diff options
| -rw-r--r-- | src/geoptimiser.c | 332 |
1 files changed, 170 insertions, 162 deletions
diff --git a/src/geoptimiser.c b/src/geoptimiser.c index 16c59f3c..7ef91c65 100644 --- a/src/geoptimiser.c +++ b/src/geoptimiser.c @@ -9,7 +9,7 @@ * Authors: * 2014-2015 Oleksandr Yefanov * 2014-2015 Valerio Mariani - * 2014-2019 Thomas White <taw@physics.org> + * 2014-2020 Thomas White <taw@physics.org> * * This file is part of CrystFEL. * @@ -54,7 +54,8 @@ #endif /* HAVE_GDK */ #endif /* HAVE_CAIRO */ -#include <detector.h> +#include <detgeom.h> +#include <datatemplate.h> #include <stream.h> #include <crystal.h> #include <image.h> @@ -145,7 +146,7 @@ struct single_pixel_displ struct gpanel { - struct panel *p; + struct detgeom_panel *p; /* Individual pixel displacements */ struct single_pixel_displ *pix_displ_list; @@ -159,6 +160,12 @@ struct gpanel }; +static void free_pixbuf_data(guchar *data, gpointer p) +{ + free(data); +} + + static GdkPixbuf *render_get_colour_scale(size_t w, size_t h, int scale) { guchar *data; @@ -177,7 +184,7 @@ static GdkPixbuf *render_get_colour_scale(size_t w, size_t h, int scale) val = y-(h/6); - render_scale(val, max, scale, &r, &g, &b); + colscale_lookup(val, max, scale, &r, &g, &b); data[3*( 0+w*(h-1-y) )+0] = 0; data[3*( 0+w*(h-1-y) )+1] = 0; @@ -187,7 +194,6 @@ static GdkPixbuf *render_get_colour_scale(size_t w, size_t h, int scale) data[3*( x+w*(h-1-y) )+1] = 255*g; data[3*( x+w*(h-1-y) )+2] = 255*b; } - } y = h/6; @@ -197,12 +203,13 @@ static GdkPixbuf *render_get_colour_scale(size_t w, size_t h, int scale) data[3*( x+w*(h-1-y) )+2] = 255; } - return gdk_pixbuf_new_from_data(data, GDK_COLORSPACE_RGB, FALSE, 8, - w, h, w*3, render_free_data, NULL); + return gdk_pixbuf_new_from_data(data, GDK_COLORSPACE_RGB, + FALSE, 8, w, h, w*3, + free_pixbuf_data, NULL); } -static void compute_x_y(double fs, double ss, struct panel *p, +static void compute_x_y(double fs, double ss, struct detgeom_panel *p, double *x, double *y) { double xs, ys; @@ -236,10 +243,14 @@ static Reflection *find_closest_reflection(struct image *image, double ds; double rfs, rss; double rx, ry; + int pn; get_detector_pos(refl, &rfs, &rss); + pn = get_panel_number(refl); - compute_x_y(rfs, rss, get_panel(refl), &rx, &ry); + compute_x_y(rfs, rss, + &image->detgeom->panels[pn], + &rx, &ry); ds = distance(rx+det_shift[0], ry+det_shift[1], fx, fy); @@ -261,40 +272,28 @@ static Reflection *find_closest_reflection(struct image *image, } -static double get_average_clen(struct image *image) +static double avg_clen(struct detgeom *det) { int i; - // FIXME! - // struct stuff_from_stream *stuff = image->stuff_from_stream; - // - // if ( stuff == NULL ) { - // ERROR("No 'stuff' from stream!\n"); - // return -1.0; - // } - // - // for ( i=0; i<stuff->n_fields; i++ ) { - // - // if ( strncmp(stuff->fields[i], "average_camera_length = ", - // 24) == 0 ) - // { - // return atof(stuff->fields[i]+24); - // } - // } - - ERROR("Failed to recover average camera length from stream file\n"); - return -1.0; + double av = 0.0; + + for ( i=0; i<det->n_panels; i++ ) { + av += det->panels[i].cnz * det->panels[i].pixel_pitch; + } + return av / i; } -static struct image *read_patterns_from_stream(Stream *st, - struct detector *det, int *n) +static struct image **read_patterns_from_stream(Stream *st, + const DataTemplate *dtempl, + int *n) { - struct image *images; + struct image **images; int n_chunks = 0; int max_images = 1024; int n_images = 0; - images = malloc(max_images * sizeof(struct image)); + images = malloc(max_images * sizeof(struct image *)); if ( images == NULL ) { ERROR("Failed to allocate memory for images.\n"); return NULL; @@ -302,28 +301,25 @@ static struct image *read_patterns_from_stream(Stream *st, do { - images[n_images].det = det; - - if ( read_chunk_2(st, &images[n_images], - STREAM_READ_REFLECTIONS - | STREAM_READ_PEAKS - | STREAM_READ_UNITCELL) != 0 ) break; + images[n_images] = stream_read_chunk(st, dtempl, + STREAM_REFLECTIONS + | STREAM_PEAKS + | STREAM_UNITCELL); + if ( images[n_images] == NULL ) break; n_chunks++; /* Number of chunks processed */ /* Reject if there are no crystals (not indexed) */ - if ( images[n_images].n_crystals == 0 ) continue; - - images[n_images].avg_clen = get_average_clen(&images[n_images]); + if ( images[n_images]->n_crystals == 0 ) continue; n_images++; /* Number of images accepted */ if ( n_images == max_images ) { - struct image *images_new; + struct image **images_new; images_new = realloc(images, - (max_images+1024)*sizeof(struct image)); + (max_images+1024)*sizeof(struct image *)); if ( images_new == NULL ) { ERROR("Failed to allocate memory for " "patterns.\n"); @@ -368,7 +364,8 @@ static struct rvec get_q_from_xyz(double rx, double ry, double dist, double l) } -static UnitCell *compute_avg_cell_parameters(struct image *images, int n) +static UnitCell *compute_avg_cell_parameters(struct image **images, + int n) { int numavc; int j, i; @@ -389,9 +386,9 @@ static UnitCell *compute_avg_cell_parameters(struct image *images, int n) double cpar[6]; int j, cri; - image = &images[i]; + image = images[i]; - for ( cri=0; cri<images->n_crystals; cri++ ) { + for ( cri=0; cri<image->n_crystals; cri++ ) { UnitCell *cell = crystal_get_cell(image->crystals[cri]); @@ -447,7 +444,7 @@ static UnitCell *compute_avg_cell_parameters(struct image *images, int n) static double pick_clen_to_use(struct geoptimiser_params *gparams, - struct image *images, int n, + struct image **images, int n, double avg_res, UnitCell *avg) { int cp, i, u; @@ -484,9 +481,9 @@ static double pick_clen_to_use(struct geoptimiser_params *gparams, int found = 0; for ( i=0; i<num_clens; i++ ) { - if ( fabs(images[cp].avg_clen - clens[i]) <0.0001 ) { + if ( fabs(avg_clen(images[cp]->detgeom) - clens[i]) <0.0001 ) { clens_population[i]++; - lambdas[i] += images[cp].lambda; + lambdas[i] += images[cp]->lambda; found = 1; break; } @@ -494,9 +491,9 @@ static double pick_clen_to_use(struct geoptimiser_params *gparams, if ( found ) continue; - clens[num_clens] = images[cp].avg_clen; + clens[num_clens] = avg_clen(images[cp]->detgeom); clens_population[num_clens] = 1; - lambdas[num_clens] = images[cp].lambda; + lambdas[num_clens] = images[cp]->lambda; num_clens++; } @@ -571,18 +568,29 @@ static double comp_median(double *arr, long n) } +static int panel_in_rigid_group(struct rigid_group *rg, + int panel_number) +{ + int i; + for ( i=0; i<rg->n_panels; i++ ) { + if ( panel_number == rg->panel_numbers[i] ) return 1; + } + return 0; +} + + +/* Go up a level in the detector hierarchy, e.g. from "dominoes" to + * "quadrants", by finding the first panel in "rg" (a rigid group of + * the finer grained type) in the collection of coarser-grained + * groups */ static int find_quad_for_connected(struct rigid_group *rg, struct rg_collection *quadrants) { - struct panel *p; int qi; - /* The quadrant for a group of connected panels is the quadrant to which - * the first panel in the connected set belongs */ - p = rg->panels[0]; - for ( qi=0; qi<quadrants->n_rigid_groups; qi++ ) { - if ( panel_is_in_rigid_group(quadrants->rigid_groups[qi], p) ) { + if ( panel_in_rigid_group(quadrants->rigid_groups[qi], + rg->panel_numbers[0]) ) { return qi; } } @@ -693,7 +701,7 @@ static int add_distance_to_list(struct gpanel *gp, get_detector_pos(refl, &rfs, &rss); - compute_x_y(rfs, rss, get_panel(refl), &crx, &cry); + compute_x_y(rfs, rss, gp->p, &crx, &cry); gp->curr_pix_displ[pix_index]->dx = fx - crx - det_shift[0]; gp->curr_pix_displ[pix_index]->dy = fy - cry - det_shift[1]; gp->curr_pix_displ[pix_index]->ne = NULL; @@ -726,7 +734,6 @@ static int count_pixels_with_min_peaks(struct gpanel *gp, int min_num_peaks, static void adjust_min_peaks_per_conn(struct rg_collection *connected, struct gpanel *gpanels, - struct detector *det, struct geoptimiser_params *gparams, struct connected_data *conn_data) { @@ -746,11 +753,11 @@ static void adjust_min_peaks_per_conn(struct rg_collection *connected, ip++ ) { int pix_count; - struct panel *p; + int pn; struct gpanel *gp; - p = connected->rigid_groups[di]->panels[ip]; - gp = &gpanels[panel_number(det, p)]; + pn = connected->rigid_groups[di]->panel_numbers[ip]; + gp = &gpanels[pn]; pix_count = count_pixels_with_min_peaks(gp, min_num_peaks, gparams->max_num_peaks_per_pix); @@ -773,9 +780,9 @@ static void adjust_min_peaks_per_conn(struct rg_collection *connected, } -static int compute_pixel_displacements(struct image *images, int n_images, +static int compute_pixel_displacements(struct image **images, + int n_images, struct gpanel *gpanels, - struct detector *det, struct rg_collection *connected, struct geoptimiser_params *gparams, double clen_to_use, @@ -788,23 +795,23 @@ static int compute_pixel_displacements(struct image *images, int n_images, for ( cp=0; cp<n_images; cp++ ) { int fi; - ImageFeatureList *flist = images[cp].features; + ImageFeatureList *flist = images[cp]->features; double det_shift[2] = {0.0, 0.0}; double shift_x, shift_y; + struct detgeom *det = images[cp]->detgeom; if ( gparams->only_best_distance ) { - if ( fabs(images[cp].avg_clen - clen_to_use) > 0.0001 ) { + if ( fabs(avg_clen(det) - clen_to_use) > 0.0001 ) { continue; } } - - crystal_get_det_shift(images[cp].crystals[0], &shift_x, + crystal_get_det_shift(images[cp]->crystals[0], &shift_x, &shift_y); - det_shift[0] = shift_x * det->panels[0].res; - det_shift[1] = shift_y * det->panels[0].res; + det_shift[0] = shift_x / det->panels[0].pixel_pitch; + det_shift[1] = shift_y / det->panels[0].pixel_pitch; - for ( fi=0; fi<image_feature_count(images[cp].features); fi++ ) { + for ( fi=0; fi<image_feature_count(images[cp]->features); fi++ ) { double min_dist; double fx, fy; @@ -818,7 +825,7 @@ static int compute_pixel_displacements(struct image *images, int n_images, &det->panels[imfe->pn], &fx, &fy); /* Find the closest reflection (from all crystals) */ - refl = find_closest_reflection(&images[cp], fx, fy, + refl = find_closest_reflection(images[cp], fx, fy, &min_dist, det_shift); if ( refl == NULL ) continue; @@ -834,8 +841,8 @@ static int compute_pixel_displacements(struct image *images, int n_images, ERROR("Error processing peak %f,%f " "(panel %s), image %s %s\n", imfe->fs, imfe->ss, gp->p->name, - images[cp].filename, - images[cp].ev); + images[cp]->filename, + images[cp]->ev); return r; } @@ -873,27 +880,25 @@ static int compute_avg_pix_displ(struct gpanel *gp, int idx, } -static int compute_avg_displacements(struct detector *det, - struct rg_collection *connected, +static int compute_avg_displacements(struct rg_collection *connected, struct connected_data *conn_data, struct gpanel *gpanels, struct geoptimiser_params *gparams) { int di, ip, ifs, iss; int pix_index, ret, max_peaks; - struct panel *p; + struct detgeom_panel *p; max_peaks = 0; for ( di=0; di<connected->n_rigid_groups; di++ ) { for ( ip=0; ip<connected->rigid_groups[di]->n_panels; ip++ ) { - int pp; + int pn; struct gpanel *gp; - p = connected->rigid_groups[di]->panels[ip]; - pp = panel_number(det, p); - gp = &gpanels[pp]; + pn = connected->rigid_groups[di]->panel_numbers[ip]; + gp = &gpanels[pn]; for ( iss=0; iss<p->h; iss++ ) { for ( ifs=0; ifs<p->w; ifs++ ) { @@ -919,7 +924,6 @@ static int compute_avg_displacements(struct detector *det, static double compute_error(struct rg_collection *connected, - struct detector *det, struct connected_data *conn_data, struct gpanel *gpanels) { @@ -929,24 +933,22 @@ static double compute_error(struct rg_collection *connected, for ( di=0;di<connected->n_rigid_groups;di++ ) { - struct panel *p; double connected_error = 0; int num_connected_error = 0; int ifs, iss; for ( ip=0; ip<connected->rigid_groups[di]->n_panels; ip++ ) { - p = connected->rigid_groups[di]->panels[ip]; + struct gpanel *gp; + int pn = connected->rigid_groups[di]->panel_numbers[ip]; - for ( iss=0; iss<p->h; iss++ ) { - for ( ifs=0; ifs<p->w; ifs++ ) { + gp = &gpanels[pn]; - int pix_index; - struct gpanel *gp; - int pp = panel_number(det, p); + for ( iss=0; iss<gp->p->h; iss++ ) { + for ( ifs=0; ifs<gp->p->w; ifs++ ) { - gp = &gpanels[pp]; - pix_index = ifs+p->w*iss; + int pix_index; + pix_index = ifs+gp->p->w*iss; if ( gp->num_pix_displ[pix_index] >= conn_data[di].num_peaks_per_pixel && @@ -1063,15 +1065,16 @@ static int compute_rot_stretch_for_empty_panels(struct rg_collection *quads, } -static void correct_rotation_and_stretch(struct rg_collection *connected, - struct detector *det, - struct gpanel *gpanels, - struct connected_data *conn_data, - double clen_to_use, - double stretch_coeff, - struct geoptimiser_params *gparams) +static DataTemplate *correct_rotation_and_stretch(struct rg_collection *connected, + const DataTemplate *dtempl, + struct gpanel *gpanels, + struct connected_data *conn_data, + double clen_to_use, + double stretch_coeff, + struct geoptimiser_params *gparams) { - +#if 0 + /* FIXME ! */ int di, ip; STATUS("Applying rotation and stretch corrections.\n"); @@ -1083,7 +1086,7 @@ static void correct_rotation_and_stretch(struct rg_collection *connected, for ( ip=0; ip<connected->rigid_groups[di]->n_panels; ip++ ) { - struct panel *p; + struct detgeom_panel *p; p = connected->rigid_groups[di]->panels[ip]; p->coffset -= (1.0-conn_data[di].cstr)*clen_to_use; @@ -1115,7 +1118,7 @@ static void correct_rotation_and_stretch(struct rg_collection *connected, for ( ip=0; ip<connected->rigid_groups[di]->n_panels; ip++ ) { - struct panel *p; + struct detgeom_panel *p; double new_fsx, new_fsy, new_ssx, new_ssy; double new_cnx, new_cny; int fs, ss; @@ -1137,7 +1140,7 @@ static void correct_rotation_and_stretch(struct rg_collection *connected, * NB All panels follow the first one */ if ( ip > 0 ) { - struct panel *p0; + struct detgeom_panel *p0; double dx_old, dy_old, dx_new, dy_new; p0 = connected->rigid_groups[di]->panels[0]; @@ -1187,14 +1190,14 @@ static void correct_rotation_and_stretch(struct rg_collection *connected, } } - +#endif + return NULL; } /* Collect together all the offsets for each group in "connected" * Only offsets which have enough peaks per pixel will be used. */ static int collate_offsets_for_rg(struct rigid_group *group, - struct detector *det, struct gpanel *gpanels, int num_peaks_per_pixel, double *list_dx, double *list_dy, int list_sz) @@ -1205,13 +1208,13 @@ static int collate_offsets_for_rg(struct rigid_group *group, for ( ip=0; ip<group->n_panels; ip++ ) { int ifs, iss; - struct panel *p = group->panels[ip]; - struct gpanel *gp = &gpanels[panel_number(det, p)]; + int pn = group->panel_numbers[ip]; + struct gpanel *gp = &gpanels[pn]; - for ( iss=0; iss<p->h; iss++ ) { - for ( ifs=0; ifs<p->w; ifs++ ) { + for ( iss=0; iss<gp->p->h; iss++ ) { + for ( ifs=0; ifs<gp->p->w; ifs++ ) { - int idx = ifs+p->w*iss; + int idx = ifs+gp->p->w*iss; if ( gp->num_pix_displ[idx] < num_peaks_per_pixel ) { continue; @@ -1258,7 +1261,6 @@ static void fill_conn_data_sh(struct connected_data *conn_data, static int compute_shift(struct rg_collection *connected, struct connected_data *conn_data, - struct detector *det, struct geoptimiser_params *gparams, struct gpanel *gpanels) { @@ -1281,7 +1283,7 @@ static int compute_shift(struct rg_collection *connected, return 1; } - ct = collate_offsets_for_rg(connected->rigid_groups[di], det, + ct = collate_offsets_for_rg(connected->rigid_groups[di], gpanels, conn_data[di].num_peaks_per_pixel, list_dx, list_dy, @@ -1389,7 +1391,8 @@ static void correct_shift(struct rg_collection *connected, struct connected_data *conn_data, double clen_to_use) { - +#if 0 + /* FIXME ! */ int di; int ip; @@ -1398,7 +1401,7 @@ static void correct_shift(struct rg_collection *connected, for ( di=0;di<connected->n_rigid_groups;di++ ) { for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) { - struct panel *p; + struct detgeom_panel *p; p = connected->rigid_groups[di]->panels[ip]; @@ -1414,12 +1417,13 @@ static void correct_shift(struct rg_collection *connected, } } } +#endif } static void scan_p1(int ip0, int ip1, struct rg_collection *connected, struct connected_data *conn_data, - struct detector *det, struct gpanel *gpanels, + struct gpanel *gpanels, int di, double min_dist, long *num_ang, int ifs0, int iss0, double c_x0, double c_y0, double cd_x0, double cd_y0, @@ -1427,11 +1431,11 @@ static void scan_p1(int ip0, int ip1, struct rg_collection *connected, { int iss1, ifs1; - struct panel *p1; + int p1; struct gpanel *gp1; - p1 = connected->rigid_groups[di]->panels[ip1]; - gp1 = &gpanels[panel_number(det, p1)]; + p1 = connected->rigid_groups[di]->panel_numbers[ip1]; + gp1 = &gpanels[p1]; int min_ss_p1, min_fs_p1; @@ -1443,19 +1447,19 @@ static void scan_p1(int ip0, int ip1, struct rg_collection *connected, min_ss_p1 = 0; } - for ( iss1=min_ss_p1; iss1<p1->h; iss1++ ) { - for ( ifs1=min_fs_p1; ifs1<p1->w; ifs1++ ) { + for ( iss1=min_ss_p1; iss1<gp1->p->h; iss1++ ) { + for ( ifs1=min_fs_p1; ifs1<gp1->p->w; ifs1++ ) { 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; - int pix_index1 = ifs1+p1->w*iss1; + int pix_index1 = ifs1+gp1->p->w*iss1; if ( gp1->num_pix_displ[pix_index1] < conn_data[di].num_peaks_per_pixel ) continue; - compute_x_y(ifs1, iss1, p1, &c_x1, &c_y1); + compute_x_y(ifs1, iss1, gp1->p, &c_x1, &c_y1); cd_x1 = c_x1 - gp1->avg_displ_x[pix_index1]; cd_y1 = c_y1 - gp1->avg_displ_y[pix_index1]; d_c_x = c_x1-c_x0; @@ -1502,28 +1506,28 @@ static void scan_p1(int ip0, int ip1, struct rg_collection *connected, /* Executed for each panel in the connected group */ static void scan_p0(int ip0, struct rg_collection *connected, struct connected_data *conn_data, - struct detector *det, struct gpanel *gpanels, + struct gpanel *gpanels, int di, double min_dist, long *num_ang, int compute, double *angles, double *stretches) { int iss0, ifs0, ip1; struct gpanel *gp; - struct panel *p0; + int p0; - p0 = connected->rigid_groups[di]->panels[ip0]; - gp = &gpanels[panel_number(det, p0)]; + p0 = connected->rigid_groups[di]->panel_numbers[ip0]; + gp = &gpanels[p0]; - for ( iss0=0; iss0<p0->h; iss0++ ) { - for ( ifs0=0; ifs0<p0->w; ifs0++ ) { + for ( iss0=0; iss0<gp->p->h; iss0++ ) { + for ( ifs0=0; ifs0<gp->p->w; ifs0++ ) { double c_x0, c_y0, cd_x0, cd_y0; - int pix_index0 = ifs0+p0->w*iss0; + int pix_index0 = ifs0+gp->p->w*iss0; if ( gp->num_pix_displ[pix_index0] < conn_data[di].num_peaks_per_pixel ) continue; - compute_x_y(ifs0, iss0, p0, &c_x0, &c_y0); + compute_x_y(ifs0, iss0, gp->p, &c_x0, &c_y0); cd_x0 = c_x0 - gp->avg_displ_x[pix_index0]; cd_y0 = c_y0 - gp->avg_displ_y[pix_index0]; @@ -1531,7 +1535,7 @@ static void scan_p0(int ip0, struct rg_collection *connected, ip1++ ) { scan_p1(ip0, ip1, connected, - conn_data, det, gpanels, di, min_dist, + conn_data, gpanels, di, min_dist, num_ang, ifs0, iss0, c_x0, c_y0, cd_x0, cd_y0, compute, angles, stretches); @@ -1544,7 +1548,6 @@ static void scan_p0(int ip0, struct rg_collection *connected, static double compute_rotation_and_stretch(struct rg_collection *connected, struct connected_data *conn_data, - struct detector *det, struct gpanel *gpanels, double dist_coeff_for_rot_str, struct geoptimiser_params *gparams) @@ -1569,7 +1572,7 @@ static double compute_rotation_and_stretch(struct rg_collection *connected, double *angles; double *stretches; - struct panel *first_p; + struct detgeom_panel *first_p; long num_ang = 0; int ip0; int num_pix_first_p; @@ -1587,7 +1590,7 @@ static double compute_rotation_and_stretch(struct rg_collection *connected, * connected->rigid_groups[di]->n_panels); for ( ip0=0; ip0<connected->rigid_groups[di]->n_panels; ip0++ ) { - scan_p0(ip0, connected, conn_data, det, gpanels, + scan_p0(ip0, connected, conn_data, gpanels, di, min_dist, &num_ang, 0, NULL, NULL); } @@ -1609,7 +1612,7 @@ static double compute_rotation_and_stretch(struct rg_collection *connected, num_ang = 0; for ( ip0=0; ip0<connected->rigid_groups[di]->n_panels; ip0++ ) { - scan_p0(ip0, connected, conn_data, det, gpanels, + scan_p0(ip0, connected, conn_data, gpanels, di, min_dist, &num_ang, 1, angles, stretches); } @@ -1706,7 +1709,7 @@ static double compute_rotation_and_stretch(struct rg_collection *connected, static void draw_panel(struct image *image, cairo_t *cr, cairo_matrix_t *basic_m, GdkPixbuf **pixbufs, int i) { - struct panel p = image->det->panels[i]; + struct detgeom_panel p = image->det->panels[i]; int w = gdk_pixbuf_get_width(pixbufs[i]); int h = gdk_pixbuf_get_height(pixbufs[i]); cairo_matrix_t m; @@ -1806,7 +1809,7 @@ static int save_data_to_png(char *filename, struct detector *det, for ( i=0; i<det->n_panels; i++ ) { int fs, ss; - struct panel *p; + struct detgeom_panel *p; p = &det->panels[i]; @@ -1916,7 +1919,7 @@ static int save_stretch_to_png(char *filename, struct detector *det, int fs, ss; float val; - struct panel *p; + struct detgeom_panel *p; p = connected->rigid_groups[di]->panels[ip]; @@ -2017,8 +2020,8 @@ int check_and_enforce_cspad_dist(struct geoptimiser_params *gparams, double dist2; double cnx2, cny2; - struct panel *ep = &det->panels[np]; - struct panel *op = &det->panels[np+1]; + struct detgeom_panel *ep = &det->panels[np]; + struct detgeom_panel *op = &det->panels[np+1]; cnx2 = ep->cnx + 197.0*ep->fsx; cny2 = ep->cny + 197.0*ep->fsy; @@ -2095,11 +2098,11 @@ int check_and_enforce_agipd_dist(struct geoptimiser_params *gparams, double dist2; double cnx2, cny2; - struct panel *ep = &det->panels[np]; + struct detgeom_panel *ep = &det->panels[np]; for ( npp=0; npp<8; npp++ ) { - struct panel *op = &det->panels[np+npp]; + struct detgeom_panel *op = &det->panels[np+npp]; cnx2 = ep->cnx + npp*dist_to_check*ep->ssx; cny2 = ep->cny + npp*dist_to_check*ep->ssy; @@ -2262,7 +2265,8 @@ static void free_displ_lists(struct gpanel *gpanels, int n) static void recompute_panel_avg_displ(struct rg_collection *connected, struct connected_data *conn_data, - struct panel *p, struct gpanel *gp, + struct detgeom_panel *p, + struct gpanel *gp, int num_peaks_per_pixel, double sh_x, double sh_y) { @@ -2303,7 +2307,7 @@ void recompute_avg_displ(struct rg_collection *connected, for (ip=0; ip<connected->rigid_groups[di]->n_panels; ip++) { - struct panel *p; + struct detgeom_panel *p; struct gpanel *gp; p = connected->rigid_groups[di]->panels[ip]; @@ -2340,7 +2344,7 @@ int optimize_geometry(struct geoptimiser_params *gparams, Stream *st, double stretch_coeff = 1.0; struct connected_data *conn_data = NULL; - struct image *images; + struct image **images; int n_images = 0; UnitCell *avg_cell; struct gpanel *gpanels; @@ -2442,7 +2446,7 @@ int optimize_geometry(struct geoptimiser_params *gparams, Stream *st, } } - images = read_patterns_from_stream(st, det, &n_images); + images = read_patterns_from_stream(st, dtempl, &n_images); if ( (n_images < 1) || (images == NULL) ) { ERROR("Error reading stream file\n"); return 1; @@ -2508,13 +2512,13 @@ int optimize_geometry(struct geoptimiser_params *gparams, Stream *st, return 1; } - if ( compute_pixel_displacements(images, n_images, gpanels, det, + if ( compute_pixel_displacements(images, n_images, gpanels, connected, gparams, clen_to_use, conn_data) ) return 1; - adjust_min_peaks_per_conn(connected, gpanels, det, gparams, conn_data); + adjust_min_peaks_per_conn(connected, gpanels, gparams, conn_data); - if ( compute_avg_displacements(det, connected, conn_data, gpanels, gparams) ) { + if ( compute_avg_displacements(connected, conn_data, gpanels, gparams) ) { free(conn_data); free(images); return 1; @@ -2591,7 +2595,7 @@ int optimize_geometry(struct geoptimiser_params *gparams, Stream *st, stretch_coeff, gparams); } - ret = compute_shift(connected, conn_data, det, gparams, gpanels); + ret = compute_shift(connected, conn_data, gparams, gpanels); if ( ret != 0 ) { free(conn_data); return 1; @@ -2666,13 +2670,16 @@ int main(int argc, char *argv[]) char *connected_coll_name = NULL; Stream *st; struct geoptimiser_params *gparams; - struct detector *det = NULL; + DataTemplate *dtempl; struct rg_collection *quadrants; struct rg_collection *connected; - struct beam_params beam; char *geometry_filename = NULL; gparams = malloc(sizeof(struct geoptimiser_params)); + if ( gparams == NULL ) { + ERROR("Couldn't allocate params\n"); + return 1; + } gparams->outfile = NULL; gparams->min_num_peaks_per_pix = 3; @@ -2830,7 +2837,7 @@ int main(int argc, char *argv[]) #endif #endif - st = open_stream_for_read(infile); + st = stream_open_for_read(infile); if ( st == NULL ) { ERROR("Failed to open input stream '%s'\n", infile); return 1; @@ -2839,31 +2846,32 @@ int main(int argc, char *argv[]) if ( geometry_filename == NULL ) { const char *stgeom = stream_geometry_file(st); if ( stgeom != NULL ) { - det = get_detector_geometry_from_string(stgeom, &beam, NULL); + dtempl = data_template_new_from_string(stgeom); } else { - ERROR("No input geometry file given, and no geometry " - "found in stream.\n"); + ERROR("No geometry found in stream. " + "Try again with --geometry=<file>.\n"); return 1; } } else { - det = get_detector_geometry(geometry_filename, &beam); + dtempl = data_template_new_from_file(geometry_filename); free(geometry_filename); } - if ( det == NULL ) { + if ( dtempl == NULL ) { ERROR("Failed to read initial detector geometry.\n"); return 1; } - quadrants = find_rigid_group_collection_by_name(det, quadrant_coll_name); + quadrants = data_template_get_rigid_groups(dtempl, + quadrant_coll_name); if ( quadrants == NULL ) { ERROR("Cannot find rigid group collection for quadrants: %s\n", quadrant_coll_name); return 1; } - connected = find_rigid_group_collection_by_name(det, - connected_coll_name); + connected = data_template_get_rigid_groups(dtempl, + connected_coll_name); if ( connected == NULL ) { ERROR("Cannot find rigid group collection for connected " "asics: %s\n", connected_coll_name); @@ -2872,7 +2880,7 @@ int main(int argc, char *argv[]) ret_val = optimize_geometry(gparams, st, det, quadrants, connected); - close_stream(st); + stream_close(st); return ret_val; } |