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-rw-r--r--doc/man/geoptimiser.18
-rw-r--r--src/geoptimiser.c2746
2 files changed, 1467 insertions, 1287 deletions
diff --git a/doc/man/geoptimiser.1 b/doc/man/geoptimiser.1
index d56bf86a..10bf6dce 100644
--- a/doc/man/geoptimiser.1
+++ b/doc/man/geoptimiser.1
@@ -87,9 +87,15 @@ Sets the minimum number of peaks that should fall within a pixel, across all ind
.PD 0
.IP "\fB-p\fR \fIn\fR"
+.IP \fB--min-num-pixels-per-conn-group=\fR\fIn\fR
+.PD
+Sets the minimum number of pixels that contribute to the geometry opimization (see the \fB--min-num-peaks-per-pixel\fR option above ) that a connected group should have for the group to be optimized independently. The default value is 100.
+
+.PD 0
+.IP "\fB-p\fR \fIn\fR"
.IP \fB--min-num-peaks-per-panel=\fR\fIn\fR
.PD
-Sets the minimum number of peaks that should appear in a panel for the panel's geometry to be optimized independently. The default value is 100.
+This option has been renamd to \fB--min-num-pixels-per-conn-group\fR. It has been deprecated and will soon be removed. It is currently mapped to the \fB--min-num-pixels-per-conn-group\fR option.
.PD 0
.IP "\fB-l\fR"
diff --git a/src/geoptimiser.c b/src/geoptimiser.c
index ba38f63c..e1d59f05 100644
--- a/src/geoptimiser.c
+++ b/src/geoptimiser.c
@@ -68,34 +68,54 @@ static void show_help(const char *s)
printf(
"Refines detector geometry.\n"
"\n"
-" -h, --help Display this help message.\n"
+" -h, --help Display this help message.\n"
"\n"
-" --version Print CrystFEL version number and\n"
-" exit.\n"
-" -i, --input=<filename> Specify stream file to be used for \n"
-" geometry optimization.\n"
-" -g. --geometry=<filename> Input detector geometry.\n"
-" -o, --output=<filename> Output detector geometry.\n"
-" -q, --quadrants=<rg_coll> Rigid group collection for quadrants.\n"
-" -c, --connected=<rg_coll> Rigid group collection for connected\n"
-" ASICs.\n"
-" --no-error-maps Do not generate error map PNGs.\n"
-" -x, --min-num-peaks-per-pixel=<num> Minimum number of peaks per pixel.\n"
-" Default: 3. \n"
-" -p, --min-num-peaks-per-panel=<num> Minimum number of peaks per pixel.\n"
-" Default: 100.\n"
-" -l, --most-freq-clen Use only the most frequent camera\n"
-" length.\n"
-" -s, --individual-dist-offset Use a distance offset for each panel.\n"
-" Default: whole-detector offset.\n"
-" --no-stretch Do not optimize distance offset.\n"
-" Default: distance offset is optimized\n"
-" -m --max-peak-dist=<num> Maximum distance between predicted and\n"
-" detected peaks (in pixels)\n"
-" Default: 4.0 pixels.\n"
+" --version Print CrystFEL version number and\n"
+" exit.\n"
+" -i, --input=<filename> Specify stream file to be used for \n"
+" geometry optimization.\n"
+" -g. --geometry=<file> Get detector geometry from file.\n"
+" -o, --output=<filename> Output stream.\n"
+" -q, --quadrants=<rg_coll> Rigid group collection for quadrants.\n"
+" -c, --connected=<rg_coll> Rigid group collection for connected\n"
+" ASICs.\n"
+" --no-error-maps Do not generate error map PNGs.\n"
+" -x, --min-num-peaks-per-pixel=<num> Minimum number of peaks per pixel.\n"
+" Default: 3. \n"
+" --min-num-peaks-per-panel=<num> DEPRECATED. This option has been\n"
+" renamed to --min-num-pixels-per-conn-group.\n"
+" -p, --min-num-pixels-per-conn-group=<num> Minimum number of useful pixels pern"
+" connected group.\n"
+" f Default: 100.\n"
+" -l, --most-freq-clen Use only the most frequent camera\n"
+" length.\n"
+" -s, --individual-dist-offset Use a distance offset for each panel.\n"
+" Default: whole-detector offset.\n"
+" --no-stretch Do not optimize distance offset.\n"
+" Default: distance offset is optimized\n"
+" -m --max-peak-dist=<num> Maximum distance between predicted and\n"
+" detected peaks (in pixels)\n"
+" Default: 4.0 pixels.\n"
);
}
+struct geoptimiser_params
+{
+ char *infile;
+ char *outfile;
+ char *geometry_filename;
+ int min_num_peaks_per_pix;
+ int min_num_pix_per_conn_group;
+ int only_best_distance;
+ int nostretch;
+ int individual_coffset;
+ int error_maps;
+ int enforce_cspad_layout;
+ int no_cspad;
+ double max_peak_dist;
+ const char *command_line;
+};
+
struct connected_data
{
@@ -127,19 +147,76 @@ struct pattern_list {
};
-struct single_pix_displ
+struct single_pixel_displ
{
double dfs;
double dss;
- struct single_pix_displ* ne;
+ struct single_pixel_displ* ne;
+};
+
+
+struct pixel_displ_list
+{
+ struct single_pixel_displ *pix_displ_list;
+ struct single_pixel_displ **curr_pix_displ;
+ int *num_pix_displ;
};
struct connected_stretch_and_angles
{
double *stretch_coeff;
- unsigned int *num_angles;
- int num_coeff;
+ long *num_angles;
+ long num_coeff;
+};
+
+struct cell_params
+{
+ double a;
+ double b;
+ double c;
+ double alpha;
+ double beta;
+ double gamma;
+};
+
+
+struct avg_displacements
+{
+ double *displ_x;
+ double *displ_y;
+ double *displ_abs;
+};
+
+
+struct avg_rot_and_stretch
+{
+ double *aver_ang;
+ double *aver_str;
+ int *aver_num_ang;
+};
+
+
+struct avg_shift
+{
+ double *aver_x;
+ double *aver_y;
+ int *aver_num_sh;
+};
+
+struct pixel_maps
+{
+ double *pix_to_x;
+ double *pix_to_y;
+};
+
+
+struct enhanced_det
+{
+ struct detector *det;
+ int width;
+ int height;
+ int num_pix;
};
@@ -176,9 +253,8 @@ static Reflection *find_closest_reflection(RefList *rlist,
for ( refl = first_refl(rlist, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) )
- {
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
double ds;
double rfs, rss;
double rx, ry;
@@ -248,7 +324,7 @@ static double extract_f_from_stuff(const char *field_name,
if ( strncmp(stuff->fields[i], field_name_plus_equal,
strlen(field_name_plus_equal)) == 0 ) {
- return atoi(stuff->fields[i]+
+ return atof(stuff->fields[i]+
strlen(field_name_plus_equal));
}
}
@@ -261,7 +337,6 @@ static double extract_f_from_stuff(const char *field_name,
static struct pattern_list *read_patterns_from_steam_file(const char *infile,
struct detector *det)
{
-
Stream *st;
struct pattern_list *pattern_list;
@@ -390,7 +465,7 @@ static struct pattern_list *read_patterns_from_steam_file(const char *infile,
patn->unit_cells = new_unit_cells;
crystal_reflist = crystal_get_reflections(
- cur.crystals[i]);
+ cur.crystals[i]);
for ( refl = first_refl(crystal_reflist, &iter);
refl != NULL;
@@ -402,7 +477,6 @@ static struct pattern_list *read_patterns_from_steam_file(const char *infile,
get_indices(refl, &h, &k, &l);
n = add_refl(patn->ref_list, h, k, l);
copy_data(n, refl);
-
}
}
@@ -445,13 +519,14 @@ static struct rvec get_q_from_xyz(double rx, double ry, double dist, double l)
}
-static void compute_avg_cell_parameters(struct pattern_list *pattern_list,
- double *avcp)
+static struct cell_params *compute_avg_cell_parameters(struct pattern_list
+ *pattern_list)
{
int numavc;
int j, i;
double minc[6];
double maxc[6];
+ double avg_cpar[6];
for (j=0; j<6; j++) {
minc[j] = 1e10;
@@ -484,7 +559,7 @@ static void compute_avg_cell_parameters(struct pattern_list *pattern_list,
cpar[5] = rad2deg(cpar[5]);
for ( j=0; j<6; j++ ) {
- avcp[j] += cpar[j];
+ avg_cpar[j] += cpar[j];
if (cpar[j]<minc[j]) minc[j] = cpar[j];
if (cpar[j]>maxc[j]) maxc[j] = cpar[j];
}
@@ -495,33 +570,41 @@ static void compute_avg_cell_parameters(struct pattern_list *pattern_list,
}
if ( numavc>0 ) {
- for ( j=0; j<6; j++ ) avcp[j] /= numavc;
+ for ( j=0; j<6; j++ ) avg_cpar[j] /= numavc;
}
+ struct cell_params *cparams = malloc(sizeof(struct cell_params));
+
+ cparams->a = avg_cpar[0];
+ cparams->b = avg_cpar[1];
+ cparams->c = avg_cpar[2];
+ cparams->alpha = avg_cpar[3];
+ cparams->beta = avg_cpar[4];
+ cparams->gamma = avg_cpar[5];
+
STATUS("Average cell coordinates:\n");
STATUS("Average a, b, c (in nm): %6.3f, %6.3f, %6.3f\n",
- avcp[0],avcp[1],avcp[2]);
+ cparams->a, cparams->b, cparams->c);
STATUS("Minimum -Maximum a, b, c:\n"
"\t%6.3f - %6.3f,\n"
"\t%6.3f - %6.3f,\n"
"\t%6.3f - %6.3f\n",
minc[0], maxc[0], minc[1], maxc[1], minc[2], maxc[2]);
STATUS("Average alpha,beta,gamma in degrees: %6.3f, %6.3f, %6.3f\n",
- avcp[3], avcp[4], avcp[5]);
+ cparams->alpha, cparams->beta, cparams->gamma);
STATUS("Minimum - Maximum alpha,beta,gamma in degrees:\n"
"\t%5.2f - %5.2f,\n"
"\t%5.2f - %5.2f,\n"
"\t%5.2f - %5.2f\n",
minc[3], maxc[3], minc[4], maxc[4], minc[5], maxc[5]);
+ return cparams;
}
-static double compute_clen_to_use(struct pattern_list *pattern_list,
- double istep, double *avcp,
- double max_peak_distance,
- int only_best_distance,
- double* min_braggp_dist)
+static double pick_clen_to_use(struct geoptimiser_params *gparams,
+ struct pattern_list *pattern_list,
+ double avg_res, struct cell_params *cparams)
{
int cp, i, u;
int num_clens;
@@ -530,9 +613,8 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
int *clens_population;
double *clens;
double *lambdas;
- double irecistep;
+ double min_braggp_dist;
double clen_to_use;
- double *braggp_dist;
struct rvec cqu;
max_clens = 1024;
@@ -586,16 +668,16 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
clens_new = realloc(clens_population,
(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) {
ERROR("Failed to allocate memory for "
"camera length list\n");
- free(clens);
- free(clens_population);
- free(lambdas);
- return -1.0;
+ free(clens);
+ free(clens_population);
+ free(lambdas);
+ return -1.0;
}
max_clens += 1024;
@@ -605,7 +687,6 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
}
clens[num_clens] = pattern_list->patterns[cp]->clen;
-
clens_population[num_clens] = 1;
lambdas[num_clens] = pattern_list->patterns[cp]->lambda;
num_clens++;
@@ -618,37 +699,34 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
}
if ( num_clens == 1 ) {
- STATUS("All patterns in the stream file have the same camera "
- "length: %f m.\n",
+ STATUS("All patterns have the same camera length: %f m.\n",
clens[0]);
} else {
STATUS("%i different camera lengths were found for the input "
- "patterns in the stream file:\n", num_clens);
+ "patterns:\n", num_clens);
}
- braggp_dist = calloc(num_clens, sizeof(double));
- *min_braggp_dist = 999999.0;
best_clen = 0;
clen_to_use = clens[0];
for ( i=0; i<num_clens; i++) {
if ( clens_population[i] >0) {
- cqu = get_q_from_xyz(1/istep, 0, clens[i], lambdas[i]);
-
- irecistep = 1/cqu.u;
-
- braggp_dist[i] = fmin(fmin(irecistep/avcp[0],
- irecistep/avcp[1]),
- irecistep/avcp[2]);
- if (braggp_dist[i] < *min_braggp_dist) {
- *min_braggp_dist = braggp_dist[i];
- }
- STATUS("Camera length %0.4f m was found %i times in the "
- "stream file.\n"
- "Corresponding minimum inter-bragg peak distance "
- "is (based on average cell parameters): "
- " %0.1f pixels.\n",
+ cqu = get_q_from_xyz(1.0/avg_res, 0, clens[i], lambdas[i]);
+
+ min_braggp_dist = fmin(fmin((1.0/cqu.u)/cparams->a,
+ (1.0/cqu.u)/cparams->b),
+ (1.0/cqu.u)/cparams->c);
+ STATUS("Camera length %0.4f m was found %i times.\n"
+ "Minimum inter-bragg peak distance (based on "
+ "average cell parameters): %0.1f pixels.\n",
clens[i], clens_population[i],
- braggp_dist[i]);
+ min_braggp_dist);
+ if ( min_braggp_dist<1.2*gparams->max_peak_dist ) {
+ STATUS("WARNING: The distance between Bragg "
+ "peaks is too small: "
+ "%0.1f < 1.2*%0.1f pixels.\n",
+ min_braggp_dist,
+ gparams->max_peak_dist);
+ }
if ( clens_population[i] > clens_population[best_clen] ) {
best_clen = i;
clen_to_use = clens[best_clen];
@@ -656,24 +734,23 @@ static double compute_clen_to_use(struct pattern_list *pattern_list,
}
}
- if ( only_best_distance ) {
- STATUS("Only the %i patterns with clen=%0.4f m will be used.\n",
+ if ( gparams->only_best_distance ) {
+ STATUS("Only %i patterns with CLEN=%0.4f m will be used.\n",
clens_population[best_clen], clen_to_use);
- *min_braggp_dist = braggp_dist[best_clen];
}
free(clens);
free(lambdas);
free(clens_population);
- free(braggp_dist);
+
return clen_to_use;
}
-static double comp_median(double *arr, unsigned int n)
+static double comp_median(double *arr, long n)
{
- int low, high, median, middle, ll, hh;
+ long low, high, median, middle, ll, hh;
double A;
if (n<1) return 0.0;
@@ -739,7 +816,7 @@ static double comp_median(double *arr, unsigned int n)
/* Re-set active partition */
if ( hh<=median ) low = ll;
- if ( hh>=median ) high = hh-1;
+ if ( hh>=median ) high = hh-1;
}
return 0.0;
@@ -767,199 +844,211 @@ static int find_quad_for_connected(struct rigid_group *rg,
}
-static void free_all_curr_pix_displ(struct single_pix_displ *all_pix_displ,
- struct single_pix_displ **curr_pix_displ,
- int num_pix_in_slab)
+static int fill_avg_pixel_displ(struct pixel_displ_list *pix_displ_list,
+ int pix_index,
+ struct avg_displacements *avg_displ)
{
- int i;
- struct single_pix_displ *curr = NULL;
- struct single_pix_displ *next = NULL;
+ double *list_fs_displ;
+ double *list_ss_displ;
+ int count = 0;
+ int ei;
+
+ list_fs_displ = calloc(pix_displ_list->num_pix_displ[pix_index],
+ sizeof(double));
+ if ( list_fs_displ == NULL ) {
+ ERROR("Failed to allocate memory for pixel statistics.\n");
+ return 1;
+ }
+ list_ss_displ = calloc(pix_displ_list->num_pix_displ[pix_index],
+ sizeof(double));
+ if ( list_ss_displ == NULL ) {
+ ERROR("Failed to allocate memory for pixel statistics.\n");
+ free(list_fs_displ);
+ return 1;
+ }
- for ( i=0; i<num_pix_in_slab; i++ ) {
+ pix_displ_list->curr_pix_displ[pix_index] =
+ &pix_displ_list->pix_displ_list[pix_index];
- curr = &all_pix_displ[i];
+ for ( ei=0; ei<pix_displ_list->num_pix_displ[pix_index]; ei++ ) {
+ struct single_pixel_displ * pixel_displ_entry;
+ pixel_displ_entry = pix_displ_list->curr_pix_displ[pix_index];
- if ( curr->ne != NULL ) {
- curr = curr->ne;
- while ( curr != NULL ) {
- next = curr->ne;
- free(curr);
- curr = next;
- }
- }
- }
+ if ( pixel_displ_entry->dfs == -10000.0 ) break;
+ list_fs_displ[count] = pixel_displ_entry->dfs;
+ list_ss_displ[count] = pixel_displ_entry->dss;
+ count++;
+ if ( pixel_displ_entry->ne == NULL ) {
+ break;
+ } else {
+ pix_displ_list->curr_pix_displ[pix_index] =
+ pix_displ_list->curr_pix_displ[pix_index]->ne;
+ }
+ }
+
+ if ( count < 1 ) {
+ free(list_fs_displ);
+ free(list_ss_displ);
+ return 0;
+ }
- free(curr_pix_displ);
- free(all_pix_displ);
+ avg_displ->displ_x[pix_index] = comp_median(list_fs_displ, count);
+ avg_displ->displ_y[pix_index] = comp_median(list_ss_displ, count);
+ avg_displ->displ_abs[pix_index] = modulus2d(avg_displ->displ_x[pix_index],
+ avg_displ->displ_y[pix_index]);
+ free(list_fs_displ);
+ free(list_ss_displ);
+
+ return 0;
}
-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)
+static int allocate_next_element(struct single_pixel_displ** curr_pix_displ,
+ int pix_index)
{
- double *cPxAfs;
- double *cPxAss;
- int cnu = 0;
-
- cPxAfs = calloc(num_pix_displ[ifs+aw*iss], sizeof(double));
- if ( cPxAfs == NULL ) {
+ curr_pix_displ[pix_index]->ne = malloc(sizeof(struct single_pixel_displ));
+ if ( curr_pix_displ[pix_index]->ne == 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];
+ curr_pix_displ[pix_index] = curr_pix_displ[pix_index]->ne;
- 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;
- }
+ return 0;
+}
+
+
+static int add_distance_to_list(struct enhanced_det *edet,
+ struct imagefeature *imfe,
+ struct pixel_displ_list *pix_displ_list,
+ Reflection *refl, double fx, double fy)
+{
+ int pix_index;
+ double rfs, rss;
+ double crx, cry;
+
+ pix_index = ((int)rint(imfe->fs) + edet->width*(int)rint(imfe->ss));
- if ( cnu < 1 ) return 0;
+ if ( pix_displ_list->num_pix_displ[pix_index]>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++;
+ int ret;
- free(cPxAfs);
- free(cPxAss);
+ ret = allocate_next_element(pix_displ_list->curr_pix_displ,
+ pix_index);
+
+ if ( ret != 0) return ret;
+
+ }
+
+ get_detector_pos(refl, &rfs, &rss);
+ compute_x_y(edet->det, rfs, rss, &crx, &cry);
+ pix_displ_list->curr_pix_displ[pix_index]->dfs = (fx-crx);
+ pix_displ_list->curr_pix_displ[pix_index]->dss = (fy-cry);
+ pix_displ_list->curr_pix_displ[pix_index]->ne = NULL;
+ pix_displ_list->num_pix_displ[pix_index]++;
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)
+static int count_pixels_with_min_peaks( struct panel *p, int min_num_peaks,
+ struct pixel_displ_list *pix_displ_list,
+ struct enhanced_det *edet)
{
- struct panel *p;
+ int pix_index;
+ int pixel_count = 0;
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;
+ pix_index = ifs+edet->width*iss;
+
+ if ( pix_displ_list->num_pix_displ[pix_index] >=
+ min_num_peaks ) {
+ pixel_count += 1;
}
}
}
- return 0;
+ return pixel_count;
}
-
-static int allocate_next_element(struct single_pix_displ** curr_pix_displ,
- int ipx)
+static void adjust_min_peaks_per_conn(struct enhanced_det *edet,
+ struct rg_collection *connected,
+ struct geoptimiser_params *gparams,
+ struct connected_data *conn_data,
+ struct pixel_displ_list *pix_displ_list)
{
- 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 min_num_peaks, di, ip;
+ struct panel *p;
- return 0;
-}
+ STATUS("Adjusting the minimum number of measurements per pixel in "
+ "order to have enough measurements for each connected group.\n");
+ for ( di=0; di<connected->n_rigid_groups; di++ ) {
-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 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 ( min_num_peaks=gparams->min_num_peaks_per_pix;
+ min_num_peaks>0; min_num_peaks-- ) {
- for (di=0; di<connected->n_rigid_groups; di++) {
+ int di_count = 0;
+
+ for (ip=0; ip<connected->rigid_groups[di]->n_panels;
+ ip++) {
+
+ int pix_count;
+
+ p = connected->rigid_groups[di]->panels[ip];
- conn_data[di].num_quad = find_quad_for_connected(
- connected->rigid_groups[di],
- quadrants);
- conn_data[di].cang = 0.0;
- conn_data[di].cstr = 1.0;
- 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;
- }
+ pix_count = count_pixels_with_min_peaks(p,
+ min_num_peaks,
+ pix_displ_list,
+ edet);
+
+ di_count += pix_count;
+ }
+ conn_data[di].n_peaks_in_conn = di_count;
+ if ( di_count >=
+ gparams->min_num_pix_per_conn_group ) {
+ conn_data[di].num_peaks_per_pixel =
+ min_num_peaks;
+ break;
+ }
+ }
- for ( ipx=0; ipx<num_pix_in_slab; ipx++ ) {
- 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;
+ STATUS("Minimum number of measurement "
+ "per pixel for connected group "
+ "%s has been set to %i\n",
+ conn_data[di].name,
+ conn_data[di].num_peaks_per_pixel);
}
+}
+
+
+static int compute_pixel_displacements(struct pattern_list *pattern_list,
+ struct enhanced_det *edet,
+ struct rg_collection *connected,
+ struct geoptimiser_params *gparams,
+ double clen_to_use,
+ struct connected_data *conn_data,
+ struct avg_displacements *avg_displ,
+ struct pixel_displ_list *pix_displ_list)
+{
+ int cp, ich;
+
+ STATUS("Computing pixel displacements.\n");
for ( cp=0; cp<pattern_list->n_patterns; cp++ ) {
ImageFeatureList *flist = pattern_list->patterns[cp]->im_list;
- if ( only_best_distance ) {
+ if ( gparams->only_best_distance ) {
if ( fabs(pattern_list->patterns[cp]->clen-clen_to_use) >
- 0.0001 ) {
+ 0.0001 ) {
continue;
}
}
@@ -970,87 +1059,99 @@ static int compute_pixel_statistics(struct pattern_list *pattern_list,
double min_dist;
double fx, fy;
- double rfs, rss;
- double crx, cry;
Reflection *refl;
+ int ret;
RefList *rlist = pattern_list->patterns[cp]->ref_list;
struct imagefeature *imfe = image_get_feature(flist, ich);
- compute_x_y(det, imfe->fs, imfe->ss, &fx, &fy);
+ compute_x_y(edet->det, imfe->fs, imfe->ss, &fx, &fy);
- refl = find_closest_reflection(rlist, fx, fy, det,
+ refl = find_closest_reflection(rlist, fx, fy, edet->det,
&min_dist);
if ( refl == NULL ) continue;
- if ( min_dist < max_peak_distance ) {
+ if ( min_dist < gparams->max_peak_dist ) {
- int ipx = ((int)rint(imfe->fs) + aw*
- (int)rint(imfe->ss));
- if ( num_pix_displ[ipx]>0 ) {
+ ret = add_distance_to_list(edet, imfe,
+ pix_displ_list,
+ refl, fx, fy);
- int ret;
+ if ( ret != 0 ) return ret;
- ret = allocate_next_element(curr_pix_displ,
- ipx);
+ }
+ }
+ }
- if ( ret != 0) return ret;
+ return 0;
+}
- }
- get_detector_pos(refl, &rfs, &rss);
- compute_x_y(det, rfs, rss, &crx, &cry);
- get_detector_pos(refl, &rfs, &rss);
- curr_pix_displ[ipx]->dfs = (fx-crx);
- curr_pix_displ[ipx]->dss = (fy-cry);
- curr_pix_displ[ipx]->ne = NULL;
- num_pix_displ[ipx]++;
- }
- }
+static int compute_avg_pix_displ(struct pixel_displ_list *pix_displ_list,
+ int num_peaks_per_pixel,int pix_index,
+ struct avg_displacements *avg_displ)
+{
+ int ret;
+
+ if ( pix_displ_list->num_pix_displ[pix_index] >=
+ num_peaks_per_pixel ) {
+
+ ret = fill_avg_pixel_displ(pix_displ_list,
+ pix_index,
+ avg_displ);
+ if ( ret !=0 ) return ret;
+ } else {
+ avg_displ->displ_x[pix_index] = -10000.0;
+ avg_displ->displ_y[pix_index] = -10000.0;
+ avg_displ->displ_abs[pix_index] = -10000.0;
}
- for ( np=min_num_peaks_per_pixel; np>0; np-- ) {
- for ( di=0; di<connected->n_rigid_groups; di++ ) {
- if ( conn_data[di].num_peaks_per_pixel>np ) {
- continue;
- }
+ return 0;
- for (ip=0; ip<connected->rigid_groups[di]->n_panels;
- ip++) {
+}
- int ret;
-
- 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);
-
- if ( ret !=0 ) return ret;
- }
+static int compute_avg_displacements(struct enhanced_det *edet,
+ struct rg_collection *connected,
+ struct pixel_displ_list *pix_displ_list,
+ struct connected_data *conn_data,
+ struct avg_displacements *avg_displ)
+{
+ int di, ip, ifs, iss;
+ int pix_index, ret;
+ struct panel *p;
+
+ for ( di=0; di<connected->n_rigid_groups; di++ ) {
+
+ for (ip=0; ip<connected->rigid_groups[di]->n_panels;
+ ip++) {
+
+ 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 ( conn_data[di].n_peaks_in_conn >=
- min_num_peaks_per_panel ) {
- conn_data[di].num_peaks_per_pixel = np;
+ pix_index = ifs+edet->width*iss;
+
+ ret = compute_avg_pix_displ(pix_displ_list,
+ conn_data[di].num_peaks_per_pixel,
+ pix_index, avg_displ);
+
+ if ( ret != 0 ) return ret;
+
+ }
}
}
- }
- return 0;
+ }
+ return 0;
}
static double compute_error(struct rg_collection *connected,
- int aw,
+ struct enhanced_det* edet,
struct connected_data *conn_data,
int *num_pix_displ,
double *displ_abs)
@@ -1072,13 +1173,17 @@ 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+aw*iss]>=
+
+ int pix_index;
+ pix_index = ifs+edet->width*iss;
+
+ if ( num_pix_displ[pix_index]>=
conn_data[di].num_peaks_per_pixel ) {
double cer;
- cer = displ_abs[ifs+aw*iss]*
- displ_abs[ifs+aw*iss];
+ cer = displ_abs[pix_index]*
+ displ_abs[pix_index];
connected_error += cer;
num_connected_error++;
total_error += cer;
@@ -1093,11 +1198,10 @@ static double compute_error(struct rg_collection *connected,
connected_error /= (double)num_connected_error;
connected_error = sqrt(connected_error);
- STATUS("Connected group %s: \n"
- " Pixels with more than %d measurements: %i "
- " Error: <delta^2> = %0.4f pixels.\n",
- conn_data[di].name, conn_data[di].num_peaks_per_pixel,
- num_connected_error,
+ STATUS("Error for connected group %s: %d pixels with "
+ "more than %d peaks: <delta^2> = %0.4f pixels.\n",
+ conn_data[di].name, num_connected_error,
+ conn_data[di].num_peaks_per_pixel,
connected_error);
}
}
@@ -1113,120 +1217,184 @@ static double compute_error(struct rg_collection *connected,
}
-static void fill_coordinate_matrices(struct detector *det, int aw,
- double *slab_to_x, double *slab_to_y)
+static struct pixel_maps *initialize_pixel_maps(struct enhanced_det *edet)
{
+
int pi;
+ struct pixel_maps *pixel_maps;
- for ( pi=0; pi<det->n_panels; pi++ ) {
+ pixel_maps = malloc(sizeof(struct pixel_maps));
+ pixel_maps->pix_to_x = malloc(edet->num_pix*sizeof(double));
+ if ( pixel_maps->pix_to_x == NULL ) {
+ free(pixel_maps);
+ return NULL;
+ }
+
+ pixel_maps->pix_to_y = malloc(edet->num_pix*sizeof(double));
+ if ( pixel_maps->pix_to_x == NULL ) {
+ ERROR("Failed to allocate memory for pixel maps.\n");
+ free(pixel_maps->pix_to_x);
+ free(pixel_maps);
+ return NULL;
+ }
+
+ for ( pi=0; pi<edet->det->n_panels; pi++ ) {
struct panel *p;
int iss, ifs;
- p = &det->panels[pi];
+ p = &edet->det->panels[pi];
- for (iss=p->min_ss; iss < p->max_ss+1; iss++) {
- for (ifs=p->min_fs; ifs < p->max_fs+1; ifs++) {
+ for (iss=p->min_ss; iss < p->max_ss+1; iss++) {
+ for (ifs=p->min_fs; ifs < p->max_fs+1; ifs++) {
double xs, ys;
+ int pix_index;
- compute_x_y(det, ifs, iss, &xs, &ys);
-
- slab_to_x[iss*aw+ifs] = xs;
- slab_to_y[iss*aw+ifs] = ys;
+ pix_index = iss*edet->width+ifs;
+ compute_x_y(edet->det, ifs, iss, &xs, &ys);
+ pixel_maps->pix_to_x[pix_index] = xs;
+ pixel_maps->pix_to_y[pix_index] = ys;
}
}
}
+
+ return pixel_maps;
}
-static int correct_empty_panels(struct rg_collection *quadrants,
- struct rg_collection *connected,
- int min_num_peaks_per_panel,
- struct connected_data *conn_data)
+void free_pixel_maps(struct pixel_maps* pixel_maps)
{
- double *aver_ang;
- double *aver_str;
- int *aver_num_ang;
+ free(pixel_maps->pix_to_x);
+ free(pixel_maps->pix_to_y);
+ free(pixel_maps);
+}
- int di,i;
- aver_ang = malloc(quadrants->n_rigid_groups*sizeof(double));
- if ( aver_ang == NULL ) {
+
+struct avg_rot_and_stretch* initialize_avg_rot_stretch(
+ int num_rigid_groups)
+{
+ int i;
+
+ struct avg_rot_and_stretch *avg_rot_str;
+
+ avg_rot_str = malloc(sizeof(struct avg_rot_and_stretch));
+ if ( avg_rot_str == NULL ) {
ERROR("Failed to allocate memory to correct empty panels.|n");
- return 1;
+ return NULL;
+ }
+
+ avg_rot_str->aver_ang = malloc(num_rigid_groups*sizeof(double));
+ if ( avg_rot_str->aver_ang == NULL ) {
+ ERROR("Failed to allocate memory to correct empty panels.|n");
+ free(avg_rot_str);
+ return NULL;
}
- aver_str = malloc(quadrants->n_rigid_groups*sizeof(double));
- if ( aver_str == NULL ) {
+
+ avg_rot_str->aver_str = malloc(num_rigid_groups*sizeof(double));
+ if ( avg_rot_str->aver_str == NULL ) {
ERROR("Failed to allocate memory to correct empty panels.|n");
- free(aver_ang);
- return 1;
+ free(avg_rot_str->aver_ang);
+ free(avg_rot_str);
+ return NULL;
}
- aver_num_ang = malloc(quadrants->n_rigid_groups*sizeof(int));
- if ( aver_num_ang == NULL ) {
+
+ avg_rot_str->aver_num_ang = malloc(num_rigid_groups*sizeof(int));
+ if ( avg_rot_str->aver_num_ang == NULL ) {
ERROR("Failed to allocate memory to correct empty panels.|n");
- free(aver_ang);
- free(aver_str);
- return 1;
+ free(avg_rot_str->aver_ang);
+ free(avg_rot_str->aver_str);
+ free(avg_rot_str);
+ return NULL;
}
- for (i=0; i<quadrants->n_rigid_groups; i++) {
- aver_ang[i] = 0;
- aver_str[i] = 0;
- aver_num_ang[i] = 0;
+ for (i=0; i<num_rigid_groups; i++) {
+ avg_rot_str->aver_ang[i] = 0.0;
+ avg_rot_str->aver_str[i] = 0.0;
+ avg_rot_str->aver_num_ang[i] = 0;
+ }
+
+ return avg_rot_str;
+}
+
+
+void free_avg_angle_and_stretches(struct avg_rot_and_stretch* avg_rot_str)
+{
+ free(avg_rot_str->aver_ang);
+ free(avg_rot_str->aver_str);
+ free(avg_rot_str->aver_num_ang);
+}
+
+
+static int compute_rot_stretch_for_empty_panels(
+ struct rg_collection *quadrants,
+ struct rg_collection *connected,
+ struct geoptimiser_params *gparams,
+ struct connected_data *conn_data)
+{
+ struct avg_rot_and_stretch *avg_rot_str;
+ int di,i;
+
+ STATUS("Computing rotation and elongation corrections for groups "
+ "without the required number of measurements.\n");
+
+ avg_rot_str = initialize_avg_rot_stretch(quadrants->n_rigid_groups);
+ if ( avg_rot_str == NULL ) {
+ return 1;
}
for (di=0; di<connected->n_rigid_groups; di++) {
- if ( conn_data[di].n_peaks_in_conn>=min_num_peaks_per_panel ) {
- aver_ang[conn_data[di].num_quad] += conn_data[di].cang;
- aver_str[conn_data[di].num_quad] += conn_data[di].cstr;
- aver_num_ang[conn_data[di].num_quad]++;
+ if ( conn_data[di].n_peaks_in_conn >=
+ gparams->min_num_pix_per_conn_group ) {
+ avg_rot_str->aver_ang[conn_data[di].num_quad] +=
+ conn_data[di].cang;
+ avg_rot_str->aver_str[conn_data[di].num_quad] +=
+ conn_data[di].cstr;
+ avg_rot_str->aver_num_ang[conn_data[di].num_quad]++;
}
}
for ( i=0; i<quadrants->n_rigid_groups; i++ ) {
- if ( aver_num_ang[i]>0 ) {
- aver_ang[i] /= (double)aver_num_ang[i];
- aver_str[i] /= (double)aver_num_ang[i];
+ if ( avg_rot_str->aver_num_ang[i] > 0 ) {
+ avg_rot_str->aver_ang[i] /=
+ (double)avg_rot_str->aver_num_ang[i];
+ avg_rot_str->aver_str[i] /=
+ (double)avg_rot_str->aver_num_ang[i];
}
}
for ( di=0; di<connected->n_rigid_groups; di++ ) {
- if ( conn_data[di].n_peaks_in_conn<min_num_peaks_per_panel ) {
- if (aver_num_ang[conn_data[di].num_quad]>0) {
+ if ( conn_data[di].n_peaks_in_conn <
+ gparams->min_num_pix_per_conn_group ) {
+ if ( avg_rot_str->aver_num_ang[conn_data[di].num_quad]
+ > 0) {
conn_data[di].cang =
- aver_ang[conn_data[di].num_quad];
+ avg_rot_str->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 degrees\n",
- conn_data[di].name,
+ avg_rot_str->aver_str[conn_data[di].num_quad];
+ STATUS("Connected group %s has only %i useful "
+ "pixels. Using average angle: %0.4f "
+ "degrees\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",
+ STATUS("Connected group %s does not have enough "
+ " peaks (%i). It will not be moved.\n",
conn_data[di].name,
conn_data[di].n_peaks_in_conn);
}
}
}
- free(aver_ang);
- free(aver_str);
- free(aver_num_ang);
-
- return 0;
+ return 0;
}
-static void correct_angle_and_stretch(struct rg_collection *connected,
- struct detector *det,
- struct connected_data *conn_data,
- double use_clen, double stretch_coeff,
- int individual_coffset)
+static void correct_corner_coordinates(struct rg_collection *connected,
+ struct connected_data *conn_data)
{
int di, ip;
@@ -1235,55 +1403,26 @@ static void correct_angle_and_stretch(struct rg_collection *connected,
for ( ip=0; ip<connected->rigid_groups[di]->n_panels; ip++ ) {
struct panel *p;
- double newx, newy;
p = connected->rigid_groups[di]->panels[ip];
- newx =
- 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 = newx;
- p->fsy = newy;
- newx =
- 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 = newx;
- p->ssy = newy;
- }
- }
-
-
- if ( individual_coffset == 0 ) {
-
- int pi;
+ if ( ip == 0 ) {
- for (pi=0; pi<det->n_panels; pi++) {
- det->panels[pi].coffset -= use_clen*(1.0-stretch_coeff);
- }
- STATUS("Using a single offset distance for the whole detector: "
- "%f m.\n", det->panels[0].coffset);
+ p->cnx *= conn_data[di].cstr;
+ p->cny *= conn_data[di].cstr;
- for ( di=0; di<connected->n_rigid_groups; di++ ) {
- conn_data[di].cstr = stretch_coeff;
- }
+ } else {
- } else {
+ struct panel *p0;
+ double delta_x, delta_y;
- STATUS("Using an individual distance for each connected group.\n");
- for ( di=0; di<connected->n_rigid_groups; di++ ) {
- for ( ip=0; ip<connected->rigid_groups[di]->n_panels;
- ip++ ) {
+ p0 = connected->rigid_groups[di]->panels[0];
- struct panel *p;
+ delta_x = p->cnx-p0->cnx/conn_data[di].cstr;
+ delta_y = p->cny-p0->cny/conn_data[di].cstr;
- p = connected->rigid_groups[di]->panels[ip];
- p->coffset -= (1.0-conn_data[di].cstr)*p->clen;
+ p->cnx = p0->cnx + delta_x;
+ p->cny = p0->cny + delta_y;
}
}
@@ -1291,90 +1430,125 @@ static void correct_angle_and_stretch(struct rg_collection *connected,
}
-static void shift_panels(struct rg_collection *connected,
- struct connected_data *conn_data)
+static void correct_rotation_and_stretch(struct rg_collection *connected,
+ struct detector *det,
+ struct connected_data *conn_data,
+ double clen_to_use,
+ double stretch_coeff,
+ struct geoptimiser_params *gparams)
{
int di, ip;
+ STATUS("Applying rotation and stretch corrections.\n");
for ( di=0; di<connected->n_rigid_groups; di++ ) {
for ( ip=0; ip<connected->rigid_groups[di]->n_panels; ip++ ) {
struct panel *p;
+ double new_fsx, new_fsy, new_ssx, new_ssy;
p = connected->rigid_groups[di]->panels[ip];
- if ( ip == 0 ) {
+ new_fsx = p->fsx*cos(conn_data[di].cang)-
+ p->fsy*sin(conn_data[di].cang);
+ new_fsy = p->fsx*sin(conn_data[di].cang)+
+ p->fsy*cos(conn_data[di].cang);
+ new_ssx = p->ssx*cos(conn_data[di].cang)-
+ p->ssy*sin(conn_data[di].cang);
+ new_ssy = p->ssx*sin(conn_data[di].cang)+
+ p->ssy*cos(conn_data[di].cang);
+ p->fsx = new_fsx;
+ p->fsy = new_fsy;
+ p->ssx = new_ssx;
+ p->ssy = new_ssy;
+ }
+ }
- p->cnx *= conn_data[di].cstr;
- p->cny *= conn_data[di].cstr;
- } else {
+ if ( gparams->individual_coffset ) {
- struct panel *p0;
- double delta_x, delta_y;
-
- p0 = connected->rigid_groups[di]->panels[0];
+ 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++ ) {
- delta_x = (p->cnx-p0->cnx/conn_data[di].cstr);
- delta_y = (p->cny-p0->cny/conn_data[di].cstr);
+ struct panel *p;
- p->cnx = p0->cnx + delta_x * cos(conn_data[di].cang)
- - delta_y * sin(conn_data[di].cang);
- p->cny = p0->cny + delta_x * sin(conn_data[di].cang)
- + delta_y * cos(conn_data[di].cang);
+ p = connected->rigid_groups[di]->panels[ip];
+ p->coffset -= (1.0-conn_data[di].cstr)*clen_to_use;
}
}
+
+ } else {
+
+ int pi;
+
+ for ( di=0; di<connected->n_rigid_groups; di++ ) {
+ conn_data[di].cstr = stretch_coeff;
+ }
+
+ for ( pi=0; pi<det->n_panels; pi++) {
+ det->panels[pi].coffset -= clen_to_use*(1.0-stretch_coeff);
+ }
+ STATUS("Using a single offset distance for the whole "
+ "detector: %f m. Stretch ceofficient: %0.4f\n",
+ det->panels[0].coffset, stretch_coeff);
}
+
+ correct_corner_coordinates(connected, conn_data);
}
-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)
+static void adjust_panel(struct connected_data *conn_data, int di, int ip,
+ struct rg_collection *connected,
+ struct pixel_maps *pixel_maps,
+ struct pixel_maps *recomputed_pixel_maps,
+ struct avg_displacements *avg_displ,
+ double stretch_coeff,
+ struct enhanced_det *edet, 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;
+ //TODO
+
+ 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] >=
+
+ int pix_index = ifs+edet->width*iss;
+
+ recomputed_pixel_maps->pix_to_x[pix_index] /= c_stretch;
+ recomputed_pixel_maps->pix_to_y[pix_index] /= c_stretch;
+ if ( num_pix_displ[pix_index] >=
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]);
+ avg_displ->displ_x[pix_index] -=
+ (pixel_maps->pix_to_x[pix_index]-
+ recomputed_pixel_maps->pix_to_x[pix_index]);
+ avg_displ->displ_y[pix_index] -=
+ (pixel_maps->pix_to_y[pix_index]-
+ recomputed_pixel_maps->pix_to_y[pix_index]);
}
}
}
}
-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,
- double stretch_coeff, int aw,
- double *displ_x, double *displ_y,
- int *num_pix_displ)
+static void adjust_displ_for_stretch(struct rg_collection *connected,
+ struct pixel_maps *pixel_maps,
+ struct pixel_maps *recomputed_pixel_maps,
+ struct connected_data *conn_data,
+ double stretch_coeff,
+ struct enhanced_det *edet,
+ struct avg_displacements *avg_displ,
+ int *num_pix_displ)
{
int di, ip;
@@ -1382,47 +1556,57 @@ 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++) {
-
- 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);
+ adjust_panel(conn_data, di, ip, connected,
+ pixel_maps, recomputed_pixel_maps,
+ avg_displ, stretch_coeff, edet,
+ num_pix_displ);
}
}
}
-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)
+static void fill_av_conn(struct rg_collection *connected, int di,
+ struct connected_data *conn_data,
+ int *num_pix_displ, struct enhanced_det *edet,
+ double *list_displ_in_conn_fs,
+ double *list_displ_in_conn_ss,
+ struct avg_displacements *avg_displ)
{
struct panel *p;
- int ifs, iss;
+ int ifs, iss, ip;
- p = connected->rigid_groups[di]->panels[ip];
+ int counter = 0;
- for ( ifs=p->min_fs; ifs<p->max_fs+1; ifs++ ) {
- for ( iss=p->min_ss; iss<p->max_ss+1; iss++ ) {
+ for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
+
+ 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++;
+ int pix_index = ifs+edet->width*iss;
+
+ if ( num_pix_displ[pix_index] >=
+ conn_data[di].num_peaks_per_pixel ) {
+ list_displ_in_conn_fs[counter] =
+ avg_displ->displ_x[pix_index];
+ list_displ_in_conn_ss[counter] =
+ avg_displ->displ_y[pix_index];
+ counter++;
+ }
}
}
}
+
+ if ( counter != conn_data[di].n_peaks_in_conn ) {
+ printf("counter: %i n_peaks_in_conn: %i\n",
+ counter, conn_data[di].n_peaks_in_conn);
+ exit(0);
+ }
}
-static void fill_con_data_sh(struct connected_data *conn_data,
+static void fill_conn_data_sh(struct connected_data *conn_data,
double *av_in_panel_fs,
double *av_in_panel_ss, int di,
double max_peak_distance)
@@ -1431,11 +1615,11 @@ static void fill_con_data_sh(struct connected_data *conn_data,
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 of considered pixels: %i, shifts (in pixels) x,y: %0.8f, %0.8f\n",
+ STATUS("Panel %s, num pixels: %i, shifts (in pixels) 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 ) {
+ 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 pixels."
" Increase the value of the max_peak_distance parameter!\n",
modulus2d(conn_data[di].sh_x, conn_data[di].sh_y),
@@ -1444,162 +1628,183 @@ static void fill_con_data_sh(struct connected_data *conn_data,
}
-static int compute_shifts(struct rg_collection *connected,
- struct connected_data *conn_data,
- int *num_pix_displ, int aw,
- int min_num_peaks_per_panel,
- double dfv, double max_peak_distance,
- double *displ_x, double *displ_y)
+static int compute_shift(struct rg_collection *connected,
+ struct connected_data *conn_data,
+ int *num_pix_displ,
+ struct enhanced_det *edet,
+ struct geoptimiser_params *gparams,
+ struct avg_displacements *avg_displ)
{
- STATUS("Computing average shifts for connected groups.\n");
+ STATUS("Computing shift corrections.\n");
- int di, ip;
+ int di;
for ( di=0; di<connected->n_rigid_groups; di++ ) {
- int cmaxfs;
- int cmaxss;
- int num_all_pixels;
- double *av_in_panel_fs;
- double *av_in_panel_ss;
+ double *list_displ_in_conn_fs;
+ double *list_displ_in_conn_ss;
- cmaxfs = connected->rigid_groups[di]->panels[0]->max_fs+1-
- connected->rigid_groups[di]->panels[0]->min_fs;
- cmaxss = connected->rigid_groups[di]->panels[0]->max_ss+1-
- connected->rigid_groups[di]->panels[0]->min_ss;
-
- num_all_pixels = cmaxfs*cmaxss*connected->rigid_groups[di]->n_panels;
-
- av_in_panel_fs = malloc(num_all_pixels*sizeof(double));
- if ( av_in_panel_fs == NULL ) {
+ list_displ_in_conn_fs = malloc(conn_data[di].n_peaks_in_conn*
+ sizeof(double));
+ if ( list_displ_in_conn_fs == NULL ) {
ERROR("Failed to allocate memory for computing shifts\n");
return 1;
}
- av_in_panel_ss = malloc(num_all_pixels*sizeof(double));
- if ( av_in_panel_ss == NULL ) {
+ list_displ_in_conn_ss = malloc(conn_data[di].n_peaks_in_conn*
+ sizeof(double));
+ if ( list_displ_in_conn_ss == NULL ) {
ERROR("Failed to allocate memory for computing shifts\n");
- free(av_in_panel_fs);
+ free(list_displ_in_conn_fs);
return 1;
}
- conn_data[di].n_peaks_in_conn = 0;
-
- for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
+ fill_av_conn(connected, di, conn_data, num_pix_displ, edet,
+ list_displ_in_conn_fs, list_displ_in_conn_ss,
+ avg_displ);
- 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 ( conn_data[di].n_peaks_in_conn>=min_num_peaks_per_panel ) {
-
- fill_con_data_sh(conn_data, av_in_panel_fs,
- av_in_panel_ss, di,
- max_peak_distance);
+ if ( conn_data[di].n_peaks_in_conn >=
+ gparams->min_num_pix_per_conn_group ) {
+ fill_conn_data_sh(conn_data, list_displ_in_conn_fs,
+ list_displ_in_conn_ss, di,
+ gparams->max_peak_dist);
} else {
- conn_data[di].sh_x = dfv;
- conn_data[di].sh_y = dfv;
+ conn_data[di].sh_x = -10000.0;
+ conn_data[di].sh_y = -10000.0;
}
- free(av_in_panel_fs);
- free(av_in_panel_ss);
- }
+ free(list_displ_in_conn_fs);
+ free(list_displ_in_conn_ss);
+ }
return 0;
}
-static int compute_shifts_for_empty_panels(struct rg_collection *quadrants,
- struct rg_collection *connected,
- struct connected_data *conn_data,
- int min_num_peaks_per_panel)
+struct avg_shift *initialize_avg_shift(int num_rigid_groups)
{
+ struct avg_shift *avg_sh;
+ int i;
- double *aver_x;
- double *aver_y;
- int *num_aver;
- int di, i;
+ avg_sh = malloc(sizeof(struct avg_shift));
+ if ( avg_sh == NULL ) {
+ ERROR("Failed to allocate memory to compute shifts for "
+ "empty panels.\n");
+ return NULL;
+ }
- // shifts for empty
- aver_x = malloc(quadrants->n_rigid_groups*sizeof(double));
- if ( aver_x == NULL ) {
+ avg_sh->aver_x = malloc(num_rigid_groups*sizeof(double));
+ if ( avg_sh->aver_x == NULL ) {
ERROR("Failed to allocate memory to compute shifts for "
"empty panels.\n");
- return 1;
+ free(avg_sh);
+ return NULL;
}
- aver_y = malloc(quadrants->n_rigid_groups*sizeof(double));
- if ( aver_y == NULL ) {
+ avg_sh->aver_y = malloc(num_rigid_groups*sizeof(double));
+ if ( avg_sh->aver_y == NULL ) {
ERROR("Failed to allocate memory to compute shifts for "
"empty panels.\n");
- free(aver_x);
- return 1;
+ free(avg_sh->aver_x);
+ free(avg_sh);
+ return NULL;
}
- num_aver = malloc(quadrants->n_rigid_groups*sizeof(int));
- if ( num_aver == NULL ) {
+ avg_sh->aver_num_sh = malloc(num_rigid_groups*sizeof(int));
+ if ( avg_sh->aver_num_sh == NULL ) {
ERROR("Failed to allocate memory to compute shifts for "
"empty panels.\n");
- free(aver_x);
- free(aver_y);
- return 1;
+ free(avg_sh->aver_x);
+ free(avg_sh->aver_y);
+ free(avg_sh);
+ return NULL;
}
- for ( i=0; i<quadrants->n_rigid_groups; i++ ) {
- aver_x[i] = 0;
- aver_y[i] = 0;
- num_aver[i] = 0;
+ for ( i=0; i<num_rigid_groups; i++ ) {
+ avg_sh->aver_x[i] = 0.0;
+ avg_sh->aver_y[i] = 0.0;
+ avg_sh->aver_num_sh[i] = 0;
}
+ return avg_sh;
+}
+
+
+void free_avg_shift(struct avg_shift *av_sh) {
+ free(av_sh->aver_x);
+ free(av_sh->aver_y);
+ free(av_sh->aver_num_sh);
+ free(av_sh);
+}
+
+
+static int compute_shift_for_empty_panels(struct rg_collection *quadrants,
+ struct rg_collection *connected,
+ struct connected_data *conn_data,
+ struct geoptimiser_params* gparams)
+{
+
+ struct avg_shift *av_sh;
+ int di, i;
+
+ STATUS("Computing shift corrections for groups without the required "
+ "number of measurements.\n");
+ av_sh = initialize_avg_shift(quadrants->n_rigid_groups);
+ if ( av_sh == NULL ) return 1;
+
for ( di=0; di<connected->n_rigid_groups; di++ ) {
- if ( conn_data[di].n_peaks_in_conn>=min_num_peaks_per_panel ) {
- aver_x[conn_data[di].num_quad] += conn_data[di].sh_x;
- aver_y[conn_data[di].num_quad] += conn_data[di].sh_y;
- num_aver[conn_data[di].num_quad]++;
+ if ( conn_data[di].n_peaks_in_conn >=
+ gparams->min_num_pix_per_conn_group ) {
+ av_sh->aver_x[conn_data[di].num_quad] +=
+ conn_data[di].sh_x;
+ av_sh->aver_y[conn_data[di].num_quad] +=
+ conn_data[di].sh_y;
+ av_sh->aver_num_sh[conn_data[di].num_quad]++;
}
}
for ( i=0; i<quadrants->n_rigid_groups; i++ ) {
- if (num_aver[i]>0) {
- aver_x[i] /= (double)num_aver[i];
- aver_y[i] /= (double)num_aver[i];
+ if (av_sh->aver_num_sh[i]>0) {
+ av_sh->aver_x[i] /= (double)av_sh->aver_num_sh[i];
+ av_sh->aver_y[i] /= (double)av_sh->aver_num_sh[i];
}
}
for (di=0; di<connected->n_rigid_groups; di++) {
- if ( conn_data[di].n_peaks_in_conn<min_num_peaks_per_panel ) {
- 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 (in pixels) X,Y: "
- "%0.2f,%0.2f\n", conn_data[di].name,
+ if ( conn_data[di].n_peaks_in_conn <
+ gparams->min_num_pix_per_conn_group ) {
+ if ( av_sh->aver_num_sh[conn_data[di].num_quad] > 0 ) {
+ conn_data[di].sh_x =
+ av_sh->aver_x[conn_data[di].num_quad];
+ conn_data[di].sh_y =
+ av_sh->aver_y[conn_data[di].num_quad];
+ STATUS("Panel %s doesn't not have eough (%i) "
+ "peaks. Using average shifts (in pixels) "
+ "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",
+ "It will not be moved.\n",
conn_data[di].name,
conn_data[di].n_peaks_in_conn);
}
}
}
- free(aver_x);
- free(aver_y);
- free(num_aver);
+ free_avg_shift(av_sh);
return 0;
}
-static void correct_shifts(struct rg_collection *connected,
- struct connected_data *conn_data,
- double dfv, double clen_to_use)
+static void correct_shift(struct rg_collection *connected,
+ struct connected_data *conn_data,
+ double clen_to_use)
{
int di;
int ip;
+ STATUS("Applying shift corrections.\n");
+
for ( di=0;di<connected->n_rigid_groups;di++ ) {
for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
@@ -1607,300 +1812,246 @@ static void correct_shifts(struct rg_collection *connected,
p = connected->rigid_groups[di]->panels[ip];
- if ( conn_data[di].sh_x>dfv+1.0 &&
- conn_data[di].sh_y > dfv+1.0 ) {
+ if ( conn_data[di].sh_x > -9999.0 &&
+ conn_data[di].sh_y > -9999.0 ) {
p->cnx -= conn_data[di].sh_x;
p->cny -= conn_data[di].sh_y;
} else {
- STATUS("For some reason connected group %s is "
- "empty! Left unchanged.\n",
- p->name);
+ STATUS("For some reason shifts for panel %s has "
+ "not been computed!\n", p->name);
}
}
}
}
-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)
+static struct connected_stretch_and_angles *initialize_connected_stretch_angles(
+ struct rg_collection *connected)
{
- 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;
- }
+ struct connected_stretch_and_angles *csaa;
- *num_ang = *num_ang+1;
- }
- }
- }
+ csaa = malloc(sizeof(struct connected_stretch_and_angles));
+ if ( csaa == NULL ) {
+ ERROR("Failed to allocate memory to compute angles and "
+ "stretch.\n");
+ return NULL;
+ }
+ 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");
+ free(csaa);
+ return NULL;
}
+ csaa->num_angles = malloc(connected->n_rigid_groups*sizeof(long));
+ if ( csaa->num_angles == NULL ) {
+ ERROR("Failed to allocate memory to compute angles and "
+ "stretch.\n");
+ free(csaa->stretch_coeff);
+ free(csaa);
+ return NULL;
+ }
+ csaa->num_coeff=0;
+ return csaa;
}
-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)
+static void scan_p1(int ip0, int ip1, struct rg_collection *connected,
+ struct avg_displacements *avg_displ,
+ struct connected_data *conn_data,
+ struct enhanced_det *edet,
+ struct pixel_maps *pixel_maps,
+ int* num_pix_displ,
+ int di, double min_dist,
+ long *num_ang, int ifs0, int iss0,
+ double c_x0, double c_y0, double cd_x0, double cd_y0,
+ int compute, double *angles, double *stretches)
{
- double coX, coY, cdX, cdY;
- if ( num_pix_displ[ifs+aw*iss]>=
- conn_data[di].num_peaks_per_pixel ) {
+ int iss1, ifs1;
- int ifs1, iss1;
- int max_fs1_tmp = p0->max_fs;
- int max_ss1_tmp = p0->max_ss;
+ struct panel *p1 = connected->rigid_groups[di]->panels[ip1];
- if ( *num_ang>=max_num_ang ) return -2;
+ int min_ss_p1, min_fs_p1;
- 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];
+ if ( ip0 == ip1 ) {
+ min_fs_p1 = ifs0;
+ min_ss_p1 = iss0;
+ } else {
+ min_fs_p1 = p1->min_fs;
+ min_ss_p1 = p1->min_ss;
+ }
- for (ifs1=ifs+1; ifs1<max_fs1_tmp+1; ifs1++) {
+ for ( iss1=min_ss_p1; iss1<p1->max_ss+1; iss1++ ) {
- if ( ifs1 == max_fs1_tmp ) {
- max_fs1_tmp = p1->max_fs;
- }
+ for ( ifs1=min_fs_p1; ifs1<p1->max_fs+1; ifs1++ ) {
- for (iss1=iss+1; iss1<max_ss1_tmp+1; iss1++) {
+ int pix_index1 = ifs1+edet->width*iss1;
+
+ if ( num_pix_displ[pix_index1]>=
+ conn_data[di].num_peaks_per_pixel ) {
- if ( iss1 == max_ss1_tmp ) {
- max_ss1_tmp = p1->max_ss;
+ double dist;
+ double c_x1, c_y1, cd_x1, cd_y1;
+ double d_c_x, d_c_y, d_cd_x, d_cd_y;
+ double len1, len2;
+
+ c_x1 = pixel_maps->pix_to_x[pix_index1];
+ c_y1 = pixel_maps->pix_to_y[pix_index1];
+ cd_x1 = c_x1 - avg_displ->displ_x[pix_index1];
+ cd_y1 = c_y1 - avg_displ->displ_y[pix_index1];
+ d_c_x = c_x1-c_x0;
+ d_c_y = c_y1-c_y0;
+ d_cd_x = cd_x1-cd_x0;
+ d_cd_y = cd_y1-cd_y0;
+
+ dist = modulus2d(d_c_x,d_c_y);
+ if ( dist < min_dist ) continue;
+
+ len1 = modulus2d(d_c_x, d_c_y);
+ len2 = modulus2d(d_cd_x, d_cd_y);
+ if ( len1<FLT_EPSILON || len2<FLT_EPSILON ) {
+ continue;
}
- if ( num_pix_displ[ifs1+aw*iss1]>=
- conn_data[di].num_peaks_per_pixel ) {
+ if (compute) {
- double dist;
- double coX1, coY1, cdX1, cdY1;
- double len1, len2;
- double scalM;
+ double scal_m;
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;
- }
+ scal_m = d_c_x * d_cd_x+
+ d_c_y * d_cd_y -
+ FLT_EPSILON;
multlen = len1*len2;
- if ( fabs(scalM)>=multlen ) {
+ if ( fabs(scal_m)>=multlen ) {
angles[*num_ang] = 0.0;
} else {
- angles[*num_ang] = 1.0;
-
- angles[*num_ang] =
- acos(scalM/multlen);
+ angles[*num_ang] = acos(scal_m
+ /multlen);
- if ((coY1-coY)*(cdX1-cdX)-
- (coX1-coX)*(cdY1-cdY) < 0) {
+ if (d_c_y * d_cd_x -
+ d_c_x * d_cd_y < 0) {
angles[*num_ang] *= -1.;
}
}
stretches[*num_ang] = len1/len2;
-
- *num_ang = *num_ang+1;
}
+
+ *num_ang = *num_ang+1;
}
}
}
- return 0;
}
+static void scan_p0(int ip0, struct rg_collection *connected,
+ struct avg_displacements *avg_displ,
+ struct connected_data *conn_data,
+ struct enhanced_det *edet,
+ struct pixel_maps *pixel_maps,
+ int* num_pix_displ,
+ int di, double min_dist,
+ long *num_ang, int compute,
+ double *angles, double *stretches)
+{
+
+ int iss0, ifs0, ip1;
+
+ struct panel *p0 = connected->rigid_groups[di]->panels[ip0];
+ for ( iss0=p0->min_ss; iss0<p0->max_ss+1; iss0++ ) {
-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 aw,
- int min_num_peaks_per_panel,
- double dist_coeff_ang_str,
- int num_peaks_per_pixel,
- double man_stretching_coeff,
- double *stretch_coeff)
+ for ( ifs0=p0->min_fs; ifs0<p0->max_fs+1; ifs0++ ) {
+
+ int pix_index0 = ifs0+edet->width*iss0;
+
+ if ( num_pix_displ[pix_index0]>=
+ conn_data[di].num_peaks_per_pixel ) {
+
+ double c_x0, c_y0, cd_x0, cd_y0;
+
+ c_x0 = pixel_maps->pix_to_x[pix_index0];
+ c_y0 = pixel_maps->pix_to_y[pix_index0];
+ cd_x0 = c_x0 - avg_displ->displ_x[pix_index0];
+ cd_y0 = c_y0 - avg_displ->displ_y[pix_index0];
+
+ for ( ip1=ip0;
+ ip1<connected->rigid_groups[di]->n_panels;
+ ip1++ ) {
+ scan_p1(ip0, ip1, connected, avg_displ,
+ conn_data, edet, pixel_maps,
+ num_pix_displ, di, min_dist,
+ num_ang, ifs0, iss0, c_x0,
+ c_y0, cd_x0, cd_y0, compute,
+ angles, stretches);
+ }
+ }
+ }
+ }
+}
+
+
+static double compute_rotation_and_stretch(struct rg_collection *connected,
+ struct connected_data *conn_data,
+ struct enhanced_det *edet,
+ int *num_pix_displ,
+ struct pixel_maps *pixel_maps,
+ struct avg_displacements *avg_displ,
+ double dist_coeff_for_rot_str,
+ struct geoptimiser_params *gparams)
{
int di;
- int num_coeff;
double stretch_cf;
struct connected_stretch_and_angles *csaa;
- csaa = malloc(sizeof(struct connected_stretch_and_angles));
+ STATUS("Computing rotation and stretch corrections.\n");
+
+ csaa = initialize_connected_stretch_angles(connected);
if ( csaa == NULL ) {
- 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");
- 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");
- free(csaa->stretch_coeff);
- free(csaa);
- return 1;
+ return -1.0;
}
- 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 ) {
+ if ( conn_data[di].n_peaks_in_conn <
+ gparams->min_num_pix_per_conn_group ) {
continue;
}
- unsigned int max_num_ang = 0;
+ long max_num_ang = 0;
+ double min_dist;
double* angles;
double* stretches;
- int cmaxfs;
- int cmaxss;
-
- struct panel *p;
- double minrad;
- int num_ang = 0;
- int ip0, ip1;
+ struct panel *first_p;
+ long num_ang = 0;
+ int ip0;
+ int num_pix_first_p;
- p = connected->rigid_groups[di]->panels[0];
+ first_p = connected->rigid_groups[di]->panels[0];
- cmaxfs = p->max_fs+1-p->min_fs;
- cmaxss = p->max_ss+1-p->min_ss;
+ num_pix_first_p = (first_p->max_fs+1-first_p->min_fs)*
+ (first_p->max_ss+1-first_p->min_ss);
// TODO: MINRAD HERE IS NOT UNIVERSAL
- minrad = dist_coeff_ang_str*sqrt(cmaxfs*cmaxss*
- connected->rigid_groups[di]->n_panels);
+ min_dist = dist_coeff_for_rot_str*sqrt(num_pix_first_p*
+ connected->rigid_groups[di]->n_panels);
for ( ip0=0; ip0<connected->rigid_groups[di]->n_panels; ip0++ ) {
- struct panel *p0 = connected->rigid_groups[di]->panels[ip0];
-
- for ( ip1=0; ip1<connected->rigid_groups[di]->n_panels;
- ip1++ ) {
-
- struct panel *p1 =
- connected->rigid_groups [di]->panels[ip1];
-
- int ifs, iss;
- int min_fs_tmp = p0->min_fs;
- int max_fs_tmp = p0->max_fs;
- int min_ss_tmp = p0->min_ss;
- int max_ss_tmp = p0->max_ss;
-
- for (ifs=min_fs_tmp; ifs<max_fs_tmp+1; ifs++) {
-
- if ( ifs == max_fs_tmp ) {
- min_fs_tmp = p1->min_fs;
- max_fs_tmp = p1->max_fs;
- }
-
- 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;
- }
-
- 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);
-
- }
- }
- }
+ scan_p0(ip0, connected, avg_displ, conn_data, edet,
+ pixel_maps, num_pix_displ, di, min_dist,
+ &num_ang, 0, NULL, NULL);
}
- max_num_ang = conn_data[di].n_peaks_in_conn*
- conn_data[di].n_peaks_in_conn;
max_num_ang = num_ang+1;
angles = malloc(max_num_ang*sizeof(double));
@@ -1910,7 +2061,7 @@ static int compute_angles_and_stretch(struct rg_collection *connected,
free(csaa->stretch_coeff);
free(csaa->num_angles);
free(csaa);
- return 1;
+ return -1.0;
}
stretches = malloc(max_num_ang*sizeof(double));
if ( stretches == NULL ) {
@@ -1920,71 +2071,25 @@ static int compute_angles_and_stretch(struct rg_collection *connected,
free(csaa->stretch_coeff);
free(csaa->num_angles);
free(csaa);
- return 1;
+ return -1.0;
}
num_ang = 0;
for ( ip0=0; ip0<connected->rigid_groups[di]->n_panels; ip0++ ) {
- struct panel *p0 = connected->rigid_groups[di]->panels[ip0];
-
- for ( ip1=0; ip1<connected->rigid_groups[di]->n_panels;
- ip1++ ) {
-
- struct panel *p1 =
- connected->rigid_groups [di]->panels[ip1];
-
- int ifs, iss;
- int min_fs_tmp = p0->min_fs;
- int max_fs_tmp = p0->max_fs;
- int min_ss_tmp = p0->min_ss;
- int max_ss_tmp = p0->max_ss;
-
- for (ifs=min_fs_tmp; ifs<max_fs_tmp+1; ifs++) {
-
- if ( ifs == max_fs_tmp ) {
- min_fs_tmp = p1->min_fs;
- max_fs_tmp = p1->max_fs;
- }
-
- 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;
- }
-
- 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;
- }
- }
- }
+ scan_p0(ip0, connected, avg_displ, conn_data, edet,
+ pixel_maps, num_pix_displ, di, min_dist,
+ &num_ang, 1, angles, stretches);
}
- if ( num_ang<1 ) continue;
- conn_data[di].cang = -comp_median(angles,num_ang);
- conn_data[di].cstr = comp_median(stretches,num_ang);
+ if ( num_ang < 1 ) continue;
+ conn_data[di].cang = -comp_median(angles, num_ang);
+ conn_data[di].cstr = comp_median(stretches, num_ang);
- STATUS("Connected group %s:\n"
- " Number of measurements: %i Angle: %0.4f deg "
- "Stretch coefficient: %0.4f\n",
- conn_data[di].name, num_ang, conn_data[di].cang,
- conn_data[di].cstr);
+ STATUS("Panel %s, num: %li, angle: %0.4f deg, stretch coeff: "
+ "%0.4f\n", conn_data[di].name, num_ang, conn_data[di].cang,
+ conn_data[di].cstr);
csaa->stretch_coeff[csaa->num_coeff] = conn_data[di].cstr;
csaa->num_angles[csaa->num_coeff] = num_ang;
@@ -1994,55 +2099,57 @@ static int compute_angles_and_stretch(struct rg_collection *connected,
free(stretches);
}
+ stretch_cf = 1.0;
+
+ printf("Computing overall stretch coefficient.\n");
- num_coeff = csaa->num_coeff;
+ if ( csaa->num_coeff>0 ) {
- stretch_cf = 1;
- if (num_coeff>0) {
+ int peaks_per_p;
- int ipp;
+ peaks_per_p = gparams->min_num_peaks_per_pix;
- for ( ipp=num_peaks_per_pixel; ipp>=0; ipp-- ) {
+ while ( peaks_per_p>=0 ) {
double total_num;
- int di;
+ long di;
+ stretch_cf = 0;
total_num = 0;
- for ( di=0; di<num_coeff; di++ ) {
- if ( conn_data[di].num_peaks_per_pixel>=ipp ) {
+ for ( di=0; di<csaa->num_coeff; di++ ) {
+ if ( conn_data[di].num_peaks_per_pixel >=
+ peaks_per_p ) {
+ stretch_cf += csaa->stretch_coeff[di]*
+ (double)csaa->num_angles[di];
total_num += csaa->num_angles[di];
}
}
- if ( total_num>1 ) {
- total_num = 1./total_num;
- } else {
- continue;
- }
- 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];
- }
+
+ if ( total_num > 0 ) {
+
+ stretch_cf /= total_num;
+
+ printf("(Using only connected groups for which "
+ "the minimum number of measurements per "
+ "pixel is %i).\n", peaks_per_p);
+ break;
}
- break;
+ peaks_per_p--;
}
}
- if ( stretch_cf<FLT_EPSILON ) {
+ if ( stretch_cf < FLT_EPSILON ) {
stretch_cf = 1.0;
}
- STATUS("The average stretch coefficient for all patterns is %0.4f\n",
+ STATUS("The global stretch coefficient for the patterns is %0.4f\n",
stretch_cf);
- if ( man_stretching_coeff>FLT_EPSILON ) {
- stretch_cf = man_stretching_coeff;
- STATUS("Using manually set stretch coefficient: %0.4f\n",
- stretch_cf);
-
+ if ( gparams->nostretch ) {
+ stretch_cf = 1.0;
+ STATUS("However, distance offset will not be optimized, so the "
+ "stretching coefficient has been set to 1.0\n");
for ( di=0; di<connected->n_rigid_groups; di++ ) {
- conn_data[di].cstr = man_stretching_coeff;
+ conn_data[di].cstr = stretch_cf;
}
}
@@ -2051,9 +2158,7 @@ static int compute_angles_and_stretch(struct rg_collection *connected,
free(csaa->num_angles);
free(csaa);
- *stretch_coeff = stretch_cf;
-
- return 0;
+ return stretch_cf;
}
@@ -2114,19 +2219,18 @@ static int unpack_slab(struct image *image)
}
for ( ss=0; ss<p->h; ss++ ) {
- for ( fs=0; fs<p->w; fs++ ) {
+ for ( fs=0; fs<p->w; fs++ ) {
- int idx;
- int cfs, css;
+ int idx;
+ int cfs, css;
- cfs = fs+p->min_fs;
- css = ss+p->min_ss;
- idx = cfs + css*image->width;
+ cfs = fs+p->min_fs;
+ css = ss+p->min_ss;
+ idx = cfs + css*image->width;
- image->dp[pi][fs+p->w*ss] = image->data[idx];
- image->bad[pi][fs+p->w*ss] = 0;
-
- }
+ image->dp[pi][fs+p->w*ss] = image->data[idx];
+ image->bad[pi][fs+p->w*ss] = 0;
+ }
}
}
@@ -2188,8 +2292,7 @@ static int draw_detector(cairo_surface_t *surf, struct image *image,
}
-static int save_data_to_png(char *filename, struct detector *det,
- int max_fs, int max_ss, double default_fill_value,
+static int save_data_to_png(char *filename, struct enhanced_det *edet,
double *data)
{
struct image im;
@@ -2201,18 +2304,18 @@ static int save_data_to_png(char *filename, struct detector *det,
cairo_status_t r;
cairo_surface_t *surf;
- im.data = malloc((max_fs+1)*(max_ss+1)*sizeof(float));
+ im.data = malloc((edet->width)*(edet->height)*sizeof(float));
if ( im.data == NULL ) {
ERROR("Failed to allocate memory to save data.\n");
return 1;
}
- im.det = det;
- im.width = max_fs+1;
- im.height = max_ss+1;
+ im.det = edet->det;
+ im.width = edet->width;
+ im.height = edet->height;
im.flags = NULL;
- for ( i=0; i<(max_fs+1)*(max_ss+1); i++) {
- if ( data[i] == default_fill_value ) {
+ for ( i=0; i<(edet->width)*(edet->height); i++) {
+ if ( data[i] == -10000.0) {
im.data[i] = 0.0;
} else if ( data[i] > 1.0) {
im.data[i] = 1.0;
@@ -2264,61 +2367,9 @@ static int save_data_to_png(char *filename, struct detector *det,
#endif /* HAVE_SAVE_TO_PNG */
-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 check_and_enforce_cspad_dist(struct detector *det, int enforce)
+int check_and_enforce_cspad_dist(struct geoptimiser_params *gparams,
+ struct detector *det)
{
int np = 0;
int num_errors_found = 0;
@@ -2334,7 +2385,7 @@ int check_and_enforce_cspad_dist(struct detector *det, int enforce)
struct panel *op = &det->panels[np+1];
dist2 = (( ep->cnx - op->cnx )*( ep->cnx - op->cnx ) +
- ( ep->cny - op->cny )*( ep->cny - op->cny ));
+ ( ep->cny - op->cny )*( ep->cny - op->cny ));
if ( dist2 > (dist_to_check+tol)*(dist_to_check+tol) ||
dist2 < (dist_to_check-tol)*(dist_to_check-tol) ) {
@@ -2345,7 +2396,7 @@ int check_and_enforce_cspad_dist(struct detector *det, int enforce)
"is outside acceptable margins.\n", ep->name,
op->name);
- if ( enforce ) {
+ if ( gparams->enforce_cspad_layout ) {
double new_op_cx, new_op_cy;
@@ -2368,7 +2419,7 @@ int check_and_enforce_cspad_dist(struct detector *det, int enforce)
STATUS("Warning: relative orientation between panels "
"%s and %s is incorrect.\n", ep->name, op->name);
- if ( enforce ) {
+ if ( gparams->enforce_cspad_layout ) {
STATUS("Enforcing relative orientation....\n");
@@ -2385,67 +2436,313 @@ int check_and_enforce_cspad_dist(struct detector *det, int enforce)
}
- }
+ }
return num_errors_found;
}
+static struct connected_data *initialize_conn_data(struct rg_collection *quadrants,
+ struct rg_collection *connected)
+{
+
+ struct connected_data *conn_data;
+
+ conn_data = malloc(connected->n_rigid_groups*
+ sizeof(struct connected_data));
+
+ int di;
+
+ for (di=0; di<connected->n_rigid_groups; di++) {
+
+ conn_data[di].num_quad = find_quad_for_connected(
+ connected->rigid_groups[di],
+ quadrants);
+ conn_data[di].cang = 0.0;
+ conn_data[di].cstr = 1.0;
+ conn_data[di].sh_x = -10000.0;
+ conn_data[di].sh_y = -10000.0;
+ 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;
+ }
+
+ return conn_data;
+}
+
+
+static struct pixel_displ_list *initialize_pixel_displacement_list(
+ struct enhanced_det *edet)
+{
+
+ struct pixel_displ_list *pix_displ_list;
+ int ipx;
+
+ pix_displ_list = malloc(sizeof(struct pixel_displ_list));
+
+ pix_displ_list->pix_displ_list = calloc(edet->num_pix,
+ sizeof(struct single_pixel_displ));
+ if ( pix_displ_list->pix_displ_list == NULL ) {
+ ERROR("Error allocating memory for pixel displacement data.\n");
+ free(pix_displ_list);
+ return NULL;
+ }
+ pix_displ_list->curr_pix_displ = calloc(edet->num_pix,
+ sizeof(struct single_pixel_displ*));
+ if ( pix_displ_list->curr_pix_displ == NULL ) {
+ ERROR("Error allocating memory for pixel displacement data.\n");
+ free(pix_displ_list->pix_displ_list);
+ free(pix_displ_list);
+ return NULL;
+ }
+ pix_displ_list->num_pix_displ = calloc(edet->num_pix, sizeof(int));
+ if ( pix_displ_list->num_pix_displ == NULL ) {
+ ERROR("Error allocating memory for pixel displacement data.\n");
+ free(pix_displ_list->curr_pix_displ);
+ free(pix_displ_list->pix_displ_list);
+ free(pix_displ_list);
+ return NULL;
+ }
+
+ for ( ipx=0; ipx<edet->num_pix; ipx++ ) {
+ pix_displ_list->pix_displ_list[ipx].dfs = -10000.0;
+ pix_displ_list->pix_displ_list[ipx].dss = -10000.0;
+ pix_displ_list->pix_displ_list[ipx].ne = NULL;
+ pix_displ_list->curr_pix_displ[ipx] = &pix_displ_list->pix_displ_list[ipx];
+ pix_displ_list->num_pix_displ[ipx] = 0;
+ }
+
+ return pix_displ_list;
+}
+
+
+static void free_pixel_displacement_list(
+ struct pixel_displ_list *pix_displ_list,
+ struct enhanced_det *edet)
+{
+ int i;
+ struct single_pixel_displ *curr = NULL;
+ struct single_pixel_displ *next = NULL;
+
+ for ( i=0; i<edet->num_pix; i++ ) {
+
+ curr = &pix_displ_list->pix_displ_list[i];
+
+ if ( curr->ne != NULL ) {
+ curr = curr->ne;
+ while ( curr != NULL ) {
+ next = curr->ne;
+ free(curr);
+ curr = next;
+ }
+ }
+ }
+
+ free(pix_displ_list->curr_pix_displ);
+ free(pix_displ_list->pix_displ_list);
+ free(pix_displ_list->num_pix_displ);
+ free(pix_displ_list);
+}
+
+
+static struct avg_displacements *initialize_average_displacement(
+ struct enhanced_det *edet)
+
+{
+ static struct avg_displacements *avg_displ;
+
+ avg_displ = malloc(sizeof(struct avg_displacements));
+ avg_displ->displ_x = calloc(edet->num_pix, sizeof(double));
+ if ( avg_displ->displ_x == NULL ) {
+ ERROR("Error allocating memory for pixel properties.\n");
+ return NULL;
+ }
+ avg_displ->displ_y = calloc(edet->num_pix, sizeof(double));
+ if ( avg_displ->displ_y == NULL ) {
+ ERROR("Error allocating memory for pixel properties.\n");
+ free(avg_displ->displ_x);
+ free(avg_displ);
+ return NULL;
+ }
+ avg_displ->displ_abs = calloc(edet->num_pix, sizeof(double));
+ if ( avg_displ->displ_abs == NULL ) {
+ ERROR("Error allocating memory for pixel properties.\n");
+ free(avg_displ->displ_x);
+ free(avg_displ->displ_y);
+ free(avg_displ);
+ return NULL;
+ }
+
+ return avg_displ;
+}
+
+
+static void free_avg_displacement(struct avg_displacements * avg_displ)
+{
+ free(avg_displ->displ_x);
+ free(avg_displ->displ_y);
+ free(avg_displ->displ_abs);
+ free(avg_displ);
+}
+
+
+static void free_pattern_list(struct pattern_list *pattern_list)
+{
+
+ int pti;
+
+ for ( pti=0; pti<pattern_list->n_patterns; pti++ ) {
+ int nuc;
+
+ 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++) {
+ cell_free(pattern_list->patterns[pti]->unit_cells[nuc]);
+ }
+ free(pattern_list->patterns[pti]->filename);
+ free(pattern_list->patterns[pti]);
+ }
+ free(pattern_list);
+}
+
+
+static int *extract_num_pix_free_displ_list(struct pixel_displ_list *pix_displ_list,
+ struct enhanced_det *edet)
+{
+ int *num_pix;
+
+ int i;
+ struct single_pixel_displ *curr = NULL;
+ struct single_pixel_displ *next = NULL;
+
+ for ( i=0; i<edet->num_pix; i++ ) {
+
+ curr = &pix_displ_list->pix_displ_list[i];
+
+ if ( curr->ne != NULL ) {
+ curr = curr->ne;
+ while ( curr != NULL ) {
+ next = curr->ne;
+ free(curr);
+ curr = next;
+ }
+ }
+ }
+
+ num_pix = pix_displ_list->num_pix_displ;
+
+ free(pix_displ_list->curr_pix_displ);
+ free(pix_displ_list->pix_displ_list);
+ free(pix_displ_list);
+
+ return num_pix;
+}
+
+
+static void recompute_panel_avg_displ(struct rg_collection *connected,
+ struct connected_data *conn_data,
+ int *num_pix_displ, int di, int ip,
+ struct enhanced_det *edet,
+ struct avg_displacements *avg_displ)
+{
+ struct panel *p;
+ int ifs, iss;
+
+ if (conn_data[di].sh_x < -9999.0) 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++ ) {
+
+ int pix_index = ifs+edet->width*iss;
+
+ if ( num_pix_displ[pix_index]>=
+ conn_data[di].num_peaks_per_pixel ) {
+ avg_displ->displ_x[pix_index] -= conn_data[di].sh_x;
+ avg_displ->displ_y[pix_index] -= conn_data[di].sh_y;
+ avg_displ->displ_abs[pix_index] = modulus2d(
+ avg_displ->displ_x[pix_index],
+ avg_displ->displ_y[pix_index]
+ );
+ } else {
+ avg_displ->displ_abs[pix_index] = -10000.0;
+ }
+ }
+ }
+}
+
+
+void recompute_avg_displ(struct rg_collection *connected,
+ struct connected_data *conn_data,
+ int *num_pix_displ,
+ struct enhanced_det *edet,
+ struct avg_displacements *avg_displ)
+{
+
+ int di, ip;
+
+ for ( di=0;di<connected->n_rigid_groups;di++ ) {
+ for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
+
+ recompute_panel_avg_displ(connected, conn_data,
+ num_pix_displ, di, ip, edet,
+ avg_displ);
+
+ }
+ }
+}
+
-int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
- struct detector *det, struct rg_collection* quadrants,
- struct rg_collection* connected,
- int min_num_peaks_per_pixel, int min_num_peaks_per_panel,
- int only_best_distance, int nostretch,
- int individual_coffset, int error_maps,
- int enforce_cspad_layout, int no_cspad,
- double max_peak_dist, const char *command_line)
+int optimize_geometry(struct geoptimiser_params *gparams,
+ struct detector *det,
+ struct rg_collection *quadrants,
+ struct rg_collection *connected)
{
- int num_pix_in_slab;
int max_fs = 0;
int max_ss = 0;
- int aw = 0;
- int pi, di, ip, pti;
- int ret1, ret2;
+ int pi;
int ret;
int write_ret;
int maybe_cspad = 0;
-
int *num_pix_displ;
double res_sum;
- double istep;
+ double avg_res;
double clen_to_use;
- double man_stretching_coeff = 0.0;
- double avc[6] = {0.,0.,0.,0.,0.,0.};
- 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;
- double totalError;
- double min_braggp_dist;
+ // only pixels which are distco*size_panel
+ // away
+ double dist_coeff_for_rot_str = 0.2;
+ double total_error;
- double* slab_to_x;
- double* slab_to_y;
- double* recomputed_slab_to_x;
- double* recomputed_slab_to_y;
- double stretch_coeff = 1;
+ struct pixel_maps *pixel_maps;
+ struct pixel_maps *recomputed_pixel_maps;
+ double stretch_coeff = 1.0;
- struct single_pix_displ *all_pix_displ;
- struct single_pix_displ **curr_pix_displ;
struct connected_data *conn_data = NULL;
struct pattern_list *pattern_list;
+ struct cell_params *cell_params;
+ struct enhanced_det edet;
+ struct avg_displacements *avg_displ;
+ struct pixel_displ_list *pix_displ_list;
- if ( nostretch ) man_stretching_coeff = 1.0;
+ STATUS("Maximum distance between peaks: %0.1f pixels.\n",
+ gparams->max_peak_dist);
- if ( det->n_panels == 64 ) {
+ STATUS("Minimum number of measurements for a pixel to be included in the "
+ "refinement: %i\n",
+ gparams->min_num_peaks_per_pix);
+ STATUS("Minimum number of measurements for connected group for accurate "
+ "estimation of position/orientation: %i\n",
+ gparams->min_num_pix_per_conn_group);
+
+ if (det->n_panels == 64 ) {
maybe_cspad = 1;
}
- if ( maybe_cspad && !no_cspad ) {
+ if ( maybe_cspad && !gparams->no_cspad ) {
int num_errors = 0;
@@ -2454,14 +2751,13 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
"connected ASICS.\n");
STATUS("If the detector is not a CSPAD, please rerun the "
"program with the --no-cspad option.\n");
- if ( enforce_cspad_layout ) {
+ if ( gparams->enforce_cspad_layout ) {
STATUS("Enforcing CSPAD layout...\n");
}
- num_errors = check_and_enforce_cspad_dist(det,
- enforce_cspad_layout);
+ num_errors = check_and_enforce_cspad_dist(gparams, det);
- if ( enforce_cspad_layout ) {
+ if ( gparams->enforce_cspad_layout ) {
int geom_wr;
@@ -2469,9 +2765,10 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
"Please restart geometry optimization using the "
"optimized geometry from this run as input geometry "
"file.\n");
- geom_wr = write_detector_geometry_2(geometry_filename,
- outfile, det,
- command_line, 1);
+ geom_wr = write_detector_geometry_2(
+ gparams->geometry_filename,
+ gparams->outfile, det,
+ gparams->command_line, 1);
if ( geom_wr != 0 ) {
ERROR("Error in writing output geometry file.\n");
return 1;
@@ -2480,9 +2777,9 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
return 0;
}
- if ( !enforce_cspad_layout && num_errors > 0 ) {
+ if ( !gparams->enforce_cspad_layout && num_errors > 0 ) {
ERROR("Relative distance and orientation of connected "
- "panels do not respect the CSPAD layout.\n"
+ "ASICS do not respect the CSPAD layout.\n"
"Geometry optimization cannot continue.\n"
"Please rerun the program with the "
"--enforce-cspad-layout option.\n");
@@ -2490,13 +2787,17 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
}
}
- pattern_list = read_patterns_from_steam_file(infile, det);
+ pattern_list = read_patterns_from_steam_file(gparams->infile, det);
if ( pattern_list->n_patterns < 1 ) {
ERROR("Error reading stream file\n");
return 1;
}
- compute_avg_cell_parameters(pattern_list, avc);
+ cell_params = compute_avg_cell_parameters(pattern_list);
+ if ( cell_params == NULL ) {
+ free(pattern_list);
+ return 1;
+ }
res_sum = 0;
for ( pi=0; pi<det->n_panels; pi++ ) {
@@ -2509,362 +2810,224 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
}
res_sum += det->panels[pi].res;
}
+ avg_res = res_sum/det->n_panels;
- istep = res_sum/det->n_panels;
-
- aw = max_fs+1;
+ edet.det = det;
+ edet.width = max_fs+1;
+ edet.height = max_ss+1;
+ edet.num_pix = (max_fs+1)*(max_ss+1);
- clen_to_use = compute_clen_to_use(pattern_list, istep, avc,
- max_peak_dist,
- only_best_distance,
- &min_braggp_dist);
+ clen_to_use = pick_clen_to_use(gparams, pattern_list, avg_res,
+ cell_params);
if ( clen_to_use == -1.0 ) return 1;
- if ( max_peak_dist == -1.0 ) {
- STATUS ("Setting maximum distance for peak search to 0.5*"
- "minimum Bragg peak distance from the data\n");
- max_peak_dist = 0.5*min_braggp_dist;
- }
- STATUS("Maximum distance for peak search: %0.1f pixels.\n", max_peak_dist);
- if ( min_braggp_dist<1.2*max_peak_dist ) {
- STATUS("WARNING: The maximum distance for peak search "
- "is too small compared to minimum Bragg peak "
- "distance: %0.1f < 1.2*%0.1f pixels.\n",
- min_braggp_dist,
- max_peak_dist);
- }
-
- STATUS("Minimum number of measurements for a pixel to be included in the "
- "refinement: %i\n",
- min_num_peaks_per_pixel);
- STATUS("Minimum number of measurements per connected group for accurate "
- "estimation of position/orientation: %i\n",
- min_num_peaks_per_panel);
-
- num_pix_in_slab = (max_fs+1)*(max_ss+1);
- displ_x = calloc(num_pix_in_slab,sizeof(double));
- if ( displ_x == NULL ) {
- ERROR("Error allocating memory for pixel properties.\n");
- return 1;
- }
- displ_y = calloc(num_pix_in_slab,sizeof(double));
- if ( displ_y == NULL ) {
- ERROR("Error allocating memory for pixel properties.\n");
- free(displ_x);
- return 1;
- }
- displ_abs = calloc(num_pix_in_slab,sizeof(double));
- if ( displ_abs == NULL ) {
- ERROR("Error allocating memory for pixel properties.\n");
- free(displ_x);
- free(displ_y);
+ avg_displ = initialize_average_displacement(&edet);
+ if ( avg_displ == NULL ) {
+ free(cell_params);
+ free(pattern_list);
return 1;
}
- slab_to_x = malloc(num_pix_in_slab*sizeof(double));
- slab_to_y = malloc(num_pix_in_slab*sizeof(double));
- if ( slab_to_x == NULL ) {
+ pixel_maps = initialize_pixel_maps(&edet);
+ if ( pixel_maps == NULL ) {
ERROR("Failed to allocate memory for pixel maps.\n");
- free(displ_x);
- free(displ_y);
- free(displ_abs);
- return 1;
- }
- slab_to_y = malloc(num_pix_in_slab*sizeof(double));
- if ( slab_to_y == NULL ) {
- ERROR("Failed to allocate memory for pixel maps.\n");
- free(displ_x);
- free(displ_y);
- free(displ_abs);
- free(slab_to_x);
+ free_avg_displacement(avg_displ);
+ free(cell_params);
+ free(pattern_list);
return 1;
}
- fill_coordinate_matrices(det, aw, slab_to_x, slab_to_y);
-
- 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);
- free(displ_y);
- free(displ_abs);
- free(slab_to_x);
- free(slab_to_y);
- return 1;
- }
- curr_pix_displ = calloc(num_pix_in_slab,
- sizeof(struct single_pix_displ*));
- if ( curr_pix_displ == NULL ) {
+ pix_displ_list = initialize_pixel_displacement_list(&edet);
+ if ( pix_displ_list == NULL ) {
ERROR("Error allocating memory for connected structure data.\n");
- free(displ_x);
- free(displ_y);
- free(displ_abs);
- free(slab_to_x);
- free(slab_to_y);
- free(all_pix_displ);
- return 1;
- }
- num_pix_displ = calloc(num_pix_in_slab, sizeof(int));
- if ( num_pix_displ == NULL ) {
- ERROR("Error allocating memory for connected structure data.\n");
- free(displ_x);
- free(displ_y);
- free(displ_abs);
- free(slab_to_x);
- free(slab_to_y);
- free(all_pix_displ);
- free(curr_pix_displ);
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
+ free(pattern_list);
return 1;
}
- conn_data = malloc(connected->n_rigid_groups*
- sizeof(struct connected_data));
+ conn_data = initialize_conn_data(quadrants, connected);
if ( conn_data == NULL ) {
ERROR("Error allocating memory for connected structure data.\n");
- free(displ_x);
- free(displ_y);
- free(displ_abs);
- free(slab_to_x);
- free(slab_to_y);
- free(all_pix_displ);
- free(curr_pix_displ);
- free(num_pix_displ);
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
+ free_pixel_displacement_list(pix_displ_list, &edet);
+ free(pattern_list);
return 1;
}
- STATUS("Computing pixel statistics.\n");
- ret = compute_pixel_statistics(pattern_list, det, connected, quadrants,
- num_pix_in_slab, max_peak_dist,
- 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,
- curr_pix_displ,
- num_pix_displ);
+
+ ret = compute_pixel_displacements(pattern_list, &edet, connected,
+ gparams, clen_to_use, conn_data,
+ avg_displ, pix_displ_list);
if ( ret != 0 ) {
- free(displ_x);
- free(displ_y);
- 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(num_pix_displ);
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
+ free_pixel_displacement_list(pix_displ_list, &edet);
free(conn_data);
+ free(pattern_list);
return 1;
}
- free_all_curr_pix_displ(all_pix_displ, curr_pix_displ, num_pix_in_slab);
- for ( pti=0; pti<pattern_list->n_patterns; pti++ ) {
- int nuc;
+ free_pattern_list(pattern_list);
- 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++) {
- cell_free(pattern_list->patterns[pti]->unit_cells[nuc]);
- }
- free(pattern_list->patterns[pti]->filename);
- free(pattern_list->patterns[pti]);
+ adjust_min_peaks_per_conn(&edet, connected, gparams, conn_data,
+ pix_displ_list);
+
+ ret = compute_avg_displacements(&edet, connected, pix_displ_list,
+ conn_data, avg_displ);
+ if ( ret != 0 ) {
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
+ free_pixel_displacement_list(pix_displ_list, &edet);
+ free(conn_data);
+ return 1;
}
- free(pattern_list);
- if ( error_maps ) {
- STATUS("Saving pixel position errors before correction.\n");
+ num_pix_displ = extract_num_pix_free_displ_list(pix_displ_list, &edet);
+
+ STATUS("Computing error before correction.\n");
+ total_error = compute_error(connected, &edet, conn_data,
+ num_pix_displ, avg_displ->displ_abs);
+
+ STATUS("Detector-wide error before correction <delta^2> = %0.4f pixels.\n",
+ total_error);
+
+ if ( gparams->error_maps ) {
+ STATUS("Saving error map before correction.\n");
#ifdef HAVE_SAVE_TO_PNG
- ret1 = save_data_to_png("error_map_before.png", det, max_fs, max_ss,
- dfv, displ_abs);
- if ( ret1!=0 ) {
+ ret = save_data_to_png("error_map_before.png", &edet,
+ avg_displ->displ_abs);
+ if ( ret != 0 ) {
ERROR("Error while writing data to file.\n");
+
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
free(conn_data);
- free(displ_x);
- free(displ_y);
- free(displ_abs);
free(num_pix_displ);
- free(slab_to_x);
- free(slab_to_y);
return 1;
}
#else /* HAVE_SAVE_TO_PNG */
- STATUS("ERROR: geoptimiser was compiled without GTK and cairo "
+ ERROR("WARNING: geoptimiser was compiled without GTK and cairo "
"support. Error maps will not be saved.\n");
#endif /* HAVE_SAVE_TO_PNG */
}
- STATUS("Computing initial error.\n");
- totalError = compute_error(connected, aw, conn_data,
- num_pix_displ, displ_abs);
-
- STATUS("The total initial error <delta^2> = %0.4f pixels.\n",
- totalError);
- STATUS("Now calculating corrections.\n");
-
- for ( di=0;di<connected->n_rigid_groups;di++ ) {
-
- conn_data[di].n_peaks_in_conn = 0;
-
- for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
-
- calculate_panel_correction(di, ip, aw, num_pix_displ,
- connected, conn_data);
- }
- }
-
- STATUS("Calculating angles and elongations.\n");
-
- ret = compute_angles_and_stretch(connected, conn_data,
- num_pix_displ,
- slab_to_x, slab_to_y,
- displ_x, displ_y,
- aw,
- min_num_peaks_per_panel,
- dist_coeff_ang_str,
- min_num_peaks_per_pixel,
- man_stretching_coeff, &stretch_coeff);
-
- if ( ret != 0 ) {
+ stretch_coeff = compute_rotation_and_stretch(connected, conn_data,
+ &edet, num_pix_displ,
+ pixel_maps, avg_displ,
+ dist_coeff_for_rot_str,
+ gparams);
+ if ( stretch_coeff < 0.0 ) {
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
free(conn_data);
- free(displ_x);
- free(displ_y);
- free(displ_abs);
free(num_pix_displ);
- free(slab_to_x);
- free(slab_to_y);
return 1;
}
- ret = correct_empty_panels(quadrants, connected, min_num_peaks_per_panel,
- conn_data);
+ ret = compute_rot_stretch_for_empty_panels(quadrants, connected,
+ gparams, conn_data);
if ( ret != 0 ) {
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
free(conn_data);
- free(displ_x);
- free(displ_y);
- free(displ_abs);
free(num_pix_displ);
- free(slab_to_x);
- free(slab_to_y);
return 1;
}
- correct_angle_and_stretch(connected, det, conn_data, clen_to_use,
- stretch_coeff, individual_coffset);
- shift_panels(connected, conn_data);
+ correct_rotation_and_stretch(connected, edet.det, conn_data,
+ clen_to_use, stretch_coeff,
+ gparams);
- recomputed_slab_to_x = malloc(num_pix_in_slab*sizeof(double));
- if ( recomputed_slab_to_x == NULL ) {
- ERROR("Failed to allocate memory for pixel maps.\n");
- free(displ_x);
- free(displ_y);
- free(displ_abs);
- free(slab_to_x);
- free(slab_to_y);
- free(num_pix_displ);
+ recomputed_pixel_maps = initialize_pixel_maps(&edet);
+ if ( recomputed_pixel_maps == NULL ) {
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
free(conn_data);
- return 1;
- }
- recomputed_slab_to_y = malloc(num_pix_in_slab*sizeof(double));
- if ( recomputed_slab_to_y == NULL ) {
- ERROR("Failed to allocate memory for pixel maps.\n");
- free(displ_x);
- free(displ_y);
- free(displ_abs);
- free(slab_to_x);
- free(slab_to_y);
free(num_pix_displ);
- free(conn_data);
- free(recomputed_slab_to_x);
return 1;
}
- fill_coordinate_matrices(det, aw, recomputed_slab_to_x,
- recomputed_slab_to_y);
+ adjust_displ_for_stretch(connected, pixel_maps,
+ recomputed_pixel_maps,
+ conn_data,
+ stretch_coeff, &edet, avg_displ,
+ num_pix_displ);
- recompute_differences(connected, slab_to_x, slab_to_y,
- recomputed_slab_to_x,
- recomputed_slab_to_y, conn_data,
- stretch_coeff, aw, displ_x, displ_y,
- num_pix_displ);
-
- 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;
-
- compute_shifts_for_empty_panels(quadrants, connected, conn_data,
- min_num_peaks_per_panel);
-
- for ( di=0;di<connected->n_rigid_groups;di++ ) {
- for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) {
-
- compute_abs_displ(connected, conn_data,
- num_pix_displ, dfv, di, ip, aw,
- displ_x, displ_y, displ_abs);
-
- }
+ ret = compute_shift(connected, conn_data, num_pix_displ, &edet,
+ gparams, avg_displ);
+ if ( ret != 0 ) {
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
+ free(conn_data);
+ free(num_pix_displ);
+ free_pixel_maps(recomputed_pixel_maps);
+ return 1;
}
- correct_shifts(connected, conn_data, dfv, clen_to_use);
+ compute_shift_for_empty_panels(quadrants, connected, conn_data,
+ gparams);
+
+ correct_shift(connected, conn_data, clen_to_use);
- if ( error_maps ) {
+ recompute_avg_displ(connected, conn_data,
+ num_pix_displ, &edet,
+ avg_displ);
+ if ( gparams->error_maps ) {
#ifdef HAVE_SAVE_TO_PNG
- STATUS("Saving pixel position errors after correction.\n");
- ret2 = save_data_to_png("error_map_after.png", det, max_fs, max_ss,
- dfv, displ_abs);
- if ( ret2 !=0 ) {
+ STATUS("Saving error map after correction.\n");
+
+ ret = save_data_to_png("error_map_after.png", &edet,
+ avg_displ->displ_abs);
+ if ( ret !=0 ) {
ERROR("Error while writing data to file.\n");
+
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
free(conn_data);
- free(displ_x);
- free(displ_y);
- free(displ_abs);
free(num_pix_displ);
- free(slab_to_x);
- free(slab_to_y);
- free(recomputed_slab_to_x);
- free(recomputed_slab_to_y);
+ free_pixel_maps(recomputed_pixel_maps);
return 1;
}
#else /* HAVE_SAVE_TO_PNG */
STATUS("ERROR: geoptimiser was compiled without GTK and cairo "
- "support. Error maps will not be saved.\n");
+ "support.\n Error maps will not be saved.\n");
#endif /* HAVE_SAVE_TO_PNG */
}
- STATUS("Computing final error.\n");
- totalError = compute_error(connected, aw, conn_data, num_pix_displ,
- displ_abs);
+ STATUS("Computing errors after correction.\n");
+ total_error = compute_error(connected, &edet, conn_data,
+ num_pix_displ, avg_displ->displ_abs);
- STATUS("The total final error <delta^2> = %0.4f pixels.\n",totalError);
+ STATUS("Detector-wide error after correction <delta^2> = %0.4f pixels.\n",
+ total_error);
- write_ret = write_detector_geometry_2(geometry_filename, outfile, det,
- command_line, 1);
+ write_ret = write_detector_geometry_2(gparams->geometry_filename,
+ gparams->outfile, edet.det,
+ gparams->command_line, 1);
if ( write_ret != 0 ) {
ERROR("Error in writing output geometry file.\n");
return 1;
}
STATUS("All done!\n");
- if ( error_maps ) {
+ if ( gparams->error_maps ) {
#ifdef HAVE_SAVE_TO_PNG
@@ -2874,65 +3037,71 @@ int optimize_geometry(char *infile, char *outfile, char *geometry_filename,
#endif /* HAVE_SAVE_TO_PNG */
}
+ free_avg_displacement(avg_displ);
+ free_pixel_maps(pixel_maps);
free(conn_data);
- free(displ_x);
- free(displ_y);
- free(displ_abs);
free(num_pix_displ);
- free(slab_to_x);
- free(slab_to_y);
- free(recomputed_slab_to_x);
- free(recomputed_slab_to_y);
+ free_pixel_maps(recomputed_pixel_maps);
return 0;
}
+
int main(int argc, char *argv[])
{
int c, i;
int ret_val;
char buffer[256];
char command_line[1024];
- char *outfile = NULL;
- char *infile = NULL;
- char *geometry_filename = NULL;
+
char *quadrant_coll_name = NULL;
char *connected_coll_name = NULL;
- int min_num_peaks_per_pixel = 3;
- int min_num_peaks_per_panel = 100;
- int only_best_distance = 0;
- int enforce_cspad_layout = 0;
- int nostretch = 0;
- int individual_coffset = 0;
- int no_cspad = 0;
- int error_maps = 1;
- double max_peak_dist = -1.0;
+ struct geoptimiser_params *gparams;
struct detector *det = NULL;
struct rg_collection *quadrants;
struct rg_collection *connected;
struct beam_params beam;
+ gparams = malloc(sizeof(struct geoptimiser_params));
+
+ gparams->outfile = NULL;
+ gparams->infile = NULL;
+ gparams->geometry_filename = NULL;
+ gparams->min_num_peaks_per_pix = 3;
+ gparams->min_num_pix_per_conn_group = 100;
+ gparams->only_best_distance = 0;
+ gparams->enforce_cspad_layout = 0;
+ gparams->nostretch = 0;
+ gparams->individual_coffset = 0;
+ gparams->no_cspad = 0;
+ gparams->error_maps = 1;
+ gparams->max_peak_dist = 4.0;
+
const struct option longopts[] = {
- /* Options with long and short versions */
- {"help", 0, NULL, 'h'},
- {"version", 0, NULL, 10 },
- {"input", 1, NULL, 'i'},
- {"output", 1, NULL, 'o'},
- {"geometry", 1, NULL, 'g'},
- {"quadrants", 1, NULL, 'q'},
- {"connected", 1, NULL, 'c'},
- {"min-num-peaks-per-pixel", 1, NULL, 'x'},
- {"min-num-peaks-per-panel", 1, NULL, 'p'},
- {"most-few-clen", 0, NULL, 'l'},
- {"max-peak-dist", 1, NULL, 'm'},
- {"individual-dist-offset", 0, NULL, 's'},
-
- /* Long-only options with no arguments */
- {"no-stretch", 0, &nostretch, 1},
- {"no-error-maps", 0, &error_maps, 0},
- {"enforce-cspad-layout", 0, &enforce_cspad_layout, 1},
- {"no-cspad", 0, &no_cspad, 1},
+ /* Options with long and short versions */
+ {"help", 0, NULL, 'h'},
+ {"version", 0, NULL, 10 },
+ {"input", 1, NULL, 'i'},
+ {"output", 1, NULL, 'o'},
+ {"geometry", 1, NULL, 'g'},
+ {"quadrants", 1, NULL, 'q'},
+ {"connected", 1, NULL, 'c'},
+ {"min-num-peaks-per-pixel", 1, NULL, 'x'},
+ {"min-num-pixels-per-conn-group", 1, NULL, 'p'},
+ {"most-few-clen", 0, NULL, 'l'},
+ {"max-peak-dist", 1, NULL, 'm'},
+ {"individual-dist-offset", 0, NULL, 's'},
+
+ /* Long-only options with no arguments */
+ {"no-stretch", 0, &gparams->nostretch, 1},
+ {"no-error-maps", 0, &gparams->error_maps, 0},
+ {"enforce-cspad-layout", 0, &gparams->enforce_cspad_layout, 1},
+ {"no-cspad", 0, &gparams->no_cspad, 1},
+
+ /* Long-only options with arguments */
+ {"min-num-peaks-per-panel", 1, NULL, 11},
+
{0, 0, NULL, 0}
};
@@ -2953,16 +3122,17 @@ int main(int argc, char *argv[])
return 0;
case 'o' :
- outfile = strdup(optarg);
+ gparams->outfile = strdup(optarg);
break;
case 'i' :
- infile = strdup(optarg);
+ gparams->infile = strdup(optarg);
break;
case 'g' :
- geometry_filename = strdup(optarg);
- det = get_detector_geometry(geometry_filename, &beam);
+ gparams->geometry_filename = strdup(optarg);
+ det = get_detector_geometry(gparams->geometry_filename,
+ &beam);
if ( det == NULL ) {
ERROR("Failed to read detector geometry from "
"'%s'\n", optarg);
@@ -2979,39 +3149,48 @@ int main(int argc, char *argv[])
break;
case 'x' :
- min_num_peaks_per_pixel = atoi(optarg);
+ gparams->min_num_peaks_per_pix = atoi(optarg);
break;
case 'p' :
- min_num_peaks_per_panel = atoi(optarg);
+ gparams->min_num_pix_per_conn_group = atoi(optarg);
break;
case 'l' :
- only_best_distance = 1;
+ gparams->only_best_distance = 1;
break;
case 'm' :
- max_peak_dist = strtof(optarg, NULL);
+ gparams->max_peak_dist = strtof(optarg, NULL);
break;
case 's' :
- individual_coffset = 1;
+ gparams->individual_coffset = 1;
+ break;
+
+ case 11:
+ ERROR("WARNING: The --min-num-peaks-per-panel option has been "
+ "renamed to --min-num-pixels-per-conn-group. The "
+ "old option has been deprecated and will "
+ "soon be removed. It is currently remapped to "
+ "--min-num-pixels-per-conn-group\n");
+ gparams->min_num_pix_per_conn_group = atoi(optarg);
break;
}
}
- if ( geometry_filename == NULL ) {
+ if ( gparams->geometry_filename == NULL ) {
ERROR("You must provide a geometry to optimize.\n");
return 1;
}
- if ( infile == NULL ) {
+ if ( gparams->infile == NULL ) {
ERROR("You must provide an input stream file.\n");
return 1;
}
- if ( outfile == NULL ) {
+ if ( gparams->outfile == NULL ) {
ERROR("You must provide an output filename.\n");
return 1;
}
@@ -3052,12 +3231,7 @@ int main(int argc, char *argv[])
}
g_type_init();
- ret_val = optimize_geometry(infile, outfile, geometry_filename, det,
- quadrants, connected, min_num_peaks_per_pixel,
- min_num_peaks_per_panel, only_best_distance,
- nostretch, individual_coffset, error_maps,
- enforce_cspad_layout, no_cspad,
- max_peak_dist, command_line);
+ ret_val = optimize_geometry(gparams, det, quadrants, connected);
return ret_val;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 08:32:25 +0000