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-rw-r--r--src/reproject.c83
1 files changed, 41 insertions, 42 deletions
diff --git a/src/reproject.c b/src/reproject.c
index e1ce13e..c41aa3f 100644
--- a/src/reproject.c
+++ b/src/reproject.c
@@ -23,24 +23,24 @@
void reproject_partner_features(ImageFeatureList *rflist, ImageRecord *image) {
int i;
-
+
for ( i=0; i<rflist->n_features; i++ ) {
-
+
//if ( !reflection_is_easy(rflist->features[i].reflection) ) continue;
-
+
double d = 0.0;
ImageFeature *partner;
int 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;
rflist->features[i].partner_d = d;
} else {
rflist->features[i].partner = NULL;
}
-
+
}
}
@@ -55,12 +55,12 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
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;
-
+
flist = image_feature_list_new();
-
+
tilt = image->tilt;
omega = image->omega;
-
+
/* 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;
@@ -71,7 +71,7 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
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;
@@ -79,19 +79,19 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
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);
-
+
reflection = reflectionlist->reflections;
do {
-
+
double xl, yl, zl;
double a, b, c;
double A1, A2, s1, s2, s;
-
+
/* Get the coordinates of the reciprocal lattice point */
xl = reflection->x;
yl = reflection->y;
zl = reflection->z;
-
+
/* Next, solve the relrod equation to calculate the excitation error */
a = 1.0;
b = -2.0*(xl*nx + yl*ny + zl*nz);
@@ -101,37 +101,37 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
s1 = 1.0/image->lambda - A1;
s2 = 1.0/image->lambda - A2;
if ( fabs(s1) < fabs(s2) ) s = s1; else s = s2;
-
+
/* Skip this reflection if s is large */
if ( fabs(s) <= smax ) {
-
+
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;
-
+
/* Calculate Bragg angle */
gx = xi - kx;
gy = yi - ky;
gz = zi - kz; /* This is the vector from the centre of the sphere to the intersection */
theta = angle_between(-kx, -ky, -kz, gx, gy, gz);
-
+
if ( theta > 0.0 ) {
-
+
double psi, disc;
-
+
//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);
@@ -154,15 +154,15 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
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 image coordinates from polar representation */
if ( image->fmode == FORMULATION_CLEN ) {
x = image->camera_len*tan(theta)*cos(psi);
@@ -178,36 +178,36 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
fprintf(stderr, "Unrecognised formulation mode in reproject_get_reflections()\n");
return NULL;
}
-
+
x += image->x_centre;
y += image->y_centre;
-
+
/* 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 */
-
+
//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 */
-
+
}
-
+
reflection = reflection->next;
-
+
} while ( reflection );
-
+
/* Partner features only if the image has a feature list. This allows the test
* program to use this function to generate simulated data. */
if ( image->features != NULL ) {
reproject_partner_features(flist, image);
}
-
+
return flist;
}
@@ -216,21 +216,21 @@ ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *
void reproject_cell_to_lattice(ControlContext *ctx) {
int i;
-
+
if ( ctx->cell_lattice ) {
reflection_list_from_new_cell(ctx->cell_lattice, ctx->cell);
} else {
ctx->cell_lattice = reflection_list_from_cell(ctx->cell);
}
-
+
displaywindow_enable_cell_functions(ctx->dw, TRUE);
-
+
/* Invalidate all the reprojected feature lists */
for ( i=0; i<ctx->images->n_images; i++ ) {
image_feature_list_free(ctx->images->images[i].rflist);
ctx->images->images[i].rflist = NULL;
}
-
+
}
/* Notify that ctx->cell has changed (also need to call displaywindow_update) */
@@ -240,4 +240,3 @@ void reproject_lattice_changed(ControlContext *ctx) {
displaywindow_update_imagestack(ctx->dw);
}
-
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-17 05:03:43 +0000