From e7cf3911104fb525159b937660a3c3b9f6d31ba7 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Mon, 7 Dec 2020 16:11:45 +0100 Subject: Get rid of ImageFeature->rx,ry,rz These needed to be kept up to date with a call to map_all_peaks every time anything changed - wavelength, detector position etc. Not doing so has already led to bugs in another branch, and probably already causes problems on this branch. This patch eliminates the rx,ry,rz completely. Anyone who needs reciprocal space coordinates for a peak is now responsible for calling detgeom_transform_coords themselves. --- libcrystfel/src/indexers/asdf.c | 11 ++++++++--- libcrystfel/src/indexers/dirax.c | 7 ++++++- libcrystfel/src/indexers/felix.c | 11 ++++++++--- libcrystfel/src/indexers/mosflm.c | 13 +++++++++---- libcrystfel/src/indexers/taketwo.c | 13 ++++++++++--- libcrystfel/src/indexers/xds.c | 13 +++++++++---- libcrystfel/src/indexers/xgandalf.c | 12 +++++++++--- 7 files changed, 59 insertions(+), 21 deletions(-) (limited to 'libcrystfel/src/indexers') diff --git a/libcrystfel/src/indexers/asdf.c b/libcrystfel/src/indexers/asdf.c index 806501cc..68b714a9 100644 --- a/libcrystfel/src/indexers/asdf.c +++ b/libcrystfel/src/indexers/asdf.c @@ -1116,14 +1116,19 @@ int run_asdf(struct image *image, void *ipriv) for ( i=0; ifeatures, i); if ( f == NULL ) continue; + detgeom_transform_coords(&image->detgeom->panels[f->pn], + f->fs, f->ss, image->lambda, + r); + reflections[N_reflections] = gsl_vector_alloc(3); - gsl_vector_set(reflections[N_reflections], 0, f->rx/1e10); - gsl_vector_set(reflections[N_reflections], 1, f->ry/1e10); - gsl_vector_set(reflections[N_reflections], 2, f->rz/1e10); + gsl_vector_set(reflections[N_reflections], 0, r[0]/1e10); + gsl_vector_set(reflections[N_reflections], 1, r[1]/1e10); + gsl_vector_set(reflections[N_reflections], 2, r[2]/1e10); N_reflections++; } diff --git a/libcrystfel/src/indexers/dirax.c b/libcrystfel/src/indexers/dirax.c index 24be87ba..a21dd7e2 100644 --- a/libcrystfel/src/indexers/dirax.c +++ b/libcrystfel/src/indexers/dirax.c @@ -490,12 +490,17 @@ static void write_drx(struct image *image) for ( i=0; ifeatures); i++ ) { struct imagefeature *f; + double r[3]; f = image_get_feature(image->features, i); if ( f == NULL ) continue; + detgeom_transform_coords(&image->detgeom->panels[f->pn], + f->fs, f->ss, image->lambda, + r); + fprintf(fh, "%10f %10f %10f %8f\n", - f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0); + r[0]/1e10, r[1]/1e10, r[2]/1e10, 1.0); } fclose(fh); diff --git a/libcrystfel/src/indexers/felix.c b/libcrystfel/src/indexers/felix.c index b94227d0..0db5ecbb 100644 --- a/libcrystfel/src/indexers/felix.c +++ b/libcrystfel/src/indexers/felix.c @@ -364,14 +364,19 @@ static void write_gve(struct image *image, struct felix_private *gp) for ( i=0; ifeatures); i++ ) { struct imagefeature *f; + double r[3]; f = image_get_feature(image->features, i); if ( f == NULL ) continue; + detgeom_transform_coords(&image->detgeom->panels[f->pn], + f->fs, f->ss, image->lambda, + r); + fprintf(fh, "%.6f %.6f %.6f 0 0 %.6f %.6f %.6f 0\n", - f->rz/1e10, f->rx/1e10, f->ry/1e10, - modulus(f->rx, f->ry, f->rz)/1e10, /* dstar */ - rad2deg(atan2(f->ry, f->rx)), 0.0); /* eta, omega */ + r[2]/1e10, r[0]/1e10, r[1]/1e10, + modulus(r[0], r[1], r[2])/1e10, /* dstar */ + rad2deg(atan2(r[1], r[0])), 0.0); /* eta, omega */ } fclose(fh); diff --git a/libcrystfel/src/indexers/mosflm.c b/libcrystfel/src/indexers/mosflm.c index bacd345f..4c1d2906 100644 --- a/libcrystfel/src/indexers/mosflm.c +++ b/libcrystfel/src/indexers/mosflm.c @@ -357,16 +357,21 @@ static void write_spt(struct image *image, const char *filename) struct imagefeature *f; double ttx, tty, x, y; + double r[3]; f = image_get_feature(image->features, i); if ( f == NULL ) continue; + detgeom_transform_coords(&image->detgeom->panels[f->pn], + f->fs, f->ss, image->lambda, + r); + ttx = angle_between_2d(0.0, 1.0, - f->rx, 1.0/image->lambda + f->rz); + r[0], 1.0/image->lambda + r[2]); tty = angle_between_2d(0.0, 1.0, - f->ry, 1.0/image->lambda + f->rz); - if ( f->rx < 0.0 ) ttx *= -1.0; - if ( f->ry < 0.0 ) tty *= -1.0; + r[1], 1.0/image->lambda + r[2]); + if ( r[0] < 0.0 ) ttx *= -1.0; + if ( r[1] < 0.0 ) tty *= -1.0; x = -tan(ttx)*FAKE_CLEN; y = tan(tty)*FAKE_CLEN; diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c index 4243adcb..18845ce5 100644 --- a/libcrystfel/src/indexers/taketwo.c +++ b/libcrystfel/src/indexers/taketwo.c @@ -2157,11 +2157,18 @@ int taketwo_index(struct image *image, void *priv) rlps = malloc((image_feature_count(image->features)+1)*sizeof(struct rvec)); for ( i=0; ifeatures); i++ ) { + + double r[3]; struct imagefeature *pk = image_get_feature(image->features, i); if ( pk == NULL ) continue; - rlps[n_rlps].u = pk->rx; - rlps[n_rlps].v = pk->ry; - rlps[n_rlps].w = pk->rz; + + detgeom_transform_coords(&image->detgeom->panels[pk->pn], + pk->fs, pk->ss, image->lambda, + r); + + rlps[n_rlps].u = r[0]; + rlps[n_rlps].v = r[1]; + rlps[n_rlps].w = r[2]; n_rlps++; } rlps[n_rlps].u = 0.0; diff --git a/libcrystfel/src/indexers/xds.c b/libcrystfel/src/indexers/xds.c index 02610d5e..76c657c6 100644 --- a/libcrystfel/src/indexers/xds.c +++ b/libcrystfel/src/indexers/xds.c @@ -213,17 +213,22 @@ static void write_spot(struct image *image) { struct imagefeature *f; double ttx, tty, x, y; + double r[3]; f = image_get_feature(image->features, i); if ( f == NULL ) continue; if ( f->intensity <= 0 ) continue; + detgeom_transform_coords(&image->detgeom->panels[f->pn], + f->fs, f->ss, image->lambda, + r); + ttx = angle_between_2d(0.0, 1.0, - f->rx, 1.0/image->lambda + f->rz); + r[0], 1.0/image->lambda + r[2]); tty = angle_between_2d(0.0, 1.0, - f->ry, 1.0/image->lambda + f->rz); - if ( f->rx < 0.0 ) ttx *= -1.0; - if ( f->ry < 0.0 ) tty *= -1.0; + r[1], 1.0/image->lambda + r[2]); + if ( r[0] < 0.0 ) ttx *= -1.0; + if ( r[1] < 0.0 ) tty *= -1.0; x = tan(ttx)*FAKE_CLEN; y = tan(tty)*FAKE_CLEN; diff --git a/libcrystfel/src/indexers/xgandalf.c b/libcrystfel/src/indexers/xgandalf.c index a0ce768d..a4773e18 100644 --- a/libcrystfel/src/indexers/xgandalf.c +++ b/libcrystfel/src/indexers/xgandalf.c @@ -92,14 +92,20 @@ int run_xgandalf(struct image *image, void *ipriv) reciprocalPeaks_1_per_A->peakCount = 0; for ( i = 0; i < peakCountMax && i < MAX_PEAK_COUNT_FOR_INDEXER; i++) { struct imagefeature *f; + double r[3]; + f = image_get_feature(image->features, i); if (f == NULL) { continue; } - reciprocalPeaks_1_per_A->coordinates_x[reciprocalPeaks_1_per_A->peakCount] = f->rx * 1e-10; - reciprocalPeaks_1_per_A->coordinates_y[reciprocalPeaks_1_per_A->peakCount] = f->ry * 1e-10; - reciprocalPeaks_1_per_A->coordinates_z[reciprocalPeaks_1_per_A->peakCount] = f->rz * 1e-10; + detgeom_transform_coords(&image->detgeom->panels[f->pn], + f->fs, f->ss, image->lambda, + r); + + reciprocalPeaks_1_per_A->coordinates_x[reciprocalPeaks_1_per_A->peakCount] = r[0] * 1e-10; + reciprocalPeaks_1_per_A->coordinates_y[reciprocalPeaks_1_per_A->peakCount] = r[1] * 1e-10; + reciprocalPeaks_1_per_A->coordinates_z[reciprocalPeaks_1_per_A->peakCount] = r[2] * 1e-10; reciprocalPeaks_1_per_A->peakCount++; } -- cgit v1.2.3