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-rw-r--r--src/geoptimiser.c1127
1 files changed, 684 insertions, 443 deletions
diff --git a/src/geoptimiser.c b/src/geoptimiser.c
index f311e9e9..46cfb887 100644
--- a/src/geoptimiser.c
+++ b/src/geoptimiser.c
@@ -284,7 +284,8 @@ static struct pattern_list *read_patterns_from_steam_file(const char *infile,
struct pattern **patterns_new;
patterns_new = realloc(pattern_list->patterns,
- (max_patterns+1024)*sizeof(struct pattern *));
+ (max_patterns+1024)*
+ sizeof(struct pattern *));
if ( patterns_new == NULL ) {
ERROR("Failed to allocate "
"memory for loaded patterns.\n");
@@ -299,7 +300,8 @@ static struct pattern_list *read_patterns_from_steam_file(const char *infile,
patn = malloc(sizeof(struct pattern));
if ( patn == NULL ) {
- ERROR("Failed to allocate memory for loaded patterns.\n");
+ ERROR("Failed to allocate memory for loaded "
+ "patterns.\n");
free(pattern_list->patterns);
free(pattern_list);
return NULL;
@@ -314,7 +316,7 @@ static struct pattern_list *read_patterns_from_steam_file(const char *infile,
avg_clen = compute_average_clen(det, &clen_from, &offset);
if ( avg_clen == -1 ) {
avg_clen = extract_f_from_stuff(clen_from,
- cur.stuff_from_stream)*1e-3;
+ cur.stuff_from_stream)*1e-3;
avg_clen += offset;
}
@@ -334,9 +336,11 @@ static struct pattern_list *read_patterns_from_steam_file(const char *infile,
cell = crystal_get_cell(cur.crystals[0]);
new_unit_cells = realloc(patn->unit_cells,
- (patn->n_unit_cells+1)*sizeof(UnitCell *));
+ (patn->n_unit_cells+1)*
+ sizeof(UnitCell *));
if ( new_unit_cells == NULL ) {
- ERROR("Failed to allocate memory for loaded patterns.\n");
+ ERROR("Failed to allocate memory for "
+ "loaded patterns.\n");
free(pattern_list->patterns);
free(pattern_list);
free(patn);
@@ -347,7 +351,8 @@ static struct pattern_list *read_patterns_from_steam_file(const char *infile,
patn->n_unit_cells++;
patn->unit_cells = new_unit_cells;
- crystal_reflist = crystal_get_reflections(cur.crystals[i]);
+ crystal_reflist = crystal_get_reflections(
+ cur.crystals[i]);
for ( refl = first_refl(crystal_reflist, &iter);
refl != NULL;
@@ -368,7 +373,8 @@ static struct pattern_list *read_patterns_from_steam_file(const char *infile,
pattern_list->n_patterns++;
if ( pattern_list->n_patterns%1000 == 0 ) {
- STATUS("Loaded %i indexed patterns from %i total patterns\n",
+ STATUS("Loaded %i indexed patterns from %i "
+ "total patterns\n",
pattern_list->n_patterns, ++n_chunks);
}
@@ -424,12 +430,13 @@ static void compute_avg_cell_parameters(struct pattern_list *pattern_list,
for ( cri=0; cri<ptn->n_unit_cells; cri++ ) {
- cell_get_parameters(ptn->unit_cells[cri], &cpar[0], // a
- &cpar[1], // b
- &cpar[2], // c
- &cpar[3], // alpha
- &cpar[4], // beta
- &cpar[5]); // gamma
+ cell_get_parameters(ptn->unit_cells[cri],
+ &cpar[0], // a
+ &cpar[1], // b
+ &cpar[2], // c
+ &cpar[3], // alpha
+ &cpar[4], // beta
+ &cpar[5]); // gamma
cpar[0] *= 1e9;
cpar[1] *= 1e9;
@@ -518,7 +525,8 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
int found = 0;
for ( i=0; i<num_clens; i++ ) {
- if ( fabs(pattern_list->patterns[cp]->clen-clens[i])<0.0001 ) {
+ if ( fabs(pattern_list->patterns[cp]->clen-clens[i])
+ <0.0001 ) {
clens_population[i]++;
lambdas[i] += pattern_list->patterns[cp]->lambda;
found = 1;
@@ -535,14 +543,14 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
double *lambdas_new;
clens_population_new = realloc(clens_population,
- (max_clens+1024)*sizeof(int));
+ (max_clens+1024)*sizeof(int));
clens_new = realloc(clens_population,
- (max_clens+1024)*sizeof(double));
+ (max_clens+1024)*sizeof(double));
lambdas_new = realloc(clens_population,
- (max_clens+1024)*sizeof(double));
+ (max_clens+1024)*sizeof(double));
- if ( clens_new == NULL || clens_population_new == NULL ||
- lambdas_new == NULL) {
+ if ( clens_new == NULL || clens_population_new == NULL
+ || lambdas_new == NULL) {
ERROR("Failed to allocate memory for "
"camera length list\n");
free(clens);
@@ -570,7 +578,8 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
}
if ( num_clens == 1 ) {
- STATUS("All patterns have the same camera length: %f\n", clens[0]);
+ STATUS("All patterns have the same camera length: %f\n",
+ clens[0]);
} else {
STATUS("%i different camera lengths were found for the input "
"patterns:\n", num_clens);
@@ -584,15 +593,17 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
irecistep = 1/cqu.u;
- min_braggp_dist = fmin(fmin(irecistep/avcp[0],irecistep/avcp[1]),
+ min_braggp_dist = fmin(fmin(irecistep/avcp[0],
+ irecistep/avcp[1]),
irecistep/avcp[2]);
STATUS("Camera length %0.4f was found %i times.\n"
- "Minimum inter-bragg peak distance (based on average cell "
- "parameters): %0.1f pixels\n",clens[i], clens_population[i],
+ "Minimum inter-bragg peak distance (based on "
+ "average cell parameters): %0.1f pixels\n",
+ clens[i], clens_population[i],
min_braggp_dist);
if ( min_braggp_dist<1.2*max_peak_distance ) {
- STATUS("WARNING: The distance between Bragg peaks is too "
- "small: "
+ STATUS("WARNING: The distance between Bragg "
+ "peaks is too small: "
"%0.1f < 1.2*%0.1f\n", min_braggp_dist,
max_peak_distance);
}
@@ -639,7 +650,8 @@ static double comp_median(double *arr, unsigned int n)
return arr[median] ;
}
- /* Find median of low, middle and high items; swap into position low */
+ // Find median of low, middle and high items; swap into position
+ // low
middle = (low + high) / 2;
if ( arr[middle]>arr[high] ) {
A = arr[middle];
@@ -657,12 +669,14 @@ static double comp_median(double *arr, unsigned int n)
arr[low] = A;
}
- /* Swap low item (now in position middle) into position (low+1) */
+ // Swap low item (now in position middle) into position
+ // (low+1)
A = arr[middle];
arr[middle] = arr[low+1];
arr[low+1] = A;
- /* Nibble from each end towards middle, swapping items when stuck */
+ // Nibble from each end towards middle, swapping items when
+ // stuck
ll = low + 1;
hh = high;
while (1) {
@@ -738,36 +752,150 @@ static void free_all_curr_pix_displ(struct single_pix_displ *all_pix_displ,
}
+static int fill_pixel_statistics(int *num_pix_displ,
+ struct single_pix_displ** curr_pix_displ,
+ struct single_pix_displ* all_pix_displ,
+ struct connected_data *conn_data,
+ int ifs, int iss, int di, int aw, int dfv,
+ double *displ_x,
+ double *displ_y, double *displ_abs)
+{
+ double *cPxAfs;
+ double *cPxAss;
+ int cnu = 0;
+
+ cPxAfs = calloc(num_pix_displ[ifs+aw*iss], sizeof(double));
+ if ( cPxAfs == NULL ) {
+ ERROR("Failed to allocate memory for pixel statistics.\n");
+ return 1;
+ }
+ cPxAss = calloc(num_pix_displ[ifs+aw*iss], sizeof(double));
+ if ( cPxAss == NULL ) {
+ ERROR("Failed to allocate memory for pixel statistics.\n");
+ free(cPxAfs);
+ return 1;
+ }
+
+ curr_pix_displ[ifs+aw*iss] = &all_pix_displ[ifs+aw*iss];
+
+ while (1) {
+ if (curr_pix_displ[ifs+aw*iss]->dfs == dfv) break;
+ cPxAfs[cnu] = curr_pix_displ[ifs+aw*iss]->dfs;
+ cPxAss[cnu] = curr_pix_displ[ifs+aw*iss]->dss;
+ cnu++;
+ if ( curr_pix_displ[ifs+aw*iss]->ne == NULL ) break;
+ curr_pix_displ[ifs+aw*iss] = curr_pix_displ[ifs+aw*iss]->ne;
+ }
+
+ if ( cnu < 1 ) return 0;
+
+ displ_x[ifs+aw*iss] = comp_median(cPxAfs, cnu);
+ displ_y[ifs+aw*iss] = comp_median(cPxAss, cnu);
+ displ_abs[ifs+aw*iss] = modulus2d(displ_x[ifs+aw*iss],
+ displ_y[ifs+aw*iss]);
+ conn_data[di].n_peaks_in_conn++;
+
+ free(cPxAfs);
+ free(cPxAss);
+
+ return 0;
+}
+
+
+
+static int compute_panel_statistics(struct rg_collection *connected,
+ int *num_pix_displ,
+ struct single_pix_displ** curr_pix_displ,
+ struct single_pix_displ* all_pix_displ,
+ struct connected_data *conn_data,
+ int di, int ip, int np,
+ double dfv,
+ int aw, double *displ_x,
+ double *displ_y, double *displ_abs)
+{
+ struct panel *p;
+ int ifs, iss;
+
+ p = connected->rigid_groups[di]->panels[ip];
+
+ for ( ifs=p->min_fs; ifs<p->max_fs+1; ifs++ ) {
+ for ( iss=p->min_ss; iss<p->max_ss+1; iss++ ) {
+ if ( num_pix_displ[ifs+aw*iss]>=np ) {
+
+ int ret;
+
+ ret = fill_pixel_statistics(num_pix_displ,
+ curr_pix_displ,
+ all_pix_displ,
+ conn_data,
+ ifs, iss, di, aw,
+ dfv, displ_x,
+ displ_y, displ_abs);
+
+ if ( ret == -2 ) {
+ break;
+ } else if ( ret != 0 ) {
+ return ret;
+ }
+
+ } else {
+ displ_x[ifs+aw*iss] = dfv;
+ displ_y[ifs+aw*iss] = dfv;
+ displ_abs[ifs+aw*iss] = dfv;
+ }
+
+ }
+ }
+ return 0;
+}
+
+
+
+static int allocate_next_element(struct single_pix_displ** curr_pix_displ,
+ int ipx)
+{
+ curr_pix_displ[ipx]->ne = malloc(sizeof(struct single_pix_displ));
+ if ( curr_pix_displ[ipx]->ne == NULL ) {
+ ERROR("Failed to allocate memory for pixel statistics.\n");
+ return 1;
+ }
+
+ curr_pix_displ[ipx] = curr_pix_displ[ipx]->ne;
+
+ return 0;
+}
+
+
static int compute_pixel_statistics(struct pattern_list *pattern_list,
- struct detector *det,
- struct rg_collection *connected,
- struct rg_collection *quadrants,
- int num_pix_in_slab,
- int max_peak_distance, int array_width,
- double default_fill_value,
- double min_num_peaks_per_pixel,
- double min_num_peaks_per_panel,
- int only_best_distance,
- double clen_to_use,
- double *slab_to_x, double *slab_to_y,
- struct connected_data *conn_data,
- double *displ_x,
- double *displ_y, double *displ_abs,
- struct single_pix_displ* all_pix_displ,
- struct single_pix_displ** curr_pix_displ,
- int *num_pix_displ)
+ struct detector *det,
+ struct rg_collection *connected,
+ struct rg_collection *quadrants,
+ int num_pix_in_slab,
+ int max_peak_distance, int aw,
+ double dfv,
+ double min_num_peaks_per_pixel,
+ double min_num_peaks_per_panel,
+ int only_best_distance,
+ double clen_to_use,
+ double *slab_to_x, double *slab_to_y,
+ struct connected_data *conn_data,
+ double *displ_x,
+ double *displ_y, double *displ_abs,
+ struct single_pix_displ* all_pix_displ,
+ struct single_pix_displ** curr_pix_displ,
+ int *num_pix_displ)
{
int ipx, cp, ich, di, ip, np;
for (di=0; di<connected->n_rigid_groups; di++) {
conn_data[di].num_quad = find_quad_for_connected(
- connected->rigid_groups[di],
- quadrants);
+ connected->rigid_groups[di],
+ quadrants);
conn_data[di].cang = 0.0;
conn_data[di].cstr = 1.0;
- conn_data[di].sh_x = default_fill_value;
- conn_data[di].sh_y = default_fill_value;
+ conn_data[di].sh_x = dfv;
+ conn_data[di].sh_y = dfv;
conn_data[di].num_peaks_per_pixel = 1;
conn_data[di].name = connected->rigid_groups[di]->name;
conn_data[di].n_peaks_in_conn = 0;
@@ -775,8 +903,8 @@ static int compute_pixel_statistics(struct pattern_list *pattern_list,
for ( ipx=0; ipx<num_pix_in_slab; ipx++ ) {
- all_pix_displ[ipx].dfs = default_fill_value;
- all_pix_displ[ipx].dss = default_fill_value;
+ all_pix_displ[ipx].dfs = dfv;
+ all_pix_displ[ipx].dss = dfv;
all_pix_displ[ipx].ne = NULL;
curr_pix_displ[ipx] = &all_pix_displ[ipx];
num_pix_displ[ipx] = 0;
@@ -787,7 +915,8 @@ static int compute_pixel_statistics(struct pattern_list *pattern_list,
ImageFeatureList *flist = pattern_list->patterns[cp]->im_list;
if ( only_best_distance ) {
- if ( fabs(pattern_list->patterns[cp]->clen-clen_to_use)>0.0001 ) {
+ if ( fabs(pattern_list->patterns[cp]->clen-clen_to_use) >
+ 0.0001 ) {
continue;
}
}
@@ -807,25 +936,25 @@ static int compute_pixel_statistics(struct pattern_list *pattern_list,
struct imagefeature *imfe = image_get_feature(flist, ich);
compute_x_y(det, imfe->fs, imfe->ss, &fx, &fy);
- refl = find_closest_reflection(rlist, fx, fy, det, &min_dist);
+ refl = find_closest_reflection(rlist, fx, fy, det,
+ &min_dist);
if ( refl == NULL ) continue;
- if ( min_dist<max_peak_distance ) {
+ if ( min_dist < max_peak_distance ) {
- int ipx = ((int)rint(imfe->fs) + array_width*
+ int ipx = ((int)rint(imfe->fs) + aw*
(int)rint(imfe->ss));
if ( num_pix_displ[ipx]>0 ) {
- curr_pix_displ[ipx]->ne = malloc(sizeof(
- struct single_pix_displ));
- if ( curr_pix_displ[ipx]->ne == NULL ) {
- ERROR("Failed to allocate memory for pixel "
- "statistics.\n");
- return 1;
- }
- curr_pix_displ[ipx] = curr_pix_displ[ipx]->ne;
+ int ret;
+
+ ret = allocate_next_element(curr_pix_displ,
+ ipx);
+
+ if ( ret != 0) return ret;
+
}
get_detector_pos(refl, &rfs, &rss);
@@ -845,78 +974,29 @@ static int compute_pixel_statistics(struct pattern_list *pattern_list,
continue;
}
- for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
+ for (ip=0; ip<connected->rigid_groups[di]->n_panels;
+ ip++) {
- struct panel *p;
- int ifs, iss;
+ int ret;
- p = connected->rigid_groups[di]->panels[ip];
+ ret = compute_panel_statistics(connected,
+ num_pix_displ,
+ curr_pix_displ,
+ all_pix_displ,
+ conn_data, di, ip,
+ np,
+ dfv,
+ aw,
+ displ_x,
+ displ_y,
+ displ_abs);
- for ( ifs=p->min_fs; ifs<p->max_fs+1; ifs++ ) {
- for ( iss=p->min_ss; iss<p->max_ss+1; iss++ ) {
- if ( num_pix_displ[ifs+array_width*iss]>=np ) {
-
- double *cPxAfs;
- double *cPxAss;
- int cnu = 0;
-
- cPxAfs = calloc(num_pix_displ[ifs+array_width*iss],
- sizeof(double));
- if ( cPxAfs == NULL ) {
- ERROR("Failed to allocate memory for "
- "pixel statistics.\n");
- return 1;
- }
- cPxAss = calloc(num_pix_displ[ifs+array_width*iss],
- sizeof(double));
- if ( cPxAss == NULL ) {
- ERROR("Failed to allocate memory for "
- "pixel statistics.\n");
- free(cPxAfs);
- return 1;
- }
-
- curr_pix_displ[ifs+array_width*iss] =
- &all_pix_displ[ifs+array_width*iss];
-
- while (1) {
- if (curr_pix_displ[ifs+array_width*iss]->dfs
- == default_fill_value) break;
- cPxAfs[cnu] =
- curr_pix_displ[ifs+array_width*iss]->dfs;
- cPxAss[cnu] =
- curr_pix_displ[ifs+array_width*iss]->dss;
- cnu++;
- if ( curr_pix_displ[ifs+array_width*iss]->ne ==
- NULL ) break;
- curr_pix_displ[ifs+array_width*iss] =
- curr_pix_displ[ifs+array_width*iss]->ne;
-
- }
-
- if ( cnu<1 ) continue;
-
- displ_x[ifs+array_width*iss] =
- comp_median(cPxAfs, cnu);
- displ_y[ifs+array_width*iss] =
- comp_median(cPxAss, cnu);
- displ_abs[ifs+array_width*iss] = modulus2d(
- displ_x[ifs+array_width*iss],
- displ_y[ifs+array_width*iss]);
- conn_data[di].n_peaks_in_conn++;
-
- free(cPxAfs);
- free(cPxAss);
-
- } else {
- displ_x[ifs+array_width*iss] = default_fill_value;
- displ_y[ifs+array_width*iss] = default_fill_value;
- displ_abs[ifs+array_width*iss] = default_fill_value;
- }
- }
- }
+ if ( ret !=0 ) return ret;
}
- if ( conn_data[di].n_peaks_in_conn>=min_num_peaks_per_panel ) {
+
+
+ if ( conn_data[di].n_peaks_in_conn >=
+ min_num_peaks_per_panel ) {
conn_data[di].num_peaks_per_pixel = np;
}
}
@@ -927,7 +1007,7 @@ static int compute_pixel_statistics(struct pattern_list *pattern_list,
static double compute_error(struct rg_collection *connected,
- int array_width,
+ int aw,
struct connected_data *conn_data,
int *num_pix_displ,
double *displ_abs)
@@ -949,13 +1029,13 @@ static double compute_error(struct rg_collection *connected,
for (ifs=p->min_fs; ifs<p->max_fs+1; ifs++) {
for (iss=p->min_ss; iss<p->max_ss+1; iss++) {
- if ( num_pix_displ[ifs+array_width*iss]>=
+ if ( num_pix_displ[ifs+aw*iss]>=
conn_data[di].num_peaks_per_pixel ) {
double cer;
- cer = displ_abs[ifs+array_width*iss]*
- displ_abs[ifs+array_width*iss];
+ cer = displ_abs[ifs+aw*iss]*
+ displ_abs[ifs+aw*iss];
connected_error += cer;
num_connected_error++;
total_error += cer;
@@ -987,7 +1067,7 @@ static double compute_error(struct rg_collection *connected,
}
-static void fill_coordinate_matrices(struct detector *det, int array_width,
+static void fill_coordinate_matrices(struct detector *det, int aw,
double *slab_to_x, double *slab_to_y)
{
int pi;
@@ -1006,8 +1086,8 @@ static void fill_coordinate_matrices(struct detector *det, int array_width,
compute_x_y(det, ifs, iss, &xs, &ys);
- slab_to_x[iss*array_width+ifs] = xs;
- slab_to_y[iss*array_width+ifs] = ys;
+ slab_to_x[iss*aw+ifs] = xs;
+ slab_to_y[iss*aw+ifs] = ys;
}
}
@@ -1070,14 +1150,19 @@ static int correct_empty_panels(struct rg_collection *quadrants,
if ( conn_data[di].n_peaks_in_conn<min_num_peaks_per_panel ) {
if (aver_num_ang[conn_data[di].num_quad]>0) {
- conn_data[di].cang = aver_ang[conn_data[di].num_quad];
- conn_data[di].cstr = aver_str[conn_data[di].num_quad];
- STATUS("Connected group %s has not enough peaks (%i). Using"
- " average angle: %0.4f\n", conn_data[di].name,
- conn_data[di].n_peaks_in_conn, conn_data[di].cang);
+ conn_data[di].cang =
+ aver_ang[conn_data[di].num_quad];
+ conn_data[di].cstr =
+ aver_str[conn_data[di].num_quad];
+ STATUS("Connected group %s has not enough peaks "
+ "(%i). Using average angle: %0.4f\n",
+ conn_data[di].name,
+ conn_data[di].n_peaks_in_conn,
+ conn_data[di].cang);
} else {
- STATUS("Connected group %s has not enough peaks (%i). Left "
- "unchanged\n", conn_data[di].name,
+ STATUS("Connected group %s has not enough peaks "
+ "(%i). Left unchanged\n",
+ conn_data[di].name,
conn_data[di].n_peaks_in_conn);
}
}
@@ -1109,15 +1194,19 @@ static void correct_angle_and_stretch(struct rg_collection *connected,
p = connected->rigid_groups[di]->panels[ip];
newx =
- p->fsx*cos(conn_data[di].cang)-p->fsy*sin(conn_data[di].cang);
+ p->fsx*cos(conn_data[di].cang)-
+ p->fsy*sin(conn_data[di].cang);
newy =
- p->fsx*sin(conn_data[di].cang)+p->fsy*cos(conn_data[di].cang);
+ p->fsx*sin(conn_data[di].cang)+
+ p->fsy*cos(conn_data[di].cang);
p->fsx = newx;
p->fsy = newy;
newx =
- p->ssx*cos(conn_data[di].cang)-p->ssy*sin(conn_data[di].cang);
+ p->ssx*cos(conn_data[di].cang)-
+ p->ssy*sin(conn_data[di].cang);
newy =
- p->ssx*sin(conn_data[di].cang)+p->ssy*cos(conn_data[di].cang);
+ p->ssx*sin(conn_data[di].cang)+
+ p->ssy*cos(conn_data[di].cang);
p->ssx = newx;
p->ssy = newy;
}
@@ -1142,7 +1231,8 @@ static void correct_angle_and_stretch(struct rg_collection *connected,
STATUS("Using individual distances for rigid panels\n");
for ( di=0; di<connected->n_rigid_groups; di++ ) {
- for ( ip=0; ip<connected->rigid_groups[di]->n_panels; ip++ ) {
+ for ( ip=0; ip<connected->rigid_groups[di]->n_panels;
+ ip++ ) {
struct panel *p;
@@ -1181,9 +1271,9 @@ static void shift_panels(struct rg_collection *connected,
p0 = connected->rigid_groups[di]->panels[0];
connected_panel_dist = modulus2d(
- p->cnx-p0->cnx/conn_data[di].cstr,
- p->cny-p0->cny/conn_data[di].cstr
- );
+ p->cnx-p0->cnx/conn_data[di].cstr,
+ p->cny-p0->cny/conn_data[di].cstr
+ );
p->cnx = p0->cnx + connected_panel_dist*p0->fsx;
p->cny = p0->cny + connected_panel_dist*p0->fsy;
@@ -1193,12 +1283,50 @@ static void shift_panels(struct rg_collection *connected,
}
+static void recompute_panel(struct connected_data *conn_data, int di, int ip,
+ struct rg_collection *connected,
+ double *slab_to_x,
+ double *slab_to_y,
+ double *recomputed_slab_to_x,
+ double *recomputed_slab_to_y,
+ double *displ_x, double *displ_y,
+ double stretch_coeff, int aw, int *num_pix_displ)
+{
+
+ double c_stretch;
+ struct panel *p;
+ int ifs, iss;
+
+ c_stretch = conn_data[di].cstr;
+
+ if ( fabs(c_stretch)<FLT_EPSILON ) c_stretch =
+ stretch_coeff;
+
+ p = connected->rigid_groups[di]->panels[ip];
+
+ for ( ifs=p->min_fs; ifs<p->max_fs+1; ifs++ ) {
+ for ( iss=p->min_ss; iss<p->max_ss+1; iss++ ) {
+ recomputed_slab_to_x[ifs+aw*iss] /= c_stretch;
+ recomputed_slab_to_y[ifs+aw*iss] /= c_stretch;
+ if ( num_pix_displ[ifs+aw*iss] >=
+ conn_data[di].num_peaks_per_pixel) {
+
+ displ_x[ifs+aw*iss] -= (slab_to_x[ifs+aw*iss]-
+ recomputed_slab_to_x[ifs+aw*iss]);
+ displ_y[ifs+aw*iss] -= (slab_to_y[ifs+aw*iss]-
+ recomputed_slab_to_y[ifs+aw*iss]);
+ }
+ }
+ }
+}
+
+
static void recompute_differences(struct rg_collection *connected,
double *slab_to_x, double *slab_to_y,
double *recomputed_slab_to_x,
double *recomputed_slab_to_y,
struct connected_data *conn_data,
- int stretch_coeff, int array_width,
+ double stretch_coeff, int aw,
double *displ_x, double *displ_y,
int *num_pix_displ)
{
@@ -1208,43 +1336,74 @@ static void recompute_differences(struct rg_collection *connected,
for ( di=0; di<connected->n_rigid_groups; di++ ) {
for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
- double c_stretch;
- struct panel *p;
- int ifs, iss;
- c_stretch = conn_data[di].cstr;
+ recompute_panel(conn_data, di, ip, connected,
+ slab_to_x, slab_to_y,
+ recomputed_slab_to_x,
+ recomputed_slab_to_y,
+ displ_x, displ_y,
+ stretch_coeff, aw, num_pix_displ);
+ }
+ }
+}
- if ( fabs(c_stretch)<FLT_EPSILON ) c_stretch = stretch_coeff;
- p = connected->rigid_groups[di]->panels[ip];
+static void fill_av_in_panel(struct rg_collection *connected, int di, int ip,
+ struct connected_data *conn_data,
+ int *num_pix_displ, int aw,
+ double *av_in_panel_fs,
+ double *av_in_panel_ss,
+ double *displ_x, double *displ_y)
+{
+ struct panel *p;
+ int ifs, iss;
- for ( ifs=p->min_fs; ifs<p->max_fs+1; ifs++ ) {
- for ( iss=p->min_ss; iss<p->max_ss+1; iss++ ) {
- recomputed_slab_to_x[ifs+array_width*iss] /= c_stretch;
- recomputed_slab_to_y[ifs+array_width*iss] /= c_stretch;
- if ( num_pix_displ[ifs+array_width*iss] >=
- conn_data[di].num_peaks_per_pixel) {
-
- displ_x[ifs+array_width*iss] -=
- (slab_to_x[ifs+array_width*iss]-
- recomputed_slab_to_x[ifs+array_width*iss]);
- displ_y[ifs+array_width*iss] -=
- (slab_to_y[ifs+array_width*iss]-
- recomputed_slab_to_y[ifs+array_width*iss]);
- }
- }
+ p = connected->rigid_groups[di]->panels[ip];
+
+ for ( ifs=p->min_fs; ifs<p->max_fs+1; ifs++ ) {
+ for ( iss=p->min_ss; iss<p->max_ss+1; iss++ ) {
+
+ if (num_pix_displ[ifs+aw*iss]>=
+ conn_data[di].num_peaks_per_pixel) {
+ av_in_panel_fs[conn_data[di].n_peaks_in_conn] =
+ displ_x[ifs+aw*iss];
+ av_in_panel_ss[conn_data[di].n_peaks_in_conn] =
+ displ_y[ifs+aw*iss];
+ conn_data[di].n_peaks_in_conn++;
}
}
}
}
+static void fill_con_data_sh(struct connected_data *conn_data,
+ double *av_in_panel_fs,
+ double *av_in_panel_ss, int di,
+ double max_peak_distance)
+{
+ conn_data[di].sh_x = comp_median(av_in_panel_fs,
+ conn_data[di].n_peaks_in_conn);
+ conn_data[di].sh_y = comp_median(av_in_panel_ss,
+ conn_data[di].n_peaks_in_conn);
+ STATUS("Panel %s, num pixels: %i, shifts X,Y: %0.8f, %0.8f\n",
+ conn_data[di].name, conn_data[di].n_peaks_in_conn,
+ conn_data[di].sh_x, conn_data[di].sh_y);
+ if ( modulus2d(conn_data[di].sh_x, conn_data[di].sh_y) >
+ 0.8*max_peak_distance ) {
+ STATUS(" WARNING: absolute shift is: %0.1f > 0.8*%0.1f. "
+ " Increase the value of the max_peak_distance parameter!\n",
+ modulus2d(conn_data[di].sh_x, conn_data[di].sh_y),
+ max_peak_distance);
+ }
+}
+
+
static int compute_shifts(struct rg_collection *connected,
struct connected_data *conn_data,
- int *num_pix_displ, int array_width,
+ int *num_pix_displ, int aw,
int min_num_peaks_per_panel,
- double default_fill_value, double max_peak_distance,
- double *displ_x, double *displ_y )
+ double dfv, double max_peak_distance,
+ double *displ_x, double *displ_y)
{
STATUS("Median for panels\n");
@@ -1281,45 +1440,21 @@ static int compute_shifts(struct rg_collection *connected,
for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
- struct panel *p;
- int ifs, iss;
-
- p = connected->rigid_groups[di]->panels[ip];
-
- for ( ifs=p->min_fs; ifs<p->max_fs+1; ifs++ ) {
- for ( iss=p->min_ss; iss<p->max_ss+1; iss++ ) {
+ fill_av_in_panel(connected, di, ip, conn_data,
+ num_pix_displ, aw, av_in_panel_fs,
+ av_in_panel_ss, displ_x, displ_y);
- if (num_pix_displ[ifs+array_width*iss]>=
- conn_data[di].num_peaks_per_pixel) {
- av_in_panel_fs[conn_data[di].n_peaks_in_conn] =
- displ_x[ifs+array_width*iss];
- av_in_panel_ss[conn_data[di].n_peaks_in_conn] =
- displ_y[ifs+array_width*iss];
- conn_data[di].n_peaks_in_conn++;
- }
- }
- }
}
if ( conn_data[di].n_peaks_in_conn>=min_num_peaks_per_panel ) {
- conn_data[di].sh_x =
- comp_median(av_in_panel_fs, conn_data[di].n_peaks_in_conn);
- conn_data[di].sh_y =
- comp_median(av_in_panel_ss, conn_data[di].n_peaks_in_conn);
- STATUS("Panel %s, num pixels: %i, shifts X,Y: %0.8f, %0.8f\n",
- conn_data[di].name, conn_data[di].n_peaks_in_conn,
- conn_data[di].sh_x, conn_data[di].sh_y);
- if ( modulus2d(conn_data[di].sh_x, conn_data[di].sh_y)>
- 0.8*max_peak_distance ) {
- STATUS(" WARNING: absolute shift is: %0.1f > 0.8*%0.1f. "
- "Increase the value of the max_peak_distance parameter!\n",
- modulus2d(conn_data[di].sh_x, conn_data[di].sh_y),
- max_peak_distance);
- }
+ fill_con_data_sh(conn_data, av_in_panel_fs,
+ av_in_panel_ss, di,
+ max_peak_distance);
+
} else {
- conn_data[di].sh_x = default_fill_value;
- conn_data[di].sh_y = default_fill_value;
+ conn_data[di].sh_x = dfv;
+ conn_data[di].sh_y = dfv;
}
free(av_in_panel_fs);
free(av_in_panel_ss);
@@ -1389,13 +1524,16 @@ static int compute_shifts_for_empty_panels(struct rg_collection *quadrants,
if ( num_aver[conn_data[di].num_quad]>0 ) {
conn_data[di].sh_x = aver_x[conn_data[di].num_quad];
conn_data[di].sh_y = aver_y[conn_data[di].num_quad];
- STATUS("Panel %s has not enough (%i) peaks. Using average "
- "shifts X,Y: %0.2f,%0.2f\n", conn_data[di].name,
+ STATUS("Panel %s has not enough (%i) peaks. "
+ "Using average shifts X,Y: %0.2f,%0.2f\n",
+ conn_data[di].name,
conn_data[di].n_peaks_in_conn,
conn_data[di].sh_x, conn_data[di].sh_y);
} else {
- STATUS("Panel %s has not enough (%i) peaks. Left unchanged\n",
- conn_data[di].name, conn_data[di].n_peaks_in_conn);
+ STATUS("Panel %s has not enough (%i) peaks. "
+ "Left unchanged.\n",
+ conn_data[di].name,
+ conn_data[di].n_peaks_in_conn);
}
}
}
@@ -1410,7 +1548,7 @@ static int compute_shifts_for_empty_panels(struct rg_collection *quadrants,
static void correct_shifts(struct rg_collection *connected,
struct connected_data *conn_data,
- double default_fill_value, double clen_to_use)
+ double dfv, double clen_to_use)
{
int di;
@@ -1423,8 +1561,8 @@ static void correct_shifts(struct rg_collection *connected,
p = connected->rigid_groups[di]->panels[ip];
- if ( conn_data[di].sh_x>default_fill_value+1.0 &&
- conn_data[di].sh_y > default_fill_value+1.0 ) {
+ if ( conn_data[di].sh_x>dfv+1.0 &&
+ conn_data[di].sh_y > dfv+1.0 ) {
p->cnx -= conn_data[di].sh_x;
p->cny -= conn_data[di].sh_y;
@@ -1438,15 +1576,176 @@ static void correct_shifts(struct rg_collection *connected,
}
-static int compute_angles_and_stretch
- (struct rg_collection *connected,
+static void a_s_counting_loop(int *num_pix_displ, int ifs, int iss,
+ int di, struct connected_data *conn_data,
+ int aw, double *slab_to_x,
+ double *slab_to_y, struct panel *p0,
+ struct panel *p1, double *displ_x,
+ double *displ_y, double minrad,
+ int *num_ang)
+{
+
+ double coX, coY, cdX, cdY;
+
+ if ( num_pix_displ[ifs+aw*iss]>=
+ conn_data[di].num_peaks_per_pixel ) {
+
+ int ifs1, iss1;
+ int max_fs1_tmp = p0->max_fs;
+ int max_ss1_tmp = p0->max_ss;
+
+ coX = slab_to_x[ifs+aw*iss];
+ coY = slab_to_y[ifs+aw*iss];
+ cdX = coX - displ_x[ifs+aw*iss];
+ cdY = coY - displ_y[ifs+aw*iss];
+
+ for (ifs1=ifs+1; ifs1<max_fs1_tmp+1; ifs1++) {
+
+ if ( ifs1 == max_fs1_tmp ) {
+ max_fs1_tmp = p1->max_fs;
+ }
+
+ for (iss1=iss+1; iss1<max_ss1_tmp+1; iss1++) {
+
+ if ( iss1 == max_ss1_tmp ) {
+ max_ss1_tmp = p1->max_ss;
+ }
+
+ if ( num_pix_displ[ifs1+aw*iss1]>=
+ conn_data[di].num_peaks_per_pixel ) {
+
+ double dist;
+ double coX1, coY1, cdX1, cdY1;
+ double len1, len2;
+
+ dist = modulus2d(ifs-ifs1,iss-iss1);
+ if ( dist < minrad ) continue;
+ coX1 = slab_to_x[ifs1+aw*iss1];
+ coY1 = slab_to_y[ifs1+aw*iss1];
+ cdX1 =
+ coX1 - displ_x[ifs1+aw*iss1];
+ cdY1 =
+ coY1 - displ_y[ifs1+aw*iss1];
+
+ len1 = modulus2d(coX1-coX, coY1-coY);
+ len2 = modulus2d(cdX1-cdX, cdY1-cdY);
+ if ( len1<FLT_EPSILON ||
+ len2<FLT_EPSILON ) {
+ continue;
+ }
+
+ *num_ang = *num_ang+1;
+ }
+ }
+ }
+ }
+}
+
+
+static int a_s_processing_loop(int *num_pix_displ, int ifs, int iss,
+ int di, struct connected_data *conn_data,
+ int aw, double *slab_to_x,
+ double *slab_to_y, struct panel *p0,
+ struct panel *p1, double *displ_x,
+ double *displ_y, double minrad,
+ int max_num_ang, int *num_ang,
+ double *angles, double *stretches)
+{
+ double coX, coY, cdX, cdY;
+
+ if ( num_pix_displ[ifs+aw*iss]>=
+ conn_data[di].num_peaks_per_pixel ) {
+
+ int ifs1, iss1;
+ int max_fs1_tmp = p0->max_fs;
+ int max_ss1_tmp = p0->max_ss;
+
+ if ( *num_ang>=max_num_ang ) return -2;
+
+ coX = slab_to_x[ifs+aw*iss];
+ coY = slab_to_y[ifs+aw*iss];
+ cdX = coX - displ_x[ifs+aw*iss];
+ cdY = coY - displ_y[ifs+aw*iss];
+
+ for (ifs1=ifs+1; ifs1<max_fs1_tmp+1; ifs1++) {
+
+ if ( ifs1 == max_fs1_tmp ) {
+ max_fs1_tmp = p1->max_fs;
+ }
+
+ for (iss1=iss+1; iss1<max_ss1_tmp+1; iss1++) {
+
+ if ( iss1 == max_ss1_tmp ) {
+ max_ss1_tmp = p1->max_ss;
+ }
+
+ if ( num_pix_displ[ifs1+aw*iss1]>=
+ conn_data[di].num_peaks_per_pixel ) {
+
+ double dist;
+ double coX1, coY1, cdX1, cdY1;
+ double len1, len2;
+ double scalM;
+ double multlen;
+
+ if ( *num_ang>=max_num_ang ) return -2;
+ dist = modulus2d(ifs-ifs1,iss-iss1);
+ if (dist<minrad) return 0;
+ coX1 = slab_to_x[ifs1+aw*iss1];
+ coY1 = slab_to_y[ifs1+aw*iss1];
+ cdX1 =
+ coX1 - displ_x[ifs1+aw*iss1];
+ cdY1 =
+ coY1 - displ_y[ifs1+aw*iss1];
+
+ len1 = modulus2d(coX1-coX, coY1-coY);
+ len2 = modulus2d(cdX1-cdX, cdY1-cdY);
+ scalM = (coX1-coX)*(cdX1-cdX)+
+ (coY1-coY)*(cdY1-cdY)-
+ FLT_EPSILON;
+ if ( len1<FLT_EPSILON ||
+ len2<FLT_EPSILON ) {
+ return 0;
+ }
+
+ multlen = len1*len2;
+ if ( fabs(scalM)>=multlen ) {
+ angles[*num_ang] = 0.0;
+ } else {
+
+ angles[*num_ang] = 1.0;
+
+ angles[*num_ang] =
+ acos(scalM/multlen);
+
+ if ((coY1-coY)*(cdX1-cdX)-
+ (coX1-coX)*(cdY1-cdY) < 0) {
+ angles[*num_ang] *= -1.;
+ }
+
+ }
+
+ stretches[*num_ang] = len1/len2;
+
+ *num_ang = *num_ang+1;
+ }
+ }
+ }
+ }
+ return 0;
+}
+
+
+
+
+static int compute_angles_and_stretch(struct rg_collection *connected,
struct connected_data *conn_data,
int *num_pix_displ,
double *slab_to_x,
double *slab_to_y,
double *displ_x,
double *displ_y,
- int array_width,
+ int aw,
int min_num_peaks_per_panel,
double dist_coeff_ang_str,
int num_peaks_per_pixel,
@@ -1461,18 +1760,21 @@ static int compute_angles_and_stretch
csaa = malloc(sizeof(struct connected_stretch_and_angles));
if ( csaa == NULL ) {
- ERROR("Failed to allocate memory to compute angles and stretch.\n");
+ ERROR("Failed to allocate memory to compute angles and "
+ "stretch.\n");
return 1;
}
csaa->stretch_coeff = malloc(connected->n_rigid_groups*sizeof(double));
if ( csaa->stretch_coeff == NULL ) {
- ERROR("Failed to allocate memory to compute angles and stretch.\n");
+ ERROR("Failed to allocate memory to compute angles and "
+ "stretch.\n");
free(csaa);
return 1;
}
csaa->num_angles = malloc(connected->n_rigid_groups*sizeof(unsigned int));
if ( csaa->num_angles == NULL ) {
- ERROR("Failed to allocate memory to compute angles and stretch.\n");
+ ERROR("Failed to allocate memory to compute angles and "
+ "stretch.\n");
free(csaa->stretch_coeff);
free(csaa);
return 1;
@@ -1481,7 +1783,9 @@ static int compute_angles_and_stretch
csaa->num_coeff=0;
for ( di=0; di<connected->n_rigid_groups; di++ ) {
- if ( conn_data[di].n_peaks_in_conn<min_num_peaks_per_panel ) continue;
+ if ( conn_data[di].n_peaks_in_conn<min_num_peaks_per_panel ) {
+ continue;
+ }
unsigned int max_num_ang = 0;
@@ -1509,9 +1813,11 @@ static int compute_angles_and_stretch
struct panel *p0 = connected->rigid_groups[di]->panels[ip0];
- for ( ip1=0; ip1<connected->rigid_groups[di]->n_panels; ip1++ ) {
+ for ( ip1=0; ip1<connected->rigid_groups[di]->n_panels;
+ ip1++ ) {
- struct panel *p1 = connected->rigid_groups [di]->panels[ip1];
+ struct panel *p1 =
+ connected->rigid_groups [di]->panels[ip1];
int ifs, iss;
int min_fs_tmp = p0->min_fs;
@@ -1526,67 +1832,21 @@ static int compute_angles_and_stretch
max_fs_tmp = p1->max_fs;
}
- for (iss=min_ss_tmp; iss<max_ss_tmp+1; iss++) {
+ for (iss=min_ss_tmp; iss<max_ss_tmp+1;
+ iss++) {
if ( iss == max_ss_tmp ) {
min_ss_tmp = p1->min_ss;
max_ss_tmp = p1->max_ss;
}
- double coX, coY, cdX, cdY;
-
- if ( num_pix_displ[ifs+array_width*iss]>=
- conn_data[di].num_peaks_per_pixel ) {
-
- int ifs1, iss1;
- int max_fs1_tmp = p0->max_fs;
- int max_ss1_tmp = p0->max_ss;
-
- coX = slab_to_x[ifs+array_width*iss];
- coY = slab_to_y[ifs+array_width*iss];
- cdX = coX - displ_x[ifs+array_width*iss];
- cdY = coY - displ_y[ifs+array_width*iss];
+ a_s_counting_loop(num_pix_displ,
+ ifs, iss, di, conn_data,
+ aw, slab_to_x, slab_to_y,
+ p0, p1, displ_x,
+ displ_y, minrad,
+ &num_ang);
- for (ifs1=ifs+1; ifs1<max_fs1_tmp+1; ifs1++) {
-
- if ( ifs1 == max_fs1_tmp ) {
- max_fs1_tmp = p1->max_fs;
- }
-
- for (iss1=iss+1; iss1<max_ss1_tmp+1; iss1++) {
-
- if ( iss1 == max_ss1_tmp ) {
- max_ss1_tmp = p1->max_ss;
- }
-
- if ( num_pix_displ[ifs1+array_width*iss1]>=
- conn_data[di].num_peaks_per_pixel ) {
-
- double dist;
- double coX1, coY1, cdX1, cdY1;
- double len1, len2;
-
- dist = modulus2d(ifs-ifs1,iss-iss1);
- if ( dist < minrad ) continue;
- coX1 = slab_to_x[ifs1+array_width*iss1];
- coY1 = slab_to_y[ifs1+array_width*iss1];
- cdX1 =
- coX1 - displ_x[ifs1+array_width*iss1];
- cdY1 =
- coY1 - displ_y[ifs1+array_width*iss1];
-
- len1 = modulus2d(coX1-coX, coY1-coY);
- len2 = modulus2d(cdX1-cdX, cdY1-cdY);
- if ( len1<FLT_EPSILON ||
- len2<FLT_EPSILON ) {
- continue;
- }
-
- num_ang++;
- }
- }
- }
- }
}
}
}
@@ -1598,7 +1858,8 @@ static int compute_angles_and_stretch
angles = malloc(max_num_ang*sizeof(double));
if ( angles == NULL ) {
- ERROR("Error in allocating memory for angle optimization\n");
+ ERROR("Error in allocating memory for angle "
+ "optimization\n");
free(csaa->stretch_coeff);
free(csaa->num_angles);
free(csaa);
@@ -1606,7 +1867,8 @@ static int compute_angles_and_stretch
}
stretches = malloc(max_num_ang*sizeof(double));
if ( stretches == NULL ) {
- ERROR("Error in allocating memory for stretch optimization\n");
+ ERROR("Error in allocating memory for stretch "
+ "optimization\n");
free(angles);
free(csaa->stretch_coeff);
free(csaa->num_angles);
@@ -1620,9 +1882,11 @@ static int compute_angles_and_stretch
struct panel *p0 = connected->rigid_groups[di]->panels[ip0];
- for ( ip1=0; ip1<connected->rigid_groups[di]->n_panels; ip1++ ) {
+ for ( ip1=0; ip1<connected->rigid_groups[di]->n_panels;
+ ip1++ ) {
- struct panel *p1 = connected->rigid_groups [di]->panels[ip1];
+ struct panel *p1 =
+ connected->rigid_groups [di]->panels[ip1];
int ifs, iss;
int min_fs_tmp = p0->min_fs;
@@ -1637,94 +1901,29 @@ static int compute_angles_and_stretch
max_fs_tmp = p1->max_fs;
}
- for (iss=min_ss_tmp; iss<max_ss_tmp+1; iss++) {
+ for (iss=min_ss_tmp; iss<max_ss_tmp+1;
+ iss++) {
+
+ int ret;
if ( iss == max_ss_tmp ) {
min_ss_tmp = p1->min_ss;
max_ss_tmp = p1->max_ss;
}
- double coX, coY, cdX, cdY;
-
- if ( num_pix_displ[ifs+array_width*iss]>=
- conn_data[di].num_peaks_per_pixel ) {
-
- int ifs1, iss1;
- int max_fs1_tmp = p0->max_fs;
- int max_ss1_tmp = p0->max_ss;
-
- if ( num_ang>=max_num_ang ) break;
-
- coX = slab_to_x[ifs+array_width*iss];
- coY = slab_to_y[ifs+array_width*iss];
- cdX = coX - displ_x[ifs+array_width*iss];
- cdY = coY - displ_y[ifs+array_width*iss];
-
- for (ifs1=ifs+1; ifs1<max_fs1_tmp+1; ifs1++) {
-
- if ( ifs1 == max_fs1_tmp ) {
- max_fs1_tmp = p1->max_fs;
- }
-
- for (iss1=iss+1; iss1<max_ss1_tmp+1; iss1++) {
-
- if ( iss1 == max_ss1_tmp ) {
- max_ss1_tmp = p1->max_ss;
- }
-
- if ( num_pix_displ[ifs1+array_width*iss1]>=
- conn_data[di].num_peaks_per_pixel ) {
-
- double dist;
- double coX1, coY1, cdX1, cdY1;
- double len1, len2;
- double scalM;
- double multlen;
-
- if ( num_ang>=max_num_ang ) break;
- dist = modulus2d(ifs-ifs1,iss-iss1);
- if (dist<minrad) continue;
- coX1 = slab_to_x[ifs1+array_width*iss1];
- coY1 = slab_to_y[ifs1+array_width*iss1];
- cdX1 =
- coX1 - displ_x[ifs1+array_width*iss1];
- cdY1 =
- coY1 - displ_y[ifs1+array_width*iss1];
-
- len1 = modulus2d(coX1-coX, coY1-coY);
- len2 = modulus2d(cdX1-cdX, cdY1-cdY);
- scalM = (coX1-coX)*(cdX1-cdX)+
- (coY1-coY)*(cdY1-cdY)-
- FLT_EPSILON;
- if ( len1<FLT_EPSILON ||
- len2<FLT_EPSILON ) {
- continue;
- }
-
- multlen = len1*len2;
- if ( fabs(scalM)>=multlen ) {
- angles[num_ang] = 0.0;
- } else {
-
- angles[num_ang] = 1.0;
-
- angles[num_ang] =
- acos(scalM/multlen);
-
- if ((coY1-coY)*(cdX1-cdX)-
- (coX1-coX)*(cdY1-cdY) < 0) {
- angles[num_ang] *= -1.;
- }
-
- }
-
- stretches[num_ang] = len1/len2;
-
- num_ang++;
- }
- }
- }
- }
+ ret = a_s_processing_loop(
+ num_pix_displ,
+ ifs, iss, di,
+ conn_data,
+ aw, slab_to_x,
+ slab_to_y,
+ p0, p1, displ_x,
+ displ_y, minrad,
+ max_num_ang,
+ &num_ang, angles,
+ stretches);
+
+ if ( ret == -2 ) break;
}
}
}
@@ -1773,8 +1972,9 @@ static int compute_angles_and_stretch
stretch_cf = 0;
for ( di=0; di<num_coeff; di++ ) {
if ( conn_data[di].num_peaks_per_pixel>=ipp ) {
- stretch_cf += total_num*csaa->stretch_coeff[di]*
- (double)csaa->num_angles[di];
+ stretch_cf +=
+ total_num*csaa->stretch_coeff[di]*
+ (double)csaa->num_angles[di];
}
}
break;
@@ -1789,7 +1989,8 @@ static int compute_angles_and_stretch
stretch_cf);
if ( man_stretching_coeff>FLT_EPSILON ) {
stretch_cf = man_stretching_coeff;
- STATUS("Using manually set stretch coefficient: %0.4f\n", stretch_cf);
+ STATUS("Using manually set stretch coefficient: %0.4f\n",
+ stretch_cf);
for ( di=0; di<connected->n_rigid_groups; di++ ) {
conn_data[di].cstr = man_stretching_coeff;
@@ -1808,7 +2009,7 @@ static int compute_angles_and_stretch
static int save_data_to_hdf5(char * filename, struct detector* det,
- int max_fs, int max_ss, double default_fill_value,
+ int max_fs, int max_ss, double dfv,
double *data)
{
struct image *im;
@@ -1833,7 +2034,7 @@ static int save_data_to_hdf5(char * filename, struct detector* det,
im->spectrum = NULL;
for ( i=0; i<(max_fs+1)*(max_ss+1); i++) {
- if ( data[i] == default_fill_value ) {
+ if ( data[i] == dfv ) {
im->data[i] = 0.0;
} else {
im->data[i] = (float)data[i];
@@ -1855,6 +2056,60 @@ static int save_data_to_hdf5(char * filename, struct detector* det,
}
+static void calculate_panel_correction(int di, int ip, int aw,
+ int *num_pix_displ,
+ struct rg_collection *connected,
+ struct connected_data *conn_data)
+{
+ struct panel *p;
+ int ifs, iss;
+
+ p = connected->rigid_groups[di]->panels[ip];
+ for (ifs=p->min_fs; ifs<p->max_fs+1; ifs++) {
+ for (iss=p->min_ss; iss<p->max_ss+1; iss++) {
+ if ( num_pix_displ[ifs+aw*iss]>=
+ conn_data[di].num_peaks_per_pixel ) {
+ conn_data[di].n_peaks_in_conn++;
+ }
+ }
+ }
+
+}
+
+
+static void compute_abs_displ(struct rg_collection *connected,
+ struct connected_data *conn_data,
+ int *num_pix_displ,
+ double dfv, int di, int ip, int aw,
+ double *displ_x,
+ double *displ_y,
+ double *displ_abs)
+{
+ struct panel *p;
+ int ifs, iss;
+
+ if (conn_data[di].sh_x < dfv+1) return;
+
+ p = connected->rigid_groups[di]->panels[ip];
+
+ for (ifs=p->min_fs; ifs<p->max_fs+1; ifs++) {
+ for (iss=p->min_ss; iss<p->max_ss+1; iss++) {
+ if ( num_pix_displ[ifs+aw*iss]>=
+ conn_data[di].num_peaks_per_pixel ) {
+ displ_x[ifs+aw*iss] -= conn_data[di].sh_x;
+ displ_y[ifs+aw*iss] -= conn_data[di].sh_y;
+ displ_abs[ifs+aw*iss] = modulus2d(
+ displ_x[ifs+aw*iss],
+ displ_y[ifs+aw*iss]
+ );
+ } else {
+ displ_abs[ifs+aw*iss] = dfv;
+ }
+ }
+ }
+}
+
+
int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
struct detector *det, struct rg_collection* quadrants,
struct rg_collection* connected,
@@ -1866,24 +2121,25 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
int num_pix_in_slab;
int max_fs = 0;
int max_ss = 0;
- int array_width = 0;
+ int aw = 0;
int pi, di, ip, pti;
int ret1, ret2, ret3;
int ret4, ret5, ret6;
int ret;
int write_ret;
+ int *num_pix_displ;
+
double res_sum;
double istep;
double clen_to_use;
double man_stretching_coeff = 0.0;
double avc[6] = {0.,0.,0.,0.,0.,0.};
- double default_fill_value = -10000.0;
- double dist_coeff_ang_str = 0.2; // for angles and stretch calculation use
- // only pixels which are distco*size_panel
- // away
-
- int *num_pix_displ;
+ double dfv = -10000.0;
+ // for angles and stretch calculation use
+ // only pixels which are distco*size_panel
+ // away
+ double dist_coeff_ang_str = 0.2;
double *displ_x;
double *displ_y;
double *displ_abs;
@@ -1894,6 +2150,7 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
double* recomputed_slab_to_x;
double* recomputed_slab_to_y;
double stretch_coeff = 1;
+
struct single_pix_displ *all_pix_displ;
struct single_pix_displ **curr_pix_displ;
struct connected_data *conn_data = NULL;
@@ -1906,8 +2163,8 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
STATUS("Minimum number of measurements for pixel to be included in the "
"refinement: %i\n",
min_num_peaks_per_pixel);
- STATUS("Minimum number of measurements for panel for accurate estimation of"
- " position/orientation: %i\n", min_num_peaks_per_panel);
+ STATUS("Minimum number of measurements for panel for accurate estimation "
+ "of position/orientation: %i\n", min_num_peaks_per_panel);
pattern_list = read_patterns_from_steam_file(infile, det);
if ( pattern_list->n_patterns < 1 ) {
@@ -1931,7 +2188,7 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
istep = res_sum/det->n_panels;
- array_width = max_fs+1;
+ aw = max_fs+1;
clen_to_use = compute_clen_to_use(pattern_list, istep, avc,
max_peak_dist,
@@ -1978,9 +2235,10 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
return 1;
}
- fill_coordinate_matrices(det, array_width, slab_to_x, slab_to_y);
+ fill_coordinate_matrices(det, aw, slab_to_x, slab_to_y);
- all_pix_displ = calloc(num_pix_in_slab, sizeof(struct single_pix_displ));
+ all_pix_displ = calloc(num_pix_in_slab,
+ sizeof(struct single_pix_displ));
if ( all_pix_displ == NULL ) {
ERROR("Error allocating memory for connected structure data.\n");
free(displ_x);
@@ -1990,7 +2248,8 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
free(slab_to_y);
return 1;
}
- curr_pix_displ = calloc(num_pix_in_slab, sizeof(struct single_pix_displ*));
+ curr_pix_displ = calloc(num_pix_in_slab,
+ sizeof(struct single_pix_displ*));
if ( curr_pix_displ == NULL ) {
ERROR("Error allocating memory for connected structure data.\n");
free(displ_x);
@@ -2014,7 +2273,8 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
return 1;
}
- conn_data = malloc(connected->n_rigid_groups*sizeof(struct connected_data));
+ conn_data = malloc(connected->n_rigid_groups*
+ sizeof(struct connected_data));
if ( conn_data == NULL ) {
ERROR("Error allocating memory for connected structure data.\n");
free(displ_x);
@@ -2031,11 +2291,14 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
STATUS("Computing pixel statistics\n");
ret = compute_pixel_statistics(pattern_list, det, connected, quadrants,
num_pix_in_slab, max_peak_dist,
- array_width, default_fill_value,
+ aw, dfv,
min_num_peaks_per_pixel,
- min_num_peaks_per_panel, only_best_distance,
- clen_to_use, slab_to_x, slab_to_y, conn_data,
- displ_x, displ_y, displ_abs, all_pix_displ,
+ min_num_peaks_per_panel,
+ only_best_distance,
+ clen_to_use, slab_to_x,
+ slab_to_y, conn_data,
+ displ_x, displ_y, displ_abs,
+ all_pix_displ,
curr_pix_displ,
num_pix_displ);
if ( ret != 0 ) {
@@ -2044,7 +2307,8 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
free(displ_abs);
free(slab_to_x);
free(slab_to_y);
- free_all_curr_pix_displ(all_pix_displ, curr_pix_displ, num_pix_in_slab);
+ free_all_curr_pix_displ(all_pix_displ, curr_pix_displ,
+ num_pix_in_slab);
free(num_pix_displ);
free(conn_data);
return 1;
@@ -2056,7 +2320,8 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
image_feature_list_free(pattern_list->patterns[pti]->im_list);
reflist_free(pattern_list->patterns[pti]->ref_list);
- for ( nuc=0; nuc<pattern_list->patterns[pti]->n_unit_cells; nuc++) {
+ for ( nuc=0; nuc<pattern_list->patterns[pti]->n_unit_cells;
+ nuc++) {
cell_free(pattern_list->patterns[pti]->unit_cells[nuc]);
}
free(pattern_list->patterns[pti]->filename);
@@ -2066,11 +2331,11 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
STATUS("Saving displacements before corrections\n");
ret1 = save_data_to_hdf5("disp_x_before.h5", det, max_fs, max_ss,
- default_fill_value, displ_x);
+ dfv, displ_x);
ret2 = save_data_to_hdf5("disp_y_before.h5", det, max_fs, max_ss,
- default_fill_value, displ_y);
+ dfv, displ_y);
ret3 = save_data_to_hdf5("disp_abs_before.h5", det, max_fs, max_ss,
- default_fill_value, displ_abs);
+ dfv, displ_abs);
if ( ret1!=0 || ret2!=0 || ret3!=0 ) {
ERROR("Error while writing data to file.\n");
free(conn_data);
@@ -2084,7 +2349,7 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
}
STATUS("Computing initial error.\n");
- totalError = compute_error(connected, array_width, conn_data,
+ totalError = compute_error(connected, aw, conn_data,
num_pix_displ, displ_abs);
STATUS("The total initial error <delta^2> = %0.4f\n", totalError);
@@ -2096,18 +2361,9 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
- struct panel *p;
- int ifs, iss;
+ calculate_panel_correction(di, ip, aw, num_pix_displ,
+ connected, conn_data);
- p = connected->rigid_groups[di]->panels[ip];
- for (ifs=p->min_fs; ifs<p->max_fs+1; ifs++) {
- for (iss=p->min_ss; iss<p->max_ss+1; iss++) {
- if ( num_pix_displ[ifs+array_width*iss]>=
- conn_data[di].num_peaks_per_pixel ) {
- conn_data[di].n_peaks_in_conn++;
- }
- }
- }
}
}
@@ -2117,7 +2373,7 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
num_pix_displ,
slab_to_x, slab_to_y,
displ_x, displ_y,
- array_width,
+ aw,
min_num_peaks_per_panel,
dist_coeff_ang_str,
min_num_peaks_per_pixel,
@@ -2178,16 +2434,17 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
return 1;
}
- fill_coordinate_matrices(det, array_width, recomputed_slab_to_x,
+ fill_coordinate_matrices(det, aw, recomputed_slab_to_x,
recomputed_slab_to_y);
- recompute_differences(connected, slab_to_x, slab_to_y, recomputed_slab_to_x,
+ recompute_differences(connected, slab_to_x, slab_to_y,
+ recomputed_slab_to_x,
recomputed_slab_to_y, conn_data,
- stretch_coeff, array_width, displ_x, displ_y,
+ stretch_coeff, aw, displ_x, displ_y,
num_pix_displ);
- ret = compute_shifts(connected, conn_data, num_pix_displ, array_width,
- min_num_peaks_per_panel, default_fill_value,
+ ret = compute_shifts(connected, conn_data, num_pix_displ, aw,
+ min_num_peaks_per_panel, dfv,
max_peak_dist, displ_x, displ_y );
if ( ret != 0 ) return 1;
@@ -2198,40 +2455,22 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
for ( di=0;di<connected->n_rigid_groups;di++ ) {
for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
- struct panel *p;
- int ifs, iss;
-
- if (conn_data[di].sh_x < default_fill_value+1) continue;
-
- p = connected->rigid_groups[di]->panels[ip];
+ compute_abs_displ(connected, conn_data,
+ num_pix_displ, dfv, di, ip, aw,
+ displ_x, displ_y, displ_abs);
- for (ifs=p->min_fs; ifs<p->max_fs+1; ifs++) {
- for (iss=p->min_ss; iss<p->max_ss+1; iss++) {
- if ( num_pix_displ[ifs+array_width*iss]>=
- conn_data[di].num_peaks_per_pixel ) {
- displ_x[ifs+array_width*iss] -= conn_data[di].sh_x;
- displ_y[ifs+array_width*iss] -= conn_data[di].sh_y;
- displ_abs[ifs+array_width*iss] = modulus2d(
- displ_x[ifs+array_width*iss],
- displ_y[ifs+array_width*iss]
- );
- } else {
- displ_abs[ifs+array_width*iss] = default_fill_value;
- }
- }
- }
}
}
- correct_shifts(connected, conn_data, default_fill_value, clen_to_use);
+ correct_shifts(connected, conn_data, dfv, clen_to_use);
STATUS("Saving displacements after corrections\n");
ret4 = save_data_to_hdf5("disp_x_after.h5", det, max_fs, max_ss,
- default_fill_value, displ_x);
+ dfv, displ_x);
ret5 = save_data_to_hdf5("disp_y_after.h5", det, max_fs, max_ss,
- default_fill_value, displ_y);
+ dfv, displ_y);
ret6 = save_data_to_hdf5("disp_abs_after.h5", det, max_fs, max_ss,
- default_fill_value, displ_abs);
+ dfv, displ_abs);
if ( ret4!=0 || ret5!=0 || ret6!=0 ) {
ERROR("Error while writing data to file.\n");
free(conn_data);
@@ -2247,7 +2486,7 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
}
STATUS("Computing final error.\n");
- totalError = compute_error(connected, array_width, conn_data, num_pix_displ,
+ totalError = compute_error(connected, aw, conn_data, num_pix_displ,
displ_abs);
STATUS("The total final error <delta^2> = %0.4f\n",totalError);
@@ -2398,7 +2637,8 @@ int main(int argc, char *argv[])
}
if ( quadrant_coll_name == NULL ) {
- ERROR("You must provide a rigid group collection for quadrants.\n");
+ ERROR("You must provide a rigid group collection for "
+ "quadrants.\n");
return 1;
}
@@ -2417,10 +2657,11 @@ int main(int argc, char *argv[])
return 1;
}
- connected = find_rigid_group_collection_by_name(det, connected_coll_name);
+ connected = find_rigid_group_collection_by_name(det,
+ connected_coll_name);
if ( connected == NULL ) {
- ERROR("Cannot find rigid group collection for connected asics: %s\n",
- connected_coll_name);
+ ERROR("Cannot find rigid group collection for connected "
+ "asics: %s\n", connected_coll_name);
return 1;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-09 02:05:41 +0000