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-rw-r--r--src/Makefile.am2
-rw-r--r--src/dirax.c59
-rw-r--r--src/dirax.h2
-rw-r--r--src/image.h5
-rw-r--r--src/index.c98
-rw-r--r--src/index.h25
-rw-r--r--src/indexamajig.c15
7 files changed, 144 insertions, 62 deletions
diff --git a/src/Makefile.am b/src/Makefile.am
index 948d2fbf..8dd6af85 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -17,7 +17,7 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
process_hkl_LDADD = @LIBS@
indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c dirax.c cell.c image.c \
- intensities.c ewald.c peaks.c
+ intensities.c ewald.c peaks.c index.c
indexamajig_LDADD = @LIBS@
if HAVE_GTK
diff --git a/src/dirax.c b/src/dirax.c
index 2db591f4..991a3813 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -323,63 +323,13 @@ static gboolean dirax_readable(GIOChannel *dirax, GIOCondition condition,
}
-static int map_position(struct image *image, double x, double y,
- double *rx, double *ry, double *rz)
-{
- /* "Input" space */
- double d;
-
- /* Angular description of reflection */
- double theta, psi, k;
-
- x -= image->x_centre;
- y -= image->y_centre;
- k = 1.0 / image->lambda;
-
- /* FIXME: Don't process lower CCD for now */
- if ( y < 0 ) return 0;
-
- if ( image->fmode == FORMULATION_CLEN ) {
-
- /* Convert pixels to metres */
- x /= image->resolution;
- y /= image->resolution; /* Convert pixels to metres */
- d = sqrt((x*x) + (y*y));
- theta = atan2(d, image->camera_len);
-
- } else if (image->fmode == FORMULATION_PIXELSIZE ) {
-
- /* Convert pixels to metres^-1 */
- x *= image->pixel_size;
- y *= image->pixel_size; /* Convert pixels to metres^-1 */
- d = sqrt((x*x) + (y*y));
- theta = atan2(d, k);
-
- } else {
- ERROR("Unrecognised formulation mode in mapping_scale.\n");
- return -1;
- }
-
- psi = atan2(y, x);
-
- *rx = k*sin(theta)*cos(psi);
- *ry = k*sin(theta)*sin(psi);
- *rz = k - k*cos(theta);
-
- return 0;
-}
-
-
-void index_pattern(struct image *image, int no_index, int dump_peaks)
+void run_dirax(struct image *image, int no_index)
{
unsigned int opts;
int saved_stderr;
FILE *fh;
int i;
- /* Do peak search and splurge out 'xfel.drx' */
- search_peaks(image, dump_peaks);
-
fh = fopen("xfel.drx", "w");
if ( !fh ) {
ERROR("Couldn't open temporary file xfel.drx\n");
@@ -390,14 +340,11 @@ void index_pattern(struct image *image, int no_index, int dump_peaks)
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
- double rx = 0.0;
- double ry = 0.0;
- double rz = 0.0;
f = image_get_feature(image->features, i);
- map_position(image, f->x, f->y, &rx, &ry, &rz);
+
fprintf(fh, "%10f %10f %10f %8f\n",
- rx/1e10, ry/1e10, rz/1e10, 1.0);
+ f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
}
fclose(fh);
diff --git a/src/dirax.h b/src/dirax.h
index 4ebad677..58a0416e 100644
--- a/src/dirax.h
+++ b/src/dirax.h
@@ -18,7 +18,7 @@
#endif
-extern void index_pattern(struct image *image, int no_index, int dump_peaks);
+extern void run_dirax(struct image *image, int no_index);
#endif /* DIRAX_H */
diff --git a/src/image.h b/src/image.h
index 9649fe8e..7cf47761 100644
--- a/src/image.h
+++ b/src/image.h
@@ -46,6 +46,11 @@ struct imagefeature {
/* Distance between this feature and its partner, if any. */
double partner_d;
+ /* Reciprocal space coordinates (m^-1 of course) of this feature */
+ double rx;
+ double ry;
+ double rz;
+
};
/* An opaque type representing a list of image features */
diff --git a/src/index.c b/src/index.c
new file mode 100644
index 00000000..c8d5dbe6
--- /dev/null
+++ b/src/index.c
@@ -0,0 +1,98 @@
+/*
+ * index.c
+ *
+ * Perform indexing (somehow)
+ *
+ * (c) 2006-2009 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+
+#include "image.h"
+#include "utils.h"
+#include "peaks.h"
+#include "dirax.h"
+
+
+static int map_position(struct image *image, double x, double y,
+ double *rx, double *ry, double *rz)
+{
+ /* "Input" space */
+ double d;
+
+ /* Angular description of reflection */
+ double theta, psi, k;
+
+ x -= image->x_centre;
+ y -= image->y_centre;
+ k = 1.0 / image->lambda;
+
+ /* FIXME: Don't process lower CCD for now */
+ if ( y < 0 ) return 0;
+
+ if ( image->fmode == FORMULATION_CLEN ) {
+
+ /* Convert pixels to metres */
+ x /= image->resolution;
+ y /= image->resolution; /* Convert pixels to metres */
+ d = sqrt((x*x) + (y*y));
+ theta = atan2(d, image->camera_len);
+
+ } else if (image->fmode == FORMULATION_PIXELSIZE ) {
+
+ /* Convert pixels to metres^-1 */
+ x *= image->pixel_size;
+ y *= image->pixel_size; /* Convert pixels to metres^-1 */
+ d = sqrt((x*x) + (y*y));
+ theta = atan2(d, k);
+
+ } else {
+ ERROR("Unrecognised formulation mode in mapping_scale.\n");
+ return -1;
+ }
+
+ psi = atan2(y, x);
+
+ *rx = k*sin(theta)*cos(psi);
+ *ry = k*sin(theta)*sin(psi);
+ *rz = k - k*cos(theta);
+
+ return 0;
+}
+
+
+void index_pattern(struct image *image, int no_index, int dump_peaks,
+ int use_dirax)
+{
+ int i;
+
+ /* Perform 'fine' peak search */
+ search_peaks(image, dump_peaks);
+
+ /* Map positions to 3D. FIXME: Handle lower detector */
+ for ( i=0; i<image_feature_count(image->features); i++ ) {
+
+ struct imagefeature *f;
+
+ f = image_get_feature(image->features, i);
+ map_position(image, f->x, f->y, &f->rx, &f->ry, &f->rz);
+
+ }
+
+ if ( use_dirax ) {
+ run_dirax(image, no_index);
+ return;
+ }
+}
diff --git a/src/index.h b/src/index.h
new file mode 100644
index 00000000..ea0b4485
--- /dev/null
+++ b/src/index.h
@@ -0,0 +1,25 @@
+/*
+ * index.h
+ *
+ * Perform indexing (somehow)
+ *
+ * (c) 2006-2009 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifndef INDEX_H
+#define INDEX_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+extern void index_pattern(struct image *image, int no_index, int dump_peaks,
+ int use_dirax);
+
+
+#endif /* INDEX_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 7c2e1b5d..7f863a65 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -23,7 +23,7 @@
#include "utils.h"
#include "hdf5-file.h"
-#include "dirax.h"
+#include "index.h"
#include "intensities.h"
#include "ewald.h"
#include "peaks.h"
@@ -39,8 +39,10 @@ static void show_help(const char *s)
"\n"
" -i, --input=<filename> Specify file containing list of images to process.\n"
" '-' means stdin, which is the default.\n"
-" --no-index Do everything else (including fine peak search),\n"
-" but don't invoke the indexing program.\n"
+" --no-index Do everything else (including fine peak search and\n"
+" writing 'xfel.drx' if DirAx is being used), but\n"
+" don't actually index.\n"
+" --dirax Use DirAx for indexing.\n"
"\n");
}
@@ -55,6 +57,7 @@ int main(int argc, char *argv[])
int n_hits;
int config_noindex = 0;
int config_dumpfound = 0;
+ int config_dirax = 0;
/* Long options */
const struct option longopts[] = {
@@ -62,6 +65,7 @@ int main(int argc, char *argv[])
{"input", 1, NULL, 'i'},
{"no-index", 0, &config_noindex, 1},
{"dump-found-peaks", 0, &config_dumpfound, 1},
+ {"dirax", 0, &config_dirax, 1},
{0, 0, NULL, 0}
};
@@ -135,7 +139,10 @@ int main(int argc, char *argv[])
if ( fom > 0 ) {
/* Calculate orientation matrix (by magic) */
- index_pattern(&image, config_noindex, config_dumpfound);
+ index_pattern(&image, config_noindex, config_dumpfound,
+ config_dirax);
+
+ if ( image.molecule == NULL ) continue;
/* View head-on (unit cell is tilted) */
image.orientation.x = 0.0;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 16:49:40 +0000