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-rw-r--r--src/Makefile.am4
-rw-r--r--src/cell.c67
-rw-r--r--src/cell.h13
-rw-r--r--src/image.c11
-rw-r--r--src/image.h8
-rw-r--r--src/relrod.c114
-rw-r--r--src/sim-main.c18
7 files changed, 140 insertions, 95 deletions
diff --git a/src/Makefile.am b/src/Makefile.am
index b480cedd..46a5e9d9 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,8 +1,8 @@
bin_PROGRAMS = template_index simulate_patterns
template_index_SOURCES = main.c relrod.c utils.c image.c cell.c
-template_index_LDADD = @LIBS@ -lm
+template_index_LDADD = @LIBS@ -lm -lgsl -lgslcblas
AM_CFLAGS = -Wall -g
simulate_patterns_SOURCES = sim-main.c relrod.c utils.c image.c cell.c
-simulate_patterns_LDADD = @LIBS@ -lm
+simulate_patterns_LDADD = @LIBS@ -lm -lgsl -lgslcblas
diff --git a/src/cell.c b/src/cell.c
index 6fa91cd3..81638016 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -16,6 +16,9 @@
#include <math.h>
#include <stdlib.h>
#include <stdio.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_blas.h>
+#include <gsl/gsl_linalg.h>
#include "cell.h"
#include "utils.h"
@@ -74,9 +77,9 @@ static void cell_update_crystallographic(UnitCell *cell)
cell->gamma = angle_between(cell->ax, cell->ay, cell->az,
cell->bx, cell->by, cell->bz);
- printf("a=%f nm\n", cell->a);
- printf("b=%f nm\n", cell->b);
- printf("c=%f nm\n", cell->c);
+ printf("a=%f nm\n", cell->a/1e9);
+ printf("b=%f nm\n", cell->b/1e9);
+ printf("c=%f nm\n", cell->c/1e9);
printf("alpha = %f deg\n", rad2deg(cell->alpha));
printf(" beta = %f deg\n", rad2deg(cell->beta));
printf("gamma = %f deg\n", rad2deg(cell->gamma));
@@ -104,7 +107,7 @@ UnitCell *cell_new()
void cell_set_parameters(UnitCell *cell, double a, double b, double c,
- double alpha, double beta, double gamma)
+ double alpha, double beta, double gamma)
{
if ( !cell ) return;
@@ -135,7 +138,7 @@ void cell_set_cartesian(UnitCell *cell,
UnitCell *cell_new_from_parameters(double a, double b, double c,
- double alpha, double beta, double gamma)
+ double alpha, double beta, double gamma)
{
UnitCell *cell;
@@ -149,9 +152,9 @@ UnitCell *cell_new_from_parameters(double a, double b, double c,
void cell_get_cartesian(UnitCell *cell,
- double *ax, double *ay, double *az,
- double *bx, double *by, double *bz,
- double *cx, double *cy, double *cz)
+ double *ax, double *ay, double *az,
+ double *bx, double *by, double *bz,
+ double *cx, double *cy, double *cz)
{
if ( !cell ) return;
@@ -159,3 +162,51 @@ void cell_get_cartesian(UnitCell *cell,
*bx = cell->bx; *by = cell->by; *bz = cell->bz;
*cx = cell->cx; *cy = cell->cy; *cz = cell->cz;
}
+
+
+void cell_get_reciprocal(UnitCell *cell,
+ double *asx, double *asy, double *asz,
+ double *bsx, double *bsy, double *bsz,
+ double *csx, double *csy, double *csz)
+{
+ int s;
+ gsl_matrix *m;
+ gsl_matrix *inv;
+ gsl_permutation *perm;
+
+ m = gsl_matrix_alloc(3, 3);
+ gsl_matrix_set(m, 0, 0, cell->ax);
+ gsl_matrix_set(m, 0, 1, cell->bx);
+ gsl_matrix_set(m, 0, 2, cell->cx);
+ gsl_matrix_set(m, 1, 0, cell->ay);
+ gsl_matrix_set(m, 1, 1, cell->by);
+ gsl_matrix_set(m, 1, 2, cell->cy);
+ gsl_matrix_set(m, 2, 0, cell->az);
+ gsl_matrix_set(m, 2, 1, cell->bz);
+ gsl_matrix_set(m, 2, 2, cell->cz);
+
+ /* Invert */
+ perm = gsl_permutation_alloc(m->size1);
+ inv = gsl_matrix_alloc(m->size1, m->size2);
+ gsl_linalg_LU_decomp(m, perm, &s);
+ gsl_linalg_LU_invert(m, perm, inv);
+ gsl_permutation_free(perm);
+ gsl_matrix_free(m);
+
+ /* Transpose */
+ gsl_matrix_transpose(inv);
+
+ *asx = gsl_matrix_get(inv, 0, 0);
+ *bsx = gsl_matrix_get(inv, 0, 1);
+ *csx = gsl_matrix_get(inv, 0, 2);
+ *asy = gsl_matrix_get(inv, 1, 0);
+ *bsy = gsl_matrix_get(inv, 1, 1);
+ *csy = gsl_matrix_get(inv, 1, 2);
+ *asz = gsl_matrix_get(inv, 2, 0);
+ *bsz = gsl_matrix_get(inv, 2, 1);
+ *csz = gsl_matrix_get(inv, 2, 2);
+
+ printf("a* = %f %f %f\n", *asx/1e9, *asy/1e9, *asz/1e9);
+ printf("b* = %f %f %f\n", *bsx/1e9, *bsy/1e9, *bsz/1e9);
+ printf("c* = %f %f %f\n", *csx/1e9, *csy/1e9, *csz/1e9);
+}
diff --git a/src/cell.h b/src/cell.h
index cd31aa66..196b9521 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -19,9 +19,9 @@
typedef struct {
/* Crystallographic representation */
- double a; /* nm */
- double b; /* nm */
- double c; /* nm */
+ double a; /* m */
+ double b; /* m */
+ double c; /* m */
double alpha; /* Radians */
double beta; /* Radians */
double gamma; /* Radians */
@@ -40,7 +40,7 @@ typedef struct {
extern UnitCell *cell_new(void);
-/* Lengths in nm, angles in radians */
+/* Lengths in m, angles in radians */
extern UnitCell *cell_new_from_parameters(double a, double b, double c,
double alpha, double beta, double gamma);
@@ -57,4 +57,9 @@ extern void cell_get_cartesian(UnitCell *cell,
double *bx, double *by, double *bz,
double *cx, double *cy, double *cz);
+extern void cell_get_reciprocal(UnitCell *cell,
+ double *asx, double *asy, double *asz,
+ double *bsx, double *bsy, double *bsz,
+ double *csx, double *csy, double *csz);
+
#endif /* CELL_H */
diff --git a/src/image.c b/src/image.c
index 8780c0dd..d3e65685 100644
--- a/src/image.c
+++ b/src/image.c
@@ -69,8 +69,8 @@ ImageList *image_list_new()
}
-void image_add_feature_reflection(ImageFeatureList *flist, double x, double y,
- struct image *parent, double intensity)
+void image_add_feature(ImageFeatureList *flist, double x, double y,
+ struct image *parent, double intensity)
{
if ( flist->features ) {
flist->features = realloc(flist->features,
@@ -93,13 +93,6 @@ void image_add_feature_reflection(ImageFeatureList *flist, double x, double y,
}
-void image_add_feature(ImageFeatureList *flist, double x, double y,
- struct image *parent, double intensity)
-{
- image_add_feature_reflection(flist, x, y, parent, intensity);
-}
-
-
ImageFeatureList *image_feature_list_new()
{
ImageFeatureList *flist;
diff --git a/src/image.h b/src/image.h
index 69b8cc79..fc8a1f2f 100644
--- a/src/image.h
+++ b/src/image.h
@@ -82,10 +82,13 @@ struct image {
typedef struct _imagelist ImageList;
+/* Image lists */
extern ImageList *image_list_new(void);
extern int image_add(ImageList *list, struct image *image);
+
+/* Feature lists */
extern ImageFeatureList *image_feature_list_new(void);
extern void image_feature_list_free(ImageFeatureList *flist);
@@ -93,11 +96,6 @@ extern void image_feature_list_free(ImageFeatureList *flist);
extern void image_add_feature(ImageFeatureList *flist, double x, double y,
struct image *parent, double intensity);
-extern void image_add_feature_reflection(ImageFeatureList *flist,
- double x, double y,
- struct image *parent,
- double intensity);
-
extern struct imagefeature *image_feature_closest(ImageFeatureList *flist,
double x, double y, double *d,
int *idx);
diff --git a/src/relrod.c b/src/relrod.c
index df4c4df3..e344133a 100644
--- a/src/relrod.c
+++ b/src/relrod.c
@@ -62,14 +62,18 @@ void get_reflections(struct image *image, UnitCell *cell)
double kx, ky, kz; /* Electron wavevector ("normal" times 1/lambda) */
double ux, uy, uz; /* "up" vector */
double rx, ry, rz; /* "right" vector */
- double ax, ay, az; /* "a" lattice parameter */
- double bx, by, bz; /* "b" lattice parameter */
- double cx, cy, cz; /* "c" lattice parameter */
+ double asx, asy, asz; /* "a*" lattice parameter */
+ double bsx, bsy, bsz; /* "b*" lattice parameter */
+ double csx, csy, csz; /* "c*" lattice parameter */
signed int h, k, l;
- flist = image_feature_list_new();
- cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+ /* Get the reciprocal unit cell */
+ cell_get_reciprocal(cell, &asx, &asy, &asz,
+ &bsx, &bsy, &bsz,
+ &csx, &csy, &csz);
+ /* Prepare list and some parameters */
+ flist = image_feature_list_new();
tilt = image->tilt;
omega = image->omega;
wavenumber = 1.0/image->lambda;
@@ -96,9 +100,9 @@ void get_reflections(struct image *image, UnitCell *cell)
double g_sq, gn;
/* Get the coordinates of the reciprocal lattice point */
- xl = h*ax + k*bx + l*cx;
- yl = h*ay + k*by + l*cy;
- zl = h*az + k*bz + l*cz;
+ xl = h*asx + k*bsx + l*csx;
+ yl = h*asy + k*bsy + l*csy;
+ zl = h*asz + k*bsz + l*csz;
g_sq = modulus_squared(xl, yl, zl);
gn = xl*nx + yl*ny + zl*nz;
@@ -119,6 +123,7 @@ void get_reflections(struct image *image, UnitCell *cell)
double gx, gy, gz;
double theta;
double x, y;
+ double dx, dy, psi;
/* Determine the intersection point */
xi = xl + s*nx; yi = yl + s*ny; zi = zl + s*nz;
@@ -130,56 +135,49 @@ void get_reflections(struct image *image, UnitCell *cell)
* the sphere to the intersection */
theta = angle_between(-kx, -ky, -kz, gx, gy, gz);
- if ( theta > 0.0 ) {
-
- double dx, dy, psi;
-
- /* 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);
-
- /* Get image coordinates from polar
- * representation */
- if ( image->fmode == FORMULATION_CLEN ) {
- x = image->camera_len*tan(theta)*cos(psi);
- y = image->camera_len*tan(theta)*sin(psi);
- x *= image->resolution;
- y *= image->resolution;
- } else if ( image->fmode==FORMULATION_PIXELSIZE ) {
- x = tan(theta)*cos(psi) / image->lambda;
- y = tan(theta)*sin(psi) / image->lambda;
- x /= image->pixel_size;
- y /= image->pixel_size;
- } else {
- fprintf(stderr,
- "Unrecognised formulation mode "
- "in get_reflections\n");
- return;
- }
-
- x += image->x_centre;
- y += image->y_centre;
-
- /* Sanity check */
- if ( (x>=0) && (x<image->width)
- && (y>=0) && (y<image->height) ) {
-
- /* 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, 1.0);
-
- } /* else it's outside the picture somewhere */
-
- } /* else this is the central beam */
-
- }
+ /* 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);
+
+ /* Get image coordinates from polar
+ * representation */
+ if ( image->fmode == FORMULATION_CLEN ) {
+ x = image->camera_len*tan(theta)*cos(psi);
+ y = image->camera_len*tan(theta)*sin(psi);
+ x *= image->resolution;
+ y *= image->resolution;
+ } else if ( image->fmode==FORMULATION_PIXELSIZE ) {
+ x = tan(theta)*cos(psi) / image->lambda;
+ y = tan(theta)*sin(psi) / image->lambda;
+ x /= image->pixel_size;
+ y /= image->pixel_size;
+ } else {
+ fprintf(stderr,
+ "Unrecognised formulation mode "
+ "in get_reflections\n");
+ return;
+ }
+
+ x += image->x_centre;
+ y += image->y_centre;
+
+ /* Sanity check */
+ if ( (x>=0) && (x<image->width)
+ && (y>=0) && (y<image->height) ) {
+
+ /* Record the reflection.
+ * Intensity should be multiplied by relrod
+ * spike function, except reprojected
+ * reflections aren't used quantitatively for
+ * anything. */
+ printf("%i %i %i\n", h,k,l);
+ image_add_feature(flist, x, y, image, 1.0);
+
+ } /* else it's outside the picture somewhere */
+
+ } /* else reflection is not excited in this orientation */
}
}
diff --git a/src/sim-main.c b/src/sim-main.c
index 38ad45bc..23ba3e99 100644
--- a/src/sim-main.c
+++ b/src/sim-main.c
@@ -61,20 +61,20 @@ int main(int argc, char *argv[])
image.tilt = 0.0;
image.omega = 0.0;
image.fmode = FORMULATION_CLEN;
- image.x_centre = 128;
- image.y_centre = 128;
- image.camera_len = 1.0; /* one metre */
- image.resolution = 5120;
- image.lambda = 0.6e-9;
+ image.x_centre = 255.5;
+ image.y_centre = 255.5;
+ image.camera_len = 0.2; /* 20 cm */
+ image.resolution = 5120; /* 512 pixels in 10 cm */
+ image.lambda = 0.2e-9; /* LCLS wavelength */
image.data = malloc(512*512*2);
image_add(list, &image);
- cell = cell_new_from_parameters(1.0,
- 1.0,
- 1.0,
+ cell = cell_new_from_parameters(28.10e-9,
+ 28.10e-9,
+ 16.52e-9,
deg2rad(90.0),
deg2rad(90.0),
- deg2rad(90.0));
+ deg2rad(120.0));
get_reflections(&image, cell);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 14:40:21 +0000