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-rw-r--r--libcrystfel/src/indexers/asdf.c11
-rw-r--r--libcrystfel/src/indexers/dirax.c7
-rw-r--r--libcrystfel/src/indexers/felix.c11
-rw-r--r--libcrystfel/src/indexers/mosflm.c13
-rw-r--r--libcrystfel/src/indexers/taketwo.c13
-rw-r--r--libcrystfel/src/indexers/xds.c13
-rw-r--r--libcrystfel/src/indexers/xgandalf.c12
7 files changed, 59 insertions, 21 deletions
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; i<n; 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);
+
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; i<image_feature_count(image->features); 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; i<image_feature_count(image->features); 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; i<image_feature_count(image->features); 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++;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-28 06:23:44 +0000