	–	float sum1=0.0, sum2=0.0;
856
857		for (i = 0; i < nx; i++)
858		{
859		for (j = 0; j < ny; j++)
860		{
861		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
862	+	if isnan(bz[j * nx + i]) continue;
863	+	if isnan(jz[j * nx + i]) continue;
864		if (bz[j * nx + i] >  0) sum1 += ( jz[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);
865		if (bz[j * nx + i] <= 0) sum2 += ( jz[j * nx + i])*(1/cdelt1)*(0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs);
866	+	err += (jz_err[j * nx + i]*jz_err[j * nx + i]);
867	+	count_mask++;
868		}
869		}
870
871	<	*totaljzptr = fabs(sum1) + fabs(sum2);  /* Units are A */
871	>	*totaljzptr    = fabs(sum1) + fabs(sum2);  /* Units are A */
872	>	*totaljz_err_ptr = sqrt(err)*(1/cdelt1)*fabs((0.00010)*(1/MUNAUGHT)*(rsun_ref/rsun_obs));
873	>	//printf("SAVNCPP=%g\n",*totaljzptr);
874	>	//printf("SAVNCPP_err=%g\n",*totaljz_err_ptr);
875	>
876		return 0;
877		}
878
879		/*===========================================*/
880	<	/* Example function 12:  Mean photospheric excess magnetic energy and total photospheric excess magnetic energy density */
880	>	/* Example function 13:  Mean photospheric excess magnetic energy and total photospheric excess magnetic energy density */
881		// The units for magnetic energy density in cgs are ergs per cubic centimeter. The formula B^2/8*PI integrated over all space, dV
882	<	// automatically yields erg per cubic centimeter for an input B in Gauss.
882	>	// automatically yields erg per cubic centimeter for an input B in Gauss. Note that the 8*PI can come out of the integral; thus,
883	>	// the integral is over B^2 dV and the 8*PI is divided at the end.
884		//
885		// Total magnetic energy is the magnetic energy density times dA, or the area, and the units are thus ergs/cm. To convert
886		// ergs per centimeter cubed to ergs per centimeter, simply multiply by the area per pixel in cm:
887	<	// erg/cm^3(CDELT1)^2(RSUN_REF/RSUN_OBS)^2(100.)^2
888	<	// = erg/cm^3(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2
889	<	// = erg/cm^3(1.30501e15)
887	>	//   erg/cm^3*(CDELT1^2)*(RSUN_REF/RSUN_OBS ^2)*(100.^2)
888	>	// = erg/cm^3*(0.5 arcsec/pix)^2(722500m/arcsec)^2(100cm/m)^2
889	>	// = erg/cm^3*(1.30501e15)
890		// = erg/cm(1/pix^2)
891
892	<	int computeFreeEnergy(float *bx, float *by, float *bpx, float *bpy, int *dims,
893	<	float *meanpotptr, float *totpotptr, int *mask, int *bitmask,
892	>	int computeFreeEnergy(float *bx_err, float *by_err, float *bx, float *by, float *bpx, float *bpy, int *dims,
893	>	float *meanpotptr, float *meanpot_err_ptr, float *totpotptr, float *totpot_err_ptr, int *mask, int *bitmask,
894		float cdelt1, double rsun_ref, double rsun_obs)
895
896		{
897	<	int nx = dims[0], ny = dims[1];
898	<	int i, j, count_mask=0;
899	<
897	>	int nx = dims[0];
898	>	int ny = dims[1];
899	>	int i = 0;
900	>	int j = 0;
901	>	int count_mask = 0;
902	>	double sum = 0.0;
903	>	double sum1 = 0.0;
904	>	double err = 0.0;
905	>	*totpotptr = 0.0;
906	>	*meanpotptr = 0.0;
907	>
908		if (nx <= 0 || ny <= 0) return 1;
733	–
734	–	*totpotptr=0.0;
735	–	*meanpotptr=0.0;
736	–	float sum=0.0;
909
910		for (i = 0; i < nx; i++)
911		{
912		for (j = 0; j < ny; j++)
913		{
914		if ( mask[j * nx + i] < 70 || bitmask[j * nx + i] < 30 ) continue;
915	<	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);
915	>	if isnan(bx[j * nx + i]) continue;
916	>	if isnan(by[j * nx + i]) continue;
917	>	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);
918	>	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])) );
919	>	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]) +
920	>	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]);
921		count_mask++;
922		}
923		}
924
925	<	*meanpotptr = (sum)/(count_mask);              /* Units are ergs per cubic centimeter */
926	<	*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 */
925	>	/* Units of meanpotptr are ergs per centimeter */
926	>	*meanpotptr      = (sum1) / (count_mask*8.*PI) ;     /* Units are ergs per cubic centimeter */
927	>	*meanpot_err_ptr = (sqrt(err)) / (count_mask*8.*PI); // error in the quantity (sum)/(count_mask)
928	>
929	>	/* Units of sum are ergs/cm^3, units of factor are cm^2/pix^2; therefore, units of totpotptr are ergs per centimeter */
930	>	*totpotptr       = (sum)/(8.*PI);
931	>	*totpot_err_ptr  = (sqrt(err))*fabs(cdelt1*cdelt1*(rsun_ref/rsun_obs)*(rsun_ref/rsun_obs)*100.0*100.0*(1/(8.*PI)));
932	>
933	>	//printf("MEANPOT=%g\n",*meanpotptr);
934	>	//printf("MEANPOT_err=%g\n",*meanpot_err_ptr);
935	>
936	>	//printf("TOTPOT=%g\n",*totpotptr);
937	>	//printf("TOTPOT_err=%g\n",*totpot_err_ptr);
938	>
939		return 0;
940		}
941
942		/*===========================================*/
943	<	/* 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 */
943	>	/* 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 */
944	>
945	>	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,
946	>	float *meanshear_angleptr, float *meanshear_angle_err_ptr, float *area_w_shear_gt_45ptr, int *mask, int *bitmask)
947	>
948
756	–	int computeShearAngle(float *bx, float *by, float *bz, float *bpx, float *bpy, float *bpz, int *dims,
757	–	float *meanshear_angleptr, float *area_w_shear_gt_45ptr,
758	–	float *meanshear_anglehptr, float *area_w_shear_gt_45hptr,
759	–	int *mask, int *bitmask)
949		{
950	<	int nx = dims[0], ny = dims[1];
951	<	int i, j;
950	>	int nx = dims[0];
951	>	int ny = dims[1];
952	>	int i = 0;
953	>	int j = 0;
954	>	float count_mask = 0;
955	>	float count = 0;
956	>	double dotproduct = 0.0;
957	>	double magnitude_potential = 0.0;
958	>	double magnitude_vector = 0.0;
959	>	double shear_angle = 0.0;
960	>	double denominator = 0.0;
961	>	double term1 = 0.0;
962	>	double term2 = 0.0;
963	>	double term3 = 0.0;
964	>	double sumsum = 0.0;
965	>	double err = 0.0;
966	>	double part1 = 0.0;
967	>	double part2 = 0.0;
968	>	double part3 = 0.0;
969	>	*area_w_shear_gt_45ptr = 0.0;
970	>	*meanshear_angleptr = 0.0;
971
972		if (nx <= 0 || ny <= 0) return 1;
765	–
766	–	*area_w_shear_gt_45ptr=0.0;
767	–	*meanshear_angleptr=0.0;
768	–	float dotproduct, magnitude_potential, magnitude_vector, shear_angle=0.0, sum = 0.0, count=0.0, count_mask=0.0;
769	–	float dotproducth, magnitude_potentialh, magnitude_vectorh, shear_angleh=0.0, sum1 = 0.0, counth = 0.0;
973
974		for (i = 0; i < nx; i++)
975		{
#	Line 777 | Line 980 | int computeShearAngle(float *bx, float *
980		if isnan(bpy[j * nx + i]) continue;
981		if isnan(bpz[j * nx + i]) continue;
982		if isnan(bz[j * nx + i]) continue;
983	<	/* For mean 3D shear angle, area with shear greater than 45*/
983	>	if isnan(bx[j * nx + i]) continue;
984	>	if isnan(by[j * nx + i]) continue;
985	>	if isnan(bx_err[j * nx + i]) continue;
986	>	if isnan(by_err[j * nx + i]) continue;
987	>	if isnan(bz_err[j * nx + i]) continue;
988	>
989	>	/* For mean 3D shear angle, percentage with shear greater than 45*/
990		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]);
991	<	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]));
992	<	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]) );
993	<	shear_angle           = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);
991	>	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]));
992	>	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]) );
993	>	//printf("dotproduct=%f\n",dotproduct);
994	>	//printf("magnitude_potential=%f\n",magnitude_potential);
995	>	//printf("magnitude_vector=%f\n",magnitude_vector);
996	>
997	>	shear_angle            = acos(dotproduct/(magnitude_potential*magnitude_vector))*(180./PI);
998	>	sumsum                  += shear_angle;
999	>	//printf("shear_angle=%f\n",shear_angle);
1000		count ++;
1001	<	sum += shear_angle ;
1001	>
1002		if (shear_angle > 45) count_mask ++;
1003	<	}
1004	<	}
1005	<
1003	>
1004	>	// For the error analysis
1005	>
1006	>	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];
1007	>	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];
1008	>	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];
1009	>
1010	>	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];
1011	>	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];
1012	>	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];
1013	>
1014	>	// denominator is squared
1015	>	denominator = part1*part1*part1*part2*(1.0-((part3*part3)/(part1*part2)));
1016	>
1017	>	err = (term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) +
1018	>	(term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) +
1019	>	(term1*term1*bx_err[j * nx + i]*bx_err[j * nx + i])/(denominator) ;
1020	>
1021	>	}
1022	>	}
1023		/* For mean 3D shear angle, area with shear greater than 45*/
1024	<	*meanshear_angleptr = (sum)/(count);              /* Units are degrees */
1025	<	printf("count_mask=%f\n",count_mask);
1026	<	printf("count=%f\n",count);
1027	<	*area_w_shear_gt_45ptr = (count_mask/(count))*(100.);  /* The area here is a fractional area -- the % of the total area */
1024	>	*meanshear_angleptr = (sumsum)/(count);                 /* Units are degrees */
1025	>	*meanshear_angle_err_ptr = (sqrt(err)/count_mask)*(180./PI);
1026	>
1027	>	/* The area here is a fractional area -- the % of the total area. This has no error associated with it. */
1028	>	*area_w_shear_gt_45ptr   = (count_mask/(count))*(100.0);
1029	>
1030	>	printf("MEANSHR=%f\n",*meanshear_angleptr);
1031	>	printf("MEANSHR_err=%f\n",*meanshear_angle_err_ptr);
1032	>	printf("SHRGT45=%f\n",*area_w_shear_gt_45ptr);
1033
1034		return 0;
1035		}
#	Line 913 | Line 1150 | void greenpot(float *bx, float *by, floa
1150
1151
1152		/*===========END OF KEIJI'S CODE =========================*/
1153	+
1154	+	char *sw_functions_version() // Returns CVS version of sw_functions.c
1155	+	{
1156	+	return strdup("$Id$");
1157	+	}
1158	+
1159		/* ---------------- end of this file ----------------*/

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