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authorThomas White <taw@bitwiz.org.uk>2009-10-23 12:00:29 +0200
committerThomas White <taw@bitwiz.org.uk>2009-10-23 12:00:29 +0200
commitf09b0fc4da61d107dffc0d45489b769326fd8a08 (patch)
tree02ebe57032f0db9e68078c6ed08d413aa8c7b323
parent2600c19c6d9b994de1cb2d5e634571a55434c707 (diff)
Restructuring ready for new simulation method
-rw-r--r--Makefile.am2
-rw-r--r--src/Makefile.am3
-rw-r--r--src/diffraction.c59
-rw-r--r--src/diffraction.h24
-rw-r--r--src/main.c19
-rw-r--r--src/templates.c183
-rw-r--r--src/templates.h29
7 files changed, 86 insertions, 233 deletions
diff --git a/Makefile.am b/Makefile.am
index 03aa63dd..f4a33f00 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,3 +1,3 @@
EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h src/relrod.h \
- src/templates.h src/utils.h
+ src/utils.h src/diffraction.h
SUBDIRS = src
diff --git a/src/Makefile.am b/src/Makefile.am
index d30736c7..3ab2d7f8 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,5 +1,4 @@
bin_PROGRAMS = pattern_sim
-pattern_sim_SOURCES = main.c relrod.c utils.c image.c cell.c hdf5-file.c \
- templates.c
+pattern_sim_SOURCES = main.c diffraction.c utils.c image.c cell.c hdf5-file.c
pattern_sim_LDADD = @LIBS@ -lm -lgsl -lgslcblas
diff --git a/src/diffraction.c b/src/diffraction.c
new file mode 100644
index 00000000..93c6a22c
--- /dev/null
+++ b/src/diffraction.c
@@ -0,0 +1,59 @@
+/*
+ * diffraction.c
+ *
+ * Calculate diffraction patterns by Fourier methods
+ *
+ * (c) 2007-2009 Thomas White <thomas.white@desy.de>
+ *
+ * pattern_sim - Simulate diffraction patterns from small crystals
+ *
+ */
+
+
+#include <stdlib.h>
+#include <math.h>
+#include <stdio.h>
+
+#include "image.h"
+#include "utils.h"
+#include "cell.h"
+
+
+static void mapping_rotate(double x, double y, double z,
+ double *ddx, double *ddy, double *ddz,
+ double omega, double tilt)
+{
+ double nx, ny, nz;
+ double x_temp, y_temp, z_temp;
+
+ /* First: rotate image clockwise until tilt axis is aligned
+ * horizontally. */
+ nx = x*cos(omega) + y*sin(omega);
+ ny = -x*sin(omega) + y*cos(omega);
+ nz = z;
+
+ /* Now, tilt about the x-axis ANTICLOCKWISE around +x, i.e. the
+ * "wrong" way. This is because the crystal is rotated in the
+ * experiment, not the Ewald sphere. */
+ x_temp = nx; y_temp = ny; z_temp = nz;
+ nx = x_temp;
+ ny = cos(tilt)*y_temp + sin(tilt)*z_temp;
+ nz = -sin(tilt)*y_temp + cos(tilt)*z_temp;
+
+ /* Finally, reverse the omega rotation to restore the location of the
+ * image in 3D space */
+ x_temp = nx; y_temp = ny; z_temp = nz;
+ nx = x_temp*cos(-omega) + y_temp*sin(-omega);
+ ny = -x_temp*sin(-omega) + y_temp*cos(-omega);
+ nz = z_temp;
+
+ *ddx = nx;
+ *ddy = ny;
+ *ddz = nz;
+}
+
+
+void get_diffraction(struct image *image, UnitCell *cell)
+{
+
+}
diff --git a/src/diffraction.h b/src/diffraction.h
new file mode 100644
index 00000000..c32e62c2
--- /dev/null
+++ b/src/diffraction.h
@@ -0,0 +1,24 @@
+/*
+ * diffraction.h
+ *
+ * Calculate diffraction patterns by Fourier methods
+ *
+ * (c) 2007-2009 Thomas White <thomas.white@desy.de>
+ *
+ * pattern_sim - Simulate diffraction patterns from small crystals
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifndef DIFFRACTION_H
+#define DIFFRACTION_H
+
+#include "image.h"
+#include "cell.h"
+
+extern void get_diffraction(struct image *image, UnitCell *cell);
+
+#endif /* DIFFRACTION_H */
diff --git a/src/main.c b/src/main.c
index 04f806f2..8ab11c85 100644
--- a/src/main.c
+++ b/src/main.c
@@ -85,24 +85,7 @@ int main(int argc, char *argv[])
memset(image.data, 0, 512*512*2);
image.tilt = deg2rad(t);
- /* Calculate reflections */
- get_reflections(&image, cell, 1.0/CRYSTAL_SIZE);
-
- /* Construct the image */
- nrefl = image_feature_count(image.rflist);
- for ( i=0; i<nrefl; i++ ) {
-
- struct imagefeature *f;
- int x, y;
-
- f = image_get_feature(image.rflist, i);
-
- x = f->x;
- y = f->y; /* Discards digits after the decimal point */
-
- image.data[y*image.width+x] = 1;
-
- }
+ get_diffraction(&image, cell);
/* Write the output file */
snprintf(filename, 32, "simulated-%.0f.h5", t);
diff --git a/src/templates.c b/src/templates.c
deleted file mode 100644
index 1ad1c95a..00000000
--- a/src/templates.c
+++ /dev/null
@@ -1,183 +0,0 @@
-/*
- * templates.c
- *
- * Handle templates
- *
- * (c) 2006-2009 Thomas White <thomas.white@desy.de>
- *
- * pattern_sim - Simulate diffraction patterns from small crystals
- *
- */
-
-
-#define _GNU_SOURCE 1
-#include <stdlib.h>
-#include <assert.h>
-#include <math.h>
-#include <stdio.h>
-
-#include "templates.h"
-#include "cell.h"
-#include "image.h"
-#include "utils.h"
-#include "relrod.h"
-
-
-struct _templatelist
-{
- int n_templates;
- struct template *templates;
-};
-
-
-struct template_feature
-{
- float x;
- float y;
- struct template_feature *next;
-};
-
-
-struct template
-{
- float omega;
- float tilt;
- struct template_feature *features;
-};
-
-
-static int template_add(TemplateList *list, struct template *template)
-{
- if ( list->templates ) {
- list->templates = realloc(list->templates,
- (list->n_templates+1)*sizeof(struct template));
- } else {
- assert(list->n_templates == 0);
- list->templates = malloc(sizeof(struct template));
- }
-
- /* Copy the data */
- list->templates[list->n_templates] = *template;
-
- list->n_templates++;
-
- return list->n_templates - 1;
-}
-
-
-static TemplateList *template_list_new()
-{
- TemplateList *list;
-
- list = malloc(sizeof(TemplateList));
-
- list->n_templates = 0;
- list->templates = NULL;
-
- return list;
-}
-
-
-TemplateList *generate_templates(UnitCell *cell, struct image params)
-{
- TemplateList *list;
- double omega, tilt;
-
- list = template_list_new();
-
- omega = deg2rad(40.0);
-
- //for ( omega=deg2rad(-180); omega<deg2rad(180); omega+=deg2rad(1) ) {
-
- params.omega = omega;
-
- for ( tilt=0; tilt<deg2rad(180); tilt+=deg2rad(1) ) {
-
- struct template t;
- struct template_feature *tfc;
- int nrefl, i;
-
- t.omega = omega;
- t.tilt = tilt;
- t.features = malloc(sizeof(struct template_feature));
- t.features->next = NULL;
- tfc = t.features;
-
- params.tilt = tilt;
- get_reflections(&params, cell, 0.01e9);
-
- nrefl = image_feature_count(params.rflist);
- for ( i=0; i<nrefl; i++ ) {
-
- struct imagefeature *f;
-
- f = image_get_feature(params.rflist, i);
-
- tfc->x = f->x;
- tfc->y = f->y;
- tfc->next = malloc(sizeof(struct template_feature));
- tfc = tfc->next;
-
- }
-
- template_add(list, &t);
-
- image_feature_list_free(params.rflist);
-
- printf("Generating templates... %+5.2f %+5.2f\r",
- rad2deg(omega), rad2deg(tilt));
-
- }
- //}
-
- printf("Generating templates... done \n");
-
- return list;
-}
-
-
-static int try_template(struct image *image, struct template template)
-{
- int fit = 0;
- struct template_feature *f;
-
- f = template.features;
- while ( f != NULL ) {
-
- int x, y;
-
- x = f->x;
- y = f->y; /* Discards digits after the decimal point */
-
- fit += image->data[y*image->width+x];
-
- f = f->next;
-
- }
-
- return fit;
-}
-
-
-int try_templates(struct image *image, TemplateList *list)
-{
- int i;
- int fit_max = 0;
- int i_max = 0;
-
- for ( i=0; i<list->n_templates; i++ ) {
-
- int fit;
-
- fit = try_template(image, list->templates[i]);
- if ( fit > fit_max ) {
- fit_max = fit;
- i_max = i;
- }
-
- }
- image->omega = list->templates[i_max].omega;
- image->tilt = list->templates[i_max].tilt;
-
- return 0;
-}
diff --git a/src/templates.h b/src/templates.h
deleted file mode 100644
index c9d053ad..00000000
--- a/src/templates.h
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * templates.h
- *
- * Handle templates
- *
- * (c) 2006-2009 Thomas White <thomas.white@desy.de>
- *
- * pattern_sim - Simulate diffraction patterns from small crystals
- *
- */
-
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#ifndef TEMPLATES_H
-#define TEMPLATES_H
-
-#include "cell.h"
-#include "image.h"
-
-/* An opaque type representing a list of templates */
-typedef struct _templatelist TemplateList;
-
-extern TemplateList *generate_templates(UnitCell *cell, struct image params);
-extern int try_templates(struct image *image, TemplateList *list);
-
-#endif /* TEMPLAETS_H */