diff options
-rw-r--r-- | src/displaywindow.c | 13 | ||||
-rw-r--r-- | src/displaywindow.h | 1 | ||||
-rw-r--r-- | src/intensities.c | 2 | ||||
-rw-r--r-- | src/refine.c | 486 | ||||
-rw-r--r-- | src/refinetest2d.c | 8 | ||||
-rw-r--r-- | src/refinetest3d1.c | 10 | ||||
-rw-r--r-- | src/refinetest3d2.c | 14 | ||||
-rw-r--r-- | src/refinetest3d3.c | 8 | ||||
-rw-r--r-- | src/reflections.h | 3 | ||||
-rw-r--r-- | src/reproject.c | 113 | ||||
-rw-r--r-- | src/reproject.h | 3 | ||||
-rw-r--r-- | src/utils.c | 4 | ||||
-rw-r--r-- | src/utils.h | 1 |
13 files changed, 324 insertions, 342 deletions
diff --git a/src/displaywindow.c b/src/displaywindow.c index 6488b34..ca3edac 100644 --- a/src/displaywindow.c +++ b/src/displaywindow.c @@ -372,7 +372,15 @@ static gint displaywindow_image_last(GtkWidget *widget, DisplayWindow *dw) } static gint displaywindow_refinestep(GtkWidget *widget, DisplayWindow *dw) { + + int old_n; + + old_n = dw->ctx->images->n_images; + dw->ctx->images->n_images = 1; + printf("WARNING: I'm only refining based on the first image\n"); refine_do_cell(dw->ctx); + dw->ctx->images->n_images = old_n; + return 0; } @@ -556,7 +564,8 @@ void displaywindow_update_imagestack(DisplayWindow *dw) { /* Perform relrod projection if necessary */ if ( !image->rflist ) { image->rflist = reproject_get_reflections(image, - dw->ctx->cell_lattice); + dw->ctx->cell_lattice, + dw->ctx); } /* Draw the reprojected peaks */ @@ -663,7 +672,7 @@ static void displaywindow_scrolltoend(DisplayWindow *dw) dw->messages_mark, 0, TRUE, 1.0, 0.0); } -static void displaywindow_message(DisplayWindow *dw, const char *text) +void displaywindow_message(DisplayWindow *dw, const char *text) { GtkTextBuffer *buffer; GtkTextIter iter; diff --git a/src/displaywindow.h b/src/displaywindow.h index a69e807..8330f7e 100644 --- a/src/displaywindow.h +++ b/src/displaywindow.h @@ -100,6 +100,7 @@ extern void displaywindow_update(DisplayWindow *dw); extern void displaywindow_update_dirax(ControlContext *ctx, DisplayWindow *dw); extern void displaywindow_error(const char *msg, DisplayWindow *dw); extern void displaywindow_enable_cell_functions(DisplayWindow *dw, gboolean g); +extern void displaywindow_message(DisplayWindow *dw, const char *text); #endif /* DISPLAYWINDOW_H */ diff --git a/src/intensities.c b/src/intensities.c index a2e19c3..f1bdf19 100644 --- a/src/intensities.c +++ b/src/intensities.c @@ -46,7 +46,7 @@ void intensities_extract(ControlContext *ctx) { ImageRecord *image; image = &ctx->images->images[i]; - if ( image->rflist == NULL ) image->rflist = reproject_get_reflections(image, ctx->cell_lattice); + if ( image->rflist == NULL ) image->rflist = reproject_get_reflections(image, ctx->cell_lattice, ctx); for ( j=0; j<image->rflist->n_features; j++ ) { diff --git a/src/refine.c b/src/refine.c index 3a61170..19f9ea3 100644 --- a/src/refine.c +++ b/src/refine.c @@ -9,7 +9,7 @@ * */ -#ifdef HAVE_CONFIG_H +#if HAVE_CONFIG_H #include <config.h> #endif @@ -36,20 +36,37 @@ #define NUM_PARAMS 9 /* Refine debug */ -#define REFINE_DEBUG 1 +#define REFINE_DEBUG_MORE 0 -/* A simplex is an array of ten of these */ -typedef struct { - double dax; double dbx; double dcx; - double day; double dby; double dcy; - double daz; double dbz; double dcz; -} SimplexVertex; +#define DELTA (0.0001e9) typedef struct { - signed int h; signed int k; signed int l; - double dx; double dy; double dz; + signed int h; signed int k; signed int l; /* Indicies of reflection */ + double dx; double dy; /* Deviation vector for this reflection in nm^-1 */ + double xx; double xy; double xz; /* x,y,z components of "image x" */ + double yx; double yy; double yz; /* x,y,z components of "image y" */ + + #if REFINE_DEBUG_MORE + int image; /* Image number this dev came from, for debugging purposes */ + double rdx; double rdy; + #endif /* REFINE_DEBUG_MORE */ + } Deviation; +static void refine_printf(DisplayWindow *dw, char *fmt, ...) { + + va_list ap; + char tmp[1024]; + + va_start(ap, fmt); + vsnprintf(tmp, 1023, fmt, ap); + va_end(ap); + + printf("%s", tmp); + displaywindow_message(dw, tmp); + +} + void refine_do_sequence(ControlContext *ctx) { double omega_offs; @@ -79,8 +96,8 @@ void refine_do_sequence(ControlContext *ctx) { reproject_lattice_changed(ctx); fit = refine_do_cell(ctx); - printf("RF: omega_offs=%f deg, fit=%f nm^-1\n", rad2deg(omega_offs), - fit/DISPFACTOR); + refine_printf(ctx->dw, " omega_offs=%f deg, fit=%f nm^-1\n", + rad2deg(omega_offs), fit/DISPFACTOR); fit_vals[idx++] = fit; if ( fit < fit_best ) { fit_best = fit; @@ -103,7 +120,8 @@ void refine_do_sequence(ControlContext *ctx) { gtk_widget_show_all(window_fit); /* Perform final refinement */ - printf("Best omega offset = %f deg (%f nm^-1)\n", rad2deg(omega_offs_best), fit_best/DISPFACTOR); + refine_printf(ctx->dw, "Best omega offset = %f deg (%f nm^-1)\n", + rad2deg(omega_offs_best), fit_best/DISPFACTOR); for ( j=0; j<ctx->images->n_images; j++ ) { ctx->images->images[j].omega += omega_offs_best; } @@ -113,7 +131,7 @@ void refine_do_sequence(ControlContext *ctx) { } -static double refine_mean_dev(Deviation *d, int nf, SimplexVertex *s, int i) { +static double refine_mean_dev(Deviation *d, int nf, Basis *devcell, int disp) { double fom = 0.0; int f; @@ -121,218 +139,148 @@ static double refine_mean_dev(Deviation *d, int nf, SimplexVertex *s, int i) { for ( f=0; f<nf; f++ ) { double xdf, ydf, zdf; + double dx, dy; + + /* Calculate 3D deviation vector */ + xdf = d[f].h*devcell->a.x + d[f].k*devcell->b.x + d[f].l*devcell->c.x; + ydf = d[f].h*devcell->a.y + d[f].k*devcell->b.y + d[f].l*devcell->c.y; + zdf = d[f].h*devcell->a.z + d[f].k*devcell->b.z + d[f].l*devcell->c.z; + + /* Project into original image */ + dx = xdf*d[f].xx + ydf*d[f].xy + zdf*d[f].xz; + dy = xdf*d[f].yx + ydf*d[f].yy + zdf*d[f].yz; + + dx -= d[f].dx; + dy -= d[f].dy; - xdf = d[f].h*s[i].dax + d[f].k*s[i].dbx + d[f].l*s[i].dcx; - ydf = d[f].h*s[i].day + d[f].k*s[i].dby + d[f].l*s[i].dcy; - zdf = d[f].h*s[i].daz + d[f].k*s[i].dbz + d[f].l*s[i].dcz; - xdf -= d[f].dx; - ydf -= d[f].dy; - zdf -= d[f].dz; + #if REFINE_DEBUG_MORE + if ( disp ) { + d[f].rdx = dx; + d[f].rdy = dy; + printf("Image %2i ref %3i %3i %3i dev %8.5f %8.5f\n", d[f].image, + d[f].h, d[f].k, d[f].l, dx/DISPFACTOR, dy/DISPFACTOR); + } + #endif /* REFINE_DEBUG_MORE */ - fom += sqrt(xdf*xdf + ydf*ydf + zdf*zdf); + fom += sqrt(dx*dx + dy*dy); } -// return fabs(s[i].dax-10.0) + fabs(s[i].day-20.0) + fabs(s[i].dbx-30.0) + fabs(s[i].dby-40.0); - return fom/nf; } -static void refine_display_simplex(SimplexVertex sv) { - - printf("%9.6f %9.6f %9.6f %9.6f %9.6f %9.6f %9.6f %9.6f %9.6f\n", - sv.dax/DISPFACTOR, sv.day/DISPFACTOR, sv.daz/DISPFACTOR, - sv.dbx/DISPFACTOR, sv.dby/DISPFACTOR, sv.dbz/DISPFACTOR, - sv.dcx/DISPFACTOR, sv.dcy/DISPFACTOR, sv.dcz/DISPFACTOR); +static void refine_cell_delta(Basis *devcell_try, int comp) { + + switch ( comp ) { + case 0 : break; + case 1 : devcell_try->a.x += DELTA; break; + case 2 : devcell_try->a.y += DELTA; break; + case 3 : devcell_try->a.z += DELTA; break; + case 4 : devcell_try->b.x += DELTA; break; + case 5 : devcell_try->b.y += DELTA; break; + case 6 : devcell_try->b.z += DELTA; break; + case 7 : devcell_try->c.x += DELTA; break; + case 8 : devcell_try->c.y += DELTA; break; + case 9 : devcell_try->c.z += DELTA; break; + case 10 : devcell_try->a.x -= DELTA; break; + case 11 : devcell_try->a.y -= DELTA; break; + case 12 : devcell_try->a.z -= DELTA; break; + case 13 : devcell_try->b.x -= DELTA; break; + case 14 : devcell_try->b.y -= DELTA; break; + case 15 : devcell_try->b.z -= DELTA; break; + case 16 : devcell_try->c.x -= DELTA; break; + case 17 : devcell_try->c.y -= DELTA; break; + case 18 : devcell_try->c.z -= DELTA; break; + default : fprintf(stderr, "refine_cell_delta: argument out of range\n"); + } } -/* Expand the simplex across from vertex v_worst by factor 'fac'. - * fac = -1 is a reflection - * fac = +n is a 1d expansion - */ -static void refine_simplex_transform(SimplexVertex *s, int v_worst, double fac) { +static void refine_show_cell(DisplayWindow *dw, Basis cell) { - SimplexVertex centre; - int i, nv; - - /* Average the coordinates of the non-worst vertices to - * get the centre of the opposite face. */ - centre.dax = 0.0; centre.day = 0.0; centre.daz = 0.0; - centre.dbx = 0.0; centre.dby = 0.0; centre.dbz = 0.0; - centre.dcx = 0.0; centre.dcy = 0.0; centre.dcz = 0.0; - nv = 0; - for ( i=0; i<=NUM_PARAMS; i++ ) { - if ( i != v_worst ) { - centre.dax += s[i].dax; centre.day += s[i].day; centre.daz += s[i].daz; - centre.dbx += s[i].dbx; centre.dby += s[i].dby; centre.dbz += s[i].dbz; - centre.dcx += s[i].dcx; centre.dcy += s[i].dcy; centre.dcz += s[i].dcz; - nv++; - } - } - centre.dax /= nv; centre.day /= nv; centre.daz /= nv; - centre.dbx /= nv; centre.dby /= nv; centre.dbz /= nv; - centre.dcx /= nv; centre.dcy /= nv; centre.dcz /= nv; - -// printf("Before transformation: "); -// refine_display_simplex(s[v_worst]); - -// printf(" Midpoint: "); -// refine_display_simplex(centre); - - /* Do the transformation */ - s[v_worst].dax = centre.dax + fac * (s[v_worst].dax - centre.dax); - s[v_worst].day = centre.day + fac * (s[v_worst].day - centre.day); - s[v_worst].daz = centre.daz + fac * (s[v_worst].daz - centre.daz); - s[v_worst].dbx = centre.dbx + fac * (s[v_worst].dbx - centre.dbx); - s[v_worst].dby = centre.dby + fac * (s[v_worst].dby - centre.dby); - s[v_worst].dbz = centre.dbz + fac * (s[v_worst].dbz - centre.dbz); - s[v_worst].dcx = centre.dcx + fac * (s[v_worst].dcx - centre.dcx); - s[v_worst].dcy = centre.dcy + fac * (s[v_worst].dcy - centre.dcy); - s[v_worst].dcz = centre.dcz + fac * (s[v_worst].dcz - centre.dcz); - - if ( REFINE_DEBUG ) { - printf(" After transformation: "); - refine_display_simplex(s[v_worst]); - } + refine_printf(dw, "a: %+10.8f %+10.8f %+10.8f\n", + cell.a.x/DISPFACTOR, cell.a.y/DISPFACTOR, cell.a.z/DISPFACTOR); + refine_printf(dw, "b: %+10.8f %+10.8f %+10.8f\n", + cell.b.x/DISPFACTOR, cell.b.y/DISPFACTOR, cell.b.z/DISPFACTOR); + refine_printf(dw, "c: %+10.8f %+10.8f %+10.8f\n", + cell.c.x/DISPFACTOR, cell.c.y/DISPFACTOR, cell.c.z/DISPFACTOR); } -/* Contract vertex v of simplex s towards vertex v_best */ -static void refine_simplex_contract(SimplexVertex *s, int v, int v_best) { - - s[v].dax = s[v_best].dax + 0.5 * (s[v].dax - s[v_best].dax); - s[v].day = s[v_best].day + 0.5 * (s[v].day - s[v_best].day); - s[v].daz = s[v_best].daz + 0.5 * (s[v].daz - s[v_best].daz); - s[v].dbx = s[v_best].dbx + 0.5 * (s[v].dbx - s[v_best].dbx); - s[v].dby = s[v_best].dby + 0.5 * (s[v].dby - s[v_best].dby); - s[v].dbz = s[v_best].dbz + 0.5 * (s[v].dbz - s[v_best].dbz); - s[v].dcx = s[v_best].dcx + 0.5 * (s[v].dcx - s[v_best].dcx); - s[v].dcy = s[v_best].dcy + 0.5 * (s[v].dcy - s[v_best].dcy); - s[v].dcz = s[v_best].dcz + 0.5 * (s[v].dcz - s[v_best].dcz); - -} +static Basis refine_test_confidence(Deviation *d, int nf) { -static double refine_iteration(SimplexVertex *s, Deviation *d, int nf) { - - int v_worst, v_best, v_second_worst, i; - double fom_worst, fom_new, fom_best, fom_second_worst; - - /* Find the least favourable vertex of the simplex */ - v_worst = 0; - fom_worst = 0.0; - v_best = 0; - fom_best = 100e9; - v_second_worst = 0; - fom_second_worst = 0.0; - if ( REFINE_DEBUG ) printf("Vertex FoM/nm^-1\n"); - for ( i=0; i<=NUM_PARAMS; i++ ) { - - double fom; - - fom = refine_mean_dev(d, nf, s, i); - - if ( REFINE_DEBUG ) printf("%6i %8f\n", i, fom/DISPFACTOR); - if ( fom > fom_worst ) { - v_second_worst = v_worst; - fom_second_worst = fom_worst; - fom_worst = fom; - v_worst = i; - } - if ( fom < fom_best ) { - fom_best = fom; - v_best = i; - } - - } - if ( REFINE_DEBUG ) printf("The worst vertex is number %i\n", v_worst); - - /* Reflect this vertex across the opposite face */ - refine_simplex_transform(s, v_worst, -1.0); - - /* Is the worst vertex any better? */ - fom_new = refine_mean_dev(d, nf, s, v_worst); - if ( REFINE_DEBUG ) printf("New mean deviation for the worst vertex after reflection is %f nm^-1\n", - fom_new/DISPFACTOR); - if ( fom_new > fom_worst ) { - - double fom_new_new; - - /* It's worse than before. Contract in 1D and see if that helps. */ - if ( REFINE_DEBUG ) printf("Worse. Trying a 1D contraction...\n"); - /* Minus puts it back on the original side of the 'good' face */ - refine_simplex_transform(s, v_worst, -0.5); - fom_new_new = refine_mean_dev(d, nf, s, v_worst); - if ( REFINE_DEBUG ) printf("Mean deviation after 1D contraction is %f nm^-1\n", - fom_new_new/DISPFACTOR); - if ( fom_new_new > fom_second_worst ) { - - int i; - - if ( REFINE_DEBUG ) printf("Not as good as the second worst vertex: contracting around the " - "best vertex (%i)\n", v_best); - for ( i=0; i<=NUM_PARAMS; i++ ) { - if ( i != v_best ) refine_simplex_contract(s, i, v_best); - } - - } - - } else if ( fom_new < fom_worst ) { - - /* It's better. Try to expand in this direction */ - double fom_new_new; - SimplexVertex save; - - if ( REFINE_DEBUG ) printf("This is better. Trying to expand...\n"); - - save = s[v_worst]; - refine_simplex_transform(s, v_worst, 2.0); /* +ve means stay on this side of the 'good' face */ - /* Better? */ - fom_new_new = refine_mean_dev(d, nf, s, v_worst); - if ( REFINE_DEBUG ) printf("Mean deviation after expansion is %f nm^-1\n", fom_new_new/DISPFACTOR); - if ( fom_new_new > fom_new ) { - /* "Got too confident" */ - s[v_worst] = save; - if ( REFINE_DEBUG ) printf("Got too confident - reverting\n"); - } else { - if ( REFINE_DEBUG ) printf("Better still. Great.\n"); - } - - } else { - - printf("No change!\n"); - - } - - /* Check convergence and return */ - fom_worst = 0.0; - fom_best = 100e9; - for ( i=0; i<=NUM_PARAMS; i++ ) { - double fom; - fom = refine_mean_dev(d, nf, s, i); - if ( fom > fom_worst ) { - fom_worst = fom; - } - if ( fom < fom_best ) { - fom_best = fom; - } - } - - printf("Simplex size: %e - %e = %e\n", fom_worst/DISPFACTOR, fom_best/DISPFACTOR, (fom_worst - fom_best)/DISPFACTOR); - - return fom_best; + Basis *devcell; + double val, new_val; + Basis confidence; + + devcell = malloc(sizeof(Basis)); + devcell->a.x = 0.0e9; devcell->b.x = 0.0e9; devcell->c.x = 0.0e9; + devcell->a.y = 0.0e9; devcell->b.y = 0.0e9; devcell->c.y = 0.0e9; + devcell->a.z = 0.0e9; devcell->b.z = 0.0e9; devcell->c.z = 0.0e9; + val = refine_mean_dev(d, nf, devcell, 0); + + devcell->a.x = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.a.x = new_val-val; + devcell->a.x = 0.0; + + devcell->a.y = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.a.y = new_val-val; + devcell->a.y = 0.0; + + devcell->a.z = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.a.z = new_val-val; + devcell->a.z = 0.0; + + devcell->b.x = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.b.x = new_val-val; + devcell->b.x = 0.0; + + devcell->b.y = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.b.y = new_val-val; + devcell->b.y = 0.0; + + devcell->b.z = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.b.z = new_val-val; + devcell->b.z = 0.0; + + devcell->c.x = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.c.x = new_val-val; + devcell->c.x = 0.0; + + devcell->c.y = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.c.y = new_val-val; + devcell->c.y = 0.0; + + devcell->c.z = 1.0e9; + new_val = refine_mean_dev(d, nf, devcell, 0); + confidence.c.z = new_val-val; + devcell->c.z = 0.0; + + return confidence; } double refine_do_cell(ControlContext *ctx) { - SimplexVertex s[10]; Deviation *d; - double delta; - int i, nf, f, it, maxiter; - const double tol = 0.001e9; /* Stopping condition */ - //const double tol = 0.001; /* For testing */ + int i, nf, f; + Basis *devcell; + Basis *devcell_try; + Basis *devcell_try_best; + double mean_dev; + double mean_dev_try; + int it; + Basis conf; + double conf_threshold; if ( !ctx->cell_lattice ) { displaywindow_error("No reciprocal unit cell has been found.", ctx->dw); @@ -352,17 +300,17 @@ double refine_do_cell(ControlContext *ctx) { if ( !ctx->images->images[i].rflist ) { ctx->images->images[i].rflist = reproject_get_reflections(&ctx->images->images[i], - ctx->cell_lattice); + ctx->cell_lattice, ctx); } for ( j=0; j<ctx->images->images[i].rflist->n_features; j++ ) { if ( ctx->images->images[i].rflist->features[j].partner != NULL ) nf++; } - printf("%i features from image %i\n", nf, i); + refine_printf(ctx->dw, "%i features from image %i\n", nf, i); } - if ( REFINE_DEBUG ) printf("RF: There are %i partnered features in total\n", nf); + refine_printf(ctx->dw, "There are %i partnered features in total\n", nf); /* Initialise the 'deviation table' */ d = malloc(nf*sizeof(Deviation)); @@ -378,7 +326,6 @@ double refine_do_cell(ControlContext *ctx) { ImageFeature *rf; double dix, diy, dx, dy; - double dlx, dly, dlz; double old_x, old_y; rf = &image->rflist->features[j]; @@ -391,23 +338,30 @@ double refine_do_cell(ControlContext *ctx) { /* Determine the difference vector */ dix = rf->partner->x - rf->x; diy = rf->partner->y - rf->y; - printf("RF: Feature %3i: %3i %3i %3i dev = %+9.5f %+9.5f px ", j, d[f].h, d[f].k, d[f].l, - dix, diy); + refine_printf(ctx->dw, "%3i: %3i: %3i %3i %3i dev %+9.5f %+9.5f px ", + i, j, d[f].h, d[f].k, d[f].l, dix, diy); old_x = rf->partner->x; old_y = rf->partner->y; rf->partner->x = dix + rf->partner->parent->x_centre; rf->partner->y = diy + rf->partner->parent->y_centre; mapping_scale(rf->partner, &dx, &dy); - mapping_rotate(dx, dy, 0.0, &dlx, &dly, &dlz, image->omega, image->tilt); rf->partner->x = old_x; rf->partner->y = old_y; double mod = sqrt(dx*dx + dy*dy)/DISPFACTOR; - printf("=> %+10.5f %+10.5f %+10.5f nm^-1 (length %10.5f nm^1)\n", dlx/DISPFACTOR, dly/DISPFACTOR, dlz/DISPFACTOR, mod); + refine_printf(ctx->dw, "= %+10.5f %+10.5f nm^-1 (length %7.5f nm^1)\n", + dx/DISPFACTOR, dy/DISPFACTOR, mod); + + d[f].dx = dx; + d[f].dy = dy; + + /* Store plane normal for use in projection later */ + mapping_rotate(1.0, 0.0, 0.0, &d[f].xx, &d[f].xy, &d[f].xz, image->omega, image->tilt); + mapping_rotate(0.0, 1.0, 0.0, &d[f].yx, &d[f].yy, &d[f].yz, image->omega, image->tilt); - d[f].dx = dlx; - d[f].dy = dly; - d[f].dz = dlz; + #if REFINE_DEBUG_MORE + d[f].image = i; + #endif /* REFINE_DEBUG_MORE */ f++; @@ -416,52 +370,90 @@ double refine_do_cell(ControlContext *ctx) { } assert( f == nf ); - /* Initialise the simplex */ - delta = 0.01e9; - s[0].dax = 0.0; s[0].dbx = 0.0; s[0].dcx = 0.0; - s[0].day = 0.0; s[0].dby = 0.0; s[0].dcy = 0.0; - s[0].daz = 0.0; s[0].dbz = 0.0; s[0].dcz = 0.0; - memcpy(&s[1], &s[0], sizeof(SimplexVertex)); s[1].dax = delta; - memcpy(&s[2], &s[0], sizeof(SimplexVertex)); s[2].day = delta; - memcpy(&s[3], &s[0], sizeof(SimplexVertex)); s[3].dbx = delta; - memcpy(&s[4], &s[0], sizeof(SimplexVertex)); s[4].dby = delta; /* 2d vertices first */ - memcpy(&s[5], &s[0], sizeof(SimplexVertex)); s[5].daz = delta; - memcpy(&s[6], &s[0], sizeof(SimplexVertex)); s[6].dbz = delta; - memcpy(&s[7], &s[0], sizeof(SimplexVertex)); s[7].dcx = delta; - memcpy(&s[8], &s[0], sizeof(SimplexVertex)); s[8].dcy = delta; - memcpy(&s[9], &s[0], sizeof(SimplexVertex)); s[9].dcz = delta; - - /* Iterate */ - maxiter = 10000; - for ( it=0; it<maxiter; it++ ) { - - double conv; + /* Initial situation */ + devcell = malloc(sizeof(Basis)); + devcell->a.x = 0.0e9; devcell->b.x = 0.0e9; devcell->c.x = 0.0e9; + devcell->a.y = 0.0e9; devcell->b.y = 0.0e9; devcell->c.y = 0.0e9; + devcell->a.z = 0.0e9; devcell->b.z = 0.0e9; devcell->c.z = 0.0e9; + mean_dev = refine_mean_dev(d, nf, devcell, 0); + refine_printf(ctx->dw, "Initial mean deviation: %13.8f nm^1\n", mean_dev/DISPFACTOR); + + /* Test confidence */ + conf = refine_test_confidence(d, nf); + + /* Determine direction of steepest gradient */ + devcell_try = malloc(sizeof(Basis)); + devcell_try_best = malloc(sizeof(Basis)); + for ( it=1; it<=10000; it++ ) { - //for ( i=0; i<5; i++ ) { - // refine_display_simplex(s[i]); - //} + int found = 0; + int comp1, comp2; - if ( REFINE_DEBUG ) printf("------------------- Simplex method iteration %i -------------------\n", it); - conv = refine_iteration(s, d, nf); - if ( conv < tol ) { - if ( REFINE_DEBUG ) printf("RF: Converged after %i iterations (%f nm^-1)\n", it, - conv/DISPFACTOR); + #if REFINE_DEBUG_MORE + refine_mean_dev(d, nf, devcell, 1); + printf(ctx->dw, "Iteration %i starts at dev %14.12f\n", it, mean_dev/DISPFACTOR); + printf(ctx->dw, "Current dev cell:\n"); + printf(ctx->dw, "a = %8.5f %8.5f %8.5f\n", + devcell->a.x/DISPFACTOR, devcell->a.y/DISPFACTOR, devcell->a.z/DISPFACTOR); + printf(ctx->dw, "b = %8.5f %8.5f %8.5f\n", + devcell->b.x/DISPFACTOR, devcell->b.y/DISPFACTOR, devcell->b.z/DISPFACTOR); + printf(ctx->dw, "c = %8.5f %8.5f %8.5f\n", + devcell->c.x/DISPFACTOR, devcell->c.y/DISPFACTOR, devcell->c.z/DISPFACTOR); + #endif /* REFINE_DEBUG_MORE */ + + for ( comp1=1; comp1<19; comp1++ ) { + for ( comp2=0; comp2<19; comp2++ ) { + + memcpy(devcell_try, devcell, sizeof(Basis)); + refine_cell_delta(devcell_try, comp1); + refine_cell_delta(devcell_try, comp2); + mean_dev_try = refine_mean_dev(d, nf, devcell_try, 0); + + /* Improvement greater than the tolerance? */ + if ( mean_dev_try < mean_dev ) { + mean_dev = mean_dev_try; + memcpy(devcell_try_best, devcell_try, sizeof(Basis)); + found = 1; + } + + } + } + if ( found ) { + memcpy(devcell, devcell_try_best, sizeof(Basis)); + } else { break; } + if ( !(it % 1000) ) { + refine_printf(ctx->dw, "After %5i iterations: mean dev = %13.8f nm^1\n", it, + mean_dev/DISPFACTOR); + } } - if ( it == maxiter ) printf("RF: Did not converge.\n"); + free(devcell_try); + free(devcell_try_best); + refine_printf(ctx->dw, "Final mean dev (%5i iterations) = %13.8f nm^1\n", it, mean_dev/DISPFACTOR); + refine_printf(ctx->dw, "Final cell deviation:\n"); + refine_show_cell(ctx->dw, *devcell); + refine_printf(ctx->dw, "Confidence:\n"); + refine_show_cell(ctx->dw, conf); /* Apply the final values to the cell */ - ctx->cell->a.x += s[0].dax; ctx->cell->b.x += s[0].dbx; ctx->cell->c.x += s[0].dcx; - ctx->cell->a.y += s[0].day; ctx->cell->b.y += s[0].dby; ctx->cell->c.y += s[0].dcy; - ctx->cell->a.z += s[0].daz; ctx->cell->b.z += s[0].dbz; ctx->cell->c.z += s[0].dcz; + conf_threshold = 2.5; + if ( conf.a.x > conf_threshold ) ctx->cell->a.x += devcell->a.x; + if ( conf.a.y > conf_threshold ) ctx->cell->a.y += devcell->a.y; + if ( conf.a.z > conf_threshold ) ctx->cell->a.z += devcell->a.z; + if ( conf.b.x > conf_threshold ) ctx->cell->b.x += devcell->b.x; + if ( conf.b.y > conf_threshold ) ctx->cell->b.y += devcell->b.y; + if ( conf.b.z > conf_threshold ) ctx->cell->b.z += devcell->b.z; + if ( conf.c.x > conf_threshold ) ctx->cell->c.x += devcell->c.x; + if ( conf.c.y > conf_threshold ) ctx->cell->c.y += devcell->c.y; + if ( conf.c.z > conf_threshold ) ctx->cell->c.z += devcell->c.z; ctx->images->images[ctx->dw->cur_image].rflist = NULL; reproject_lattice_changed(ctx); displaywindow_update(ctx->dw); - return refine_mean_dev(d, nf, s, 0); + return mean_dev; } diff --git a/src/refinetest2d.c b/src/refinetest2d.c index 1c30348..2b09ef4 100644 --- a/src/refinetest2d.c +++ b/src/refinetest2d.c @@ -107,6 +107,7 @@ int main(int argc, char *argv[]) { ctx->x_centre = 256; ctx->y_centre = 256; ctx->pixel_size = 5e7; + ctx->reflectionlist = reflectionlist_new(); image_add(ctx->images, NULL, 512, 512, deg2rad(0.0), ctx); ctx->images->images[0].features = image_feature_list_new(); @@ -121,7 +122,7 @@ int main(int argc, char *argv[]) { cell_real->c.x = 0.0e9; cell_real->c.y = 0.0e9; cell_real->c.z = 5.0e9; /* The "real" reflections */ reflections_real = reflection_list_from_cell(cell_real); - ctx->images->images[0].features = reproject_get_reflections(&ctx->images->images[0], reflections_real); + ctx->images->images[0].features = reproject_get_reflections(&ctx->images->images[0], reflections_real, ctx); // printf("RT: %i test features generated.\n", ctx->images->images[0].features->n_features); /* The "model" cell to be refined */ @@ -131,13 +132,13 @@ int main(int argc, char *argv[]) { ctx->cell->c.x = 0.1e9; ctx->cell->c.y = 0.1e9; ctx->cell->c.z = 5.3e9; ctx->cell_lattice = reflection_list_from_cell(ctx->cell); ctx->cell_lattice = reflection_list_from_cell(ctx->cell); - ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice); + ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice, ctx); reproject_partner_features(ctx->images->images[0].rflist, &ctx->images->images[0]); refine_do_cell(ctx); image_feature_list_free(ctx->images->images[0].rflist); reflection_list_from_new_cell(ctx->cell_lattice, ctx->cell); - ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice); + ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice, ctx); fail = check_cell(ctx->cell, cell_real); @@ -157,6 +158,7 @@ void displaywindow_update_imagestack(DisplayWindow *dw) { }; void displaywindow_enable_cell_functions(DisplayWindow *dw, gboolean g) { }; void displaywindow_update(DisplayWindow *dw) { }; void displaywindow_error(const char *msg, DisplayWindow *dw) { }; +void displaywindow_message(DisplayWindow *dw, const char *text) { }; guint gtk_value_graph_get_type() { return 0; }; GtkWidget *gtk_value_graph_new() { return NULL; }; void gtk_value_graph_set_data(GtkValueGraph *vg, double *data, unsigned int n) { }; diff --git a/src/refinetest3d1.c b/src/refinetest3d1.c index cd8cc84..6dfc74a 100644 --- a/src/refinetest3d1.c +++ b/src/refinetest3d1.c @@ -114,6 +114,7 @@ int main(int argc, char *argv[]) { ctx->x_centre = 256; ctx->y_centre = 256; ctx->pixel_size = 5e7; + ctx->reflectionlist = reflectionlist_new(); image_add(ctx->images, NULL, 512, 512, deg2rad(00.0), ctx); ctx->images->images[0].features = image_feature_list_new(); image_add(ctx->images, NULL, 512, 512, deg2rad(90.0), ctx); @@ -133,8 +134,8 @@ int main(int argc, char *argv[]) { cell_real->c.x = 0.0e9; cell_real->c.y = 0.0e9; cell_real->c.z = 5.0e9; /* The "real" reflections */ reflections_real = reflection_list_from_cell(cell_real); - ctx->images->images[0].features = reproject_get_reflections(&ctx->images->images[0], reflections_real); - ctx->images->images[1].features = reproject_get_reflections(&ctx->images->images[1], reflections_real); + ctx->images->images[0].features = reproject_get_reflections(&ctx->images->images[0], reflections_real, ctx); + ctx->images->images[1].features = reproject_get_reflections(&ctx->images->images[1], reflections_real, ctx); //ctx->images->images[2].features = reproject_get_reflections(&ctx->images->images[2], reflections_real); /* The "model" cell to be refined */ @@ -143,9 +144,9 @@ int main(int argc, char *argv[]) { ctx->cell->b.x = 0.1e9; ctx->cell->b.y = 5.0e9; ctx->cell->b.z = 0.1e9; ctx->cell->c.x = 0.1e9; ctx->cell->c.y = 0.1e9; ctx->cell->c.z = 5.0e9; ctx->cell_lattice = reflection_list_from_cell(ctx->cell); - ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice); + ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice, ctx); reproject_partner_features(ctx->images->images[0].rflist, &ctx->images->images[0]); - ctx->images->images[1].rflist = reproject_get_reflections(&ctx->images->images[1], ctx->cell_lattice); + ctx->images->images[1].rflist = reproject_get_reflections(&ctx->images->images[1], ctx->cell_lattice, ctx); reproject_partner_features(ctx->images->images[1].rflist, &ctx->images->images[1]); //ctx->images->images[2].rflist = reproject_get_reflections(&ctx->images->images[2], ctx->cell_lattice); //reproject_partner_features(ctx->images->images[2].rflist, &ctx->images->images[2]); @@ -173,6 +174,7 @@ void displaywindow_update_imagestack(DisplayWindow *dw) { }; void displaywindow_enable_cell_functions(DisplayWindow *dw, gboolean g) { }; void displaywindow_update(DisplayWindow *dw) { }; void displaywindow_error(const char *msg, DisplayWindow *dw) { }; +void displaywindow_message(DisplayWindow *dw, const char *text) { }; guint gtk_value_graph_get_type() { return 0; }; GtkWidget *gtk_value_graph_new() { return NULL; }; void gtk_value_graph_set_data(GtkValueGraph *vg, double *data, unsigned int n) { }; diff --git a/src/refinetest3d2.c b/src/refinetest3d2.c index 38ea72e..cffe7f2 100644 --- a/src/refinetest3d2.c +++ b/src/refinetest3d2.c @@ -126,6 +126,7 @@ int main(int argc, char *argv[]) { ctx->x_centre = 256; ctx->y_centre = 256; ctx->pixel_size = 5e7; + ctx->reflectionlist = reflectionlist_new(); image_add(ctx->images, NULL, 512, 512, deg2rad(00.0), ctx); ctx->images->images[0].features = image_feature_list_new(); image_add(ctx->images, NULL, 512, 512, deg2rad(90.0), ctx); @@ -145,9 +146,9 @@ int main(int argc, char *argv[]) { cell_real->c.x = 0.0e9; cell_real->c.y = 0.0e9; cell_real->c.z = 5.0e9; /* The "real" reflections */ reflections_real = reflection_list_from_cell(cell_real); - ctx->images->images[0].features = reproject_get_reflections(&ctx->images->images[0], reflections_real); - ctx->images->images[1].features = reproject_get_reflections(&ctx->images->images[1], reflections_real); - ctx->images->images[2].features = reproject_get_reflections(&ctx->images->images[2], reflections_real); + ctx->images->images[0].features = reproject_get_reflections(&ctx->images->images[0], reflections_real, ctx); + ctx->images->images[1].features = reproject_get_reflections(&ctx->images->images[1], reflections_real, ctx); + ctx->images->images[2].features = reproject_get_reflections(&ctx->images->images[2], reflections_real, ctx); /* The "model" cell to be refined */ ctx->cell = malloc(sizeof(Basis)); @@ -155,11 +156,11 @@ int main(int argc, char *argv[]) { ctx->cell->b.x = 0.1e9; ctx->cell->b.y = 5.0e9; ctx->cell->b.z = 0.1e9; ctx->cell->c.x = 0.1e9; ctx->cell->c.y = 0.1e9; ctx->cell->c.z = 5.0e9; ctx->cell_lattice = reflection_list_from_cell(ctx->cell); - ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice); + ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice, ctx); reproject_partner_features(ctx->images->images[0].rflist, &ctx->images->images[0]); - ctx->images->images[1].rflist = reproject_get_reflections(&ctx->images->images[1], ctx->cell_lattice); + ctx->images->images[1].rflist = reproject_get_reflections(&ctx->images->images[1], ctx->cell_lattice, ctx); reproject_partner_features(ctx->images->images[1].rflist, &ctx->images->images[1]); - ctx->images->images[2].rflist = reproject_get_reflections(&ctx->images->images[2], ctx->cell_lattice); + ctx->images->images[2].rflist = reproject_get_reflections(&ctx->images->images[2], ctx->cell_lattice, ctx); reproject_partner_features(ctx->images->images[2].rflist, &ctx->images->images[2]); refine_do_cell(ctx); @@ -185,6 +186,7 @@ void displaywindow_update_imagestack(DisplayWindow *dw) { }; void displaywindow_enable_cell_functions(DisplayWindow *dw, gboolean g) { }; void displaywindow_update(DisplayWindow *dw) { }; void displaywindow_error(const char *msg, DisplayWindow *dw) { }; +void displaywindow_message(DisplayWindow *dw, const char *text) { }; guint gtk_value_graph_get_type() { return 0; }; GtkWidget *gtk_value_graph_new() { return NULL; }; void gtk_value_graph_set_data(GtkValueGraph *vg, double *data, unsigned int n) { }; diff --git a/src/refinetest3d3.c b/src/refinetest3d3.c index de8a792..65705a8 100644 --- a/src/refinetest3d3.c +++ b/src/refinetest3d3.c @@ -127,6 +127,7 @@ int main(int argc, char *argv[]) { ctx->x_centre = 256; ctx->y_centre = 256; ctx->pixel_size = 5e7; + ctx->reflectionlist = reflectionlist_new(); for ( i=0; i<=90; i++ ) { image_add(ctx->images, NULL, 512, 512, deg2rad(i), ctx); ctx->images->images[i].features = image_feature_list_new(); @@ -144,7 +145,8 @@ int main(int argc, char *argv[]) { /* The "real" reflections */ reflections_real = reflection_list_from_cell(cell_real); for ( i=0; i<=90; i++ ) { - ctx->images->images[i].features = reproject_get_reflections(&ctx->images->images[i], reflections_real); + ctx->images->images[i].features = reproject_get_reflections(&ctx->images->images[i], reflections_real, + ctx); } /* The "model" cell to be refined */ @@ -154,7 +156,8 @@ int main(int argc, char *argv[]) { ctx->cell->c.x = 0.1e9; ctx->cell->c.y = 0.1e9; ctx->cell->c.z = 5.0e9; ctx->cell_lattice = reflection_list_from_cell(ctx->cell); for ( i=0; i<ctx->images->n_images; i++ ) { - ctx->images->images[i].rflist = reproject_get_reflections(&ctx->images->images[i], ctx->cell_lattice); + ctx->images->images[i].rflist = reproject_get_reflections(&ctx->images->images[i], ctx->cell_lattice, + ctx); reproject_partner_features(ctx->images->images[i].rflist, &ctx->images->images[i]); } @@ -181,6 +184,7 @@ void displaywindow_update_imagestack(DisplayWindow *dw) { }; void displaywindow_enable_cell_functions(DisplayWindow *dw, gboolean g) { }; void displaywindow_update(DisplayWindow *dw) { }; void displaywindow_error(const char *msg, DisplayWindow *dw) { }; +void displaywindow_message(DisplayWindow *dw, const char *text) { }; guint gtk_value_graph_get_type() { return 0; }; GtkWidget *gtk_value_graph_new() { return NULL; }; void gtk_value_graph_set_data(GtkValueGraph *vg, double *data, unsigned int n) { }; diff --git a/src/reflections.h b/src/reflections.h index 8fafe4b..e51c530 100644 --- a/src/reflections.h +++ b/src/reflections.h @@ -22,7 +22,8 @@ typedef enum { REFLECTION_MARKER, REFLECTION_VECTOR_MARKER_1, REFLECTION_VECTOR_MARKER_2, - REFLECTION_VECTOR_MARKER_3 + REFLECTION_VECTOR_MARKER_3, + REFLECTION_VECTOR_MARKER_4 } ReflectionType; typedef struct reflection_struct { diff --git a/src/reproject.c b/src/reproject.c index e1ce13e..48f60da 100644 --- a/src/reproject.c +++ b/src/reproject.c @@ -18,6 +18,7 @@ #include "imagedisplay.h" #include "displaywindow.h" #include "image.h" +#include "mapping.h" /* Attempt to find partners from the feature list of "image" for each feature in "flist". */ void reproject_partner_features(ImageFeatureList *rflist, ImageRecord *image) { @@ -32,7 +33,8 @@ void reproject_partner_features(ImageFeatureList *rflist, ImageRecord *image) { ImageFeature *partner; int idx; - partner = image_feature_closest(image->features, rflist->features[i].x, rflist->features[i].y, &d, &idx); + partner = image_feature_closest(image->features, rflist->features[i].x, rflist->features[i].y, + &d, &idx); if ( (d <= 20.0) && partner ) { rflist->features[i].partner = partner; @@ -45,61 +47,57 @@ void reproject_partner_features(ImageFeatureList *rflist, ImageRecord *image) { } -ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *reflectionlist) { +ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *reflectionlist, ControlContext *ctx) { ImageFeatureList *flist; Reflection *reflection; double smax = 0.1e9; - double tilt, omega; - double nx, ny, nz, nxt, nyt, nzt; /* "normal" vector (and calculation intermediates) */ + double tilt, omega, k; + double nx, ny, nz; /* "normal" vector */ double kx, ky, kz; /* Electron wavevector ("normal" times 1/lambda */ - double ux, uy, uz, uxt, uyt, uzt; /* "up" vector (and calculation intermediates) */ - //int done_debug = 0; - + double ux, uy, uz; /* "up" vector */ + double rx, ry, rz; /* "right" vector */ + flist = image_feature_list_new(); tilt = image->tilt; omega = image->omega; + k = 1.0/image->lambda; - /* Calculate the (normalised) incident electron wavevector - * n is rotated "into" the reconstruction, so only one omega step. */ - nxt = 0.0; nyt = 0.0; nzt = 1.0; - nx = nxt; ny = cos(tilt)*nyt + sin(tilt)*nzt; nz = -sin(tilt)*nyt + cos(tilt)*nzt; - nxt = nx; nyt = ny; nzt = nz; - nx = nxt*cos(-omega) + nyt*sin(-omega); ny = -nxt*sin(-omega) + nyt*cos(-omega); nz = nzt; + /* Calculate the (normalised) incident electron wavevector */ + mapping_rotate(0.0, 0.0, 1.0, &nx, &ny, &nz, omega, tilt); kx = nx / image->lambda; ky = ny / image->lambda; kz = nz / image->lambda; /* This is the centre of the Ewald sphere */ - //reflection_add(ctx->reflectionlist, kx, ky, kz, 1, REFLECTION_VECTOR_MARKER_1); - /* Determine where "up" is - * See above. */ - uxt = 0.0; uyt = 1.0; uzt = 0.0; - ux = uxt; uy = cos(tilt)*uyt + sin(tilt)*uzt; uz = -sin(tilt)*uyt + cos(tilt)*uzt; - uxt = ux; uyt = uy; uzt = uz; - ux = uxt*cos(-omega) + uyt*-sin(omega); uy = -uxt*sin(omega) + uyt*cos(omega); uz = uzt; - //reflection_add(ctx->reflectionlist, ux*50e9, uy*50e9, uz*50e9, 1, REFLECTION_VECTOR_MARKER_2); + /* Determine where "up" is */ + mapping_rotate(0.0, 1.0, 0.0, &ux, &uy, &uz, omega, tilt); + + /* Determine where "right" is */ + mapping_rotate(1.0, 0.0, 0.0, &rx, &ry, &rz, omega, tilt); reflection = reflectionlist->reflections; do { double xl, yl, zl; double a, b, c; - double A1, A2, s1, s2, s; + double s1, s2, s, t; + double g_sq, gn; /* Get the coordinates of the reciprocal lattice point */ xl = reflection->x; yl = reflection->y; zl = reflection->z; + g_sq = modulus_squared(xl, yl, zl); + gn = xl*nx + yl*ny + zl*nz; /* Next, solve the relrod equation to calculate the excitation error */ a = 1.0; - b = -2.0*(xl*nx + yl*ny + zl*nz); - c = xl*xl + yl*yl + zl*zl - 1.0/(image->lambda*image->lambda); - A1 = (-b + sqrt(b*b-4.0*a*c))/(2.0*a); - A2 = (-b - sqrt(b*b-4.0*a*c))/(2.0*a); - s1 = 1.0/image->lambda - A1; - s2 = 1.0/image->lambda - A2; + b = 2.0*(gn - k); + c = -2.0*gn*k + g_sq; + t = -0.5*(b + sign(b)*sqrt(b*b - 4.0*a*c)); + s1 = t/a; + s2 = c/t; if ( fabs(s1) < fabs(s2) ) s = s1; else s = s2; /* Skip this reflection if s is large */ @@ -107,10 +105,8 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList * double xi, yi, zi; double gx, gy, gz; - double cx, cy, cz; double theta; double x, y; - double rx, ry, rz; /* Determine the intersection point */ xi = xl + s*nx; yi = yl + s*ny; zi = zl + s*nz; @@ -123,45 +119,12 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList * if ( theta > 0.0 ) { - double psi, disc; + double dx, dy, psi; - //reflection_add(ctx->reflectionlist, xl, yl, zl, 1, REFLECTION_GENERATED); - //reflection_add(ctx->reflectionlist, xi, yi, zi, 1, REFLECTION_MARKER); - - /* Calculate azimuth of point in image (clockwise from "up", will be changed later) */ - cx = yi*nz-zi*ny; cy = nx*zi-nz*xi; cz = ny*xi-nx*yi; /* c = i x n */ - psi = angle_between(cx, cy, cz, ux, uy, uz); - - /* Finally, resolve the +/- Pi ambiguity from the previous step */ - rx = cy*nz-cz*ny; ry = nx*cz-nz*cx; rz = ny*cx-nx*cy; /* r = [i x n] x n */ - disc = angle_between(rx, ry, rz, ux, uy, uz); - // if ( (i==20) && !done_debug ) { - // reflection_add(ctx->reflectionlist, xi, yi, zi, 1, REFLECTION_VECTOR_MARKER_3); - // reflection_add(ctx->reflectionlist, cx, cy, cz, 1, REFLECTION_VECTOR_MARKER_4); - // reflection_add(ctx->reflectionlist, rx, ry, rz, 1, REFLECTION_VECTOR_MARKER_4); - // printf("psi=%f deg, disc=%f deg\n", rad2deg(psi), rad2deg(disc)); - // } - if ( (psi >= M_PI_2) && (disc >= M_PI_2) ) { - psi -= M_PI_2; /* Case 1 */ - // if ( (i==20) && !done_debug ) printf("case 1\n"); - } else if ( (psi >= M_PI_2) && (disc < M_PI_2) ) { - psi = 3*M_PI_2 - psi; /* Case 2 */ - // if ( (i==20) && !done_debug ) printf("case 2\n"); - } else if ( (psi < M_PI_2) && (disc < M_PI_2) ) { - psi = 3*M_PI_2 - psi; /* Case 3 */ - // if ( (i==20) && !done_debug ) printf("case 3\n"); - } else if ( (psi < M_PI_2) && (disc >= M_PI_2) ) { - psi = 3*M_PI_2 + psi; /* Case 4 */ - // if ( (i==20) && !done_debug ) printf("case 4\n"); - } - - // if ( (i==20) && !done_debug ) printf("final psi=%f clockwise from 'up'\n", rad2deg(psi)); - psi = M_PI_2 - psi; /* Anticlockwise from "+x" instead of clockwise from "up" */ - // if ( (i==20) && !done_debug ) printf("final psi=%f anticlockwise from +x\n", rad2deg(psi)); - - psi += omega; - // if ( (i==20) && !done_debug ) printf("final psi=%f anticlockwise from +tilt axis\n", rad2deg(psi)); - // if ( (i==20) && !done_debug ) done_debug = 1; + /* Calculate azimuth of point in image (anticlockwise from +x) */ + dx = xi*rx + yi*ry + zi*rz; + dy = xi*ux + yi*uy + zi*uz; + psi = atan2(dy, dx); /* Calculate image coordinates from polar representation */ if ( image->fmode == FORMULATION_CLEN ) { @@ -175,7 +138,7 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList * x /= image->pixel_size; y /= image->pixel_size; } else { - fprintf(stderr, "Unrecognised formulation mode in reproject_get_reflections()\n"); + fprintf(stderr, "Unrecognised formulation mode in reproject_get_reflections\n"); return NULL; } @@ -185,13 +148,13 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList * /* Sanity check */ if ( (x>=0) && (x<image->width) && (y>=0) && (y<image->height) ) { - /* Record the reflection */ - image_add_feature_reflection(flist, x, y, image, reflection->intensity, reflection); - /* Intensity should be multiplied by relrod spike function except - * reprojected reflections aren't used quantitatively for anything */ + /* Record the reflection + * Intensity should be multiplied by relrod spike function except + * reprojected reflections aren't used quantitatively for anything + */ + image_add_feature_reflection(flist, x, y, image, + reflection->intensity, reflection); - //printf("Reflection at %f, %f\n", x, y); - } /* else it's outside the picture somewhere */ } /* else this is the central beam so don't worry about it */ diff --git a/src/reproject.h b/src/reproject.h index 93f010a..37eb84d 100644 --- a/src/reproject.h +++ b/src/reproject.h @@ -19,7 +19,8 @@ #include "control.h" #include "image.h" -extern ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *reflectionlist); +extern ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *reflectionlist, + ControlContext *ctx); extern void reproject_partner_features(ImageFeatureList *rflist, ImageRecord *image); extern void reproject_cell_to_lattice(ControlContext *ctx); extern void reproject_lattice_changed(ControlContext *ctx); diff --git a/src/utils.c b/src/utils.c index 30a6e34..01b14d9 100644 --- a/src/utils.c +++ b/src/utils.c @@ -39,6 +39,10 @@ double modulus(double x, double y, double z) { return sqrt(x*x + y*y + z*z); } +double modulus_squared(double x, double y, double z) { + return x*x + y*y + z*z; +} + double distance3d(double x1, double y1, double z1, double x2, double y2, double z2) { return modulus(x1-x2, y1-y2, z1-z2); } diff --git a/src/utils.h b/src/utils.h index 5c2e586..29ebf01 100644 --- a/src/utils.h +++ b/src/utils.h @@ -23,6 +23,7 @@ extern unsigned int biggest(signed int a, signed int b); extern unsigned int smallest(signed int a, signed int b); extern double distance(double x1, double y1, double x2, double y2); extern double modulus(double x, double y, double z); +extern double modulus_squared(double x, double y, double z); extern double angle_between(double x1, double y1, double z1, double x2, double y2, double z2); extern double angle_between_d(double x1, double y1, double z1, double x2, double y2, double z2); extern double lambda(double voltage); |