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authorThomas White <taw@physics.org>2010-01-12 14:17:13 +0100
committerThomas White <taw@physics.org>2010-01-12 14:17:13 +0100
commit0b17be9c96c4082b7cf2334c6a2cc35bb6a5814c (patch)
tree6702c7a63f06c988e740736026b18a74760c7803
parent419d5533423ca402ffce44e2e2a05d62c5ba1804 (diff)
Complete indexing functionality
-rw-r--r--src/Makefile.am3
-rw-r--r--src/dirax.c49
-rw-r--r--src/dirax.h2
-rw-r--r--src/displaywindow.c12
-rw-r--r--src/image.h3
-rw-r--r--src/indexamajig.c18
6 files changed, 60 insertions, 27 deletions
diff --git a/src/Makefile.am b/src/Makefile.am
index 978ab602..9010373c 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -16,7 +16,8 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
reflections.c
process_hkl_LDADD = @LIBS@
-indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c dirax.c cell.c image.c
+indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c dirax.c cell.c image.c \
+ intensities.c ewald.c
indexamajig_LDADD = @LIBS@
if HAVE_GTK
diff --git a/src/dirax.c b/src/dirax.c
index 0c509e06..8606ff44 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -33,6 +33,7 @@
#include "image.h"
#include "dirax.h"
#include "utils.h"
+#include "sfac.h"
typedef enum {
@@ -67,10 +68,13 @@ static void dirax_parseline(const char *line, struct image *image)
if ( line[i] == 'R' ) rf = 1;
if ( (line[i] == 'D') && rf ) {
image->dirax_read_cell = 1;
- if ( image->cell ) {
- free(image->cell);
+ if ( image->molecule == NULL ) {
+ image->molecule = malloc(sizeof(struct molecule));
+ } else if ( image->molecule->cell ) {
+ free(image->molecule->cell);
+ free(image->molecule);
}
- image->cell = cell_new();
+ image->molecule->cell = cell_new();
return;
}
i++;
@@ -79,24 +83,27 @@ static void dirax_parseline(const char *line, struct image *image)
/* Parse unit cell vectors as appropriate */
if ( image->dirax_read_cell == 1 ) {
/* First row of unit cell values */
- float x1, x2, x3;
- sscanf(line, "%f %f %f", &x1, &x2, &x3);
- cell_set_cartesian_x(image->cell, x1*1e10, x2*1e10, x3*1e10);
+ float x1, x2, x3, d;
+ sscanf(line, "%f %f %f %f %f %f", &d, &d, &d, &x1, &x2, &x3);
+ cell_set_cartesian_x(image->molecule->cell,
+ x1*1e-10, x2*1e-10, x3*1e-10);
image->dirax_read_cell++;
return;
} else if ( image->dirax_read_cell == 2 ) {
/* First row of unit cell values */
- float y1, y2, y3;
- sscanf(line, "%f %f %f", &y1, &y2, &y3);
- cell_set_cartesian_y(image->cell, y1*1e10, y2*1e10, y3*1e10);
+ float y1, y2, y3, d;
+ sscanf(line, "%f %f %f %f %f %f", &d, &d, &d, &y1, &y2, &y3);
+ cell_set_cartesian_y(image->molecule->cell,
+ y1*1e-10, y2*1e-10, y3*1e-10);
image->dirax_read_cell++;
return;
} else if ( image->dirax_read_cell == 3 ) {
/* First row of unit cell values */
- float z1, z2, z3;
- sscanf(line, "%f %f %f", &z1, &z2, &z3);
- cell_set_cartesian_z(image->cell, z1*1e10, z2*1e10, z3*1e10);
- STATUS("Read a reciprocal unit cell from DirAx\n");
+ float z1, z2, z3, d;
+ sscanf(line, "%f %f %f %f %f %f", &d, &d, &d, &z1, &z2, &z3);
+ cell_set_cartesian_z(image->molecule->cell,
+ z1*1e-10, z2*1e-10, z3*1e-10);
+ STATUS("Read a direct space unit cell from DirAx\n");
/* FIXME: Do something */
image->dirax_read_cell = 0;
return;
@@ -172,6 +179,7 @@ static void dirax_send_next(struct image *image)
default: {
image->dirax_step = 0;
STATUS("DirAx is idle\n");
+ g_main_loop_quit(image->dirax_ml);
}
}
@@ -371,7 +379,7 @@ static int map_position(struct image *image, double x, double y,
#define PEAK_WINDOW_SIZE (10)
-static void search_peaks(struct image *image)
+static void search_peaks(struct image *image, int dump_peaks)
{
FILE *fh;
int x, y, width, height;
@@ -478,7 +486,9 @@ static void search_peaks(struct image *image)
double rz = 0.0;
/* Map and record reflection */
- printf("%i %i\n", x, y);
+ if ( dump_peaks ) {
+ printf("%i %i\n", x, y);
+ }
image_add_feature(image->features,
mask_x, mask_y, image, 1.0);
@@ -497,14 +507,13 @@ static void search_peaks(struct image *image)
}
-void index_pattern(struct image *image, int no_index)
+void index_pattern(struct image *image, int no_index, int dump_peaks)
{
unsigned int opts;
int saved_stderr;
- GMainLoop *ml;
/* Do peak search and splurge out 'xfel.drx' */
- search_peaks(image);
+ search_peaks(image, dump_peaks);
if ( no_index ) return;
@@ -548,8 +557,8 @@ void index_pattern(struct image *image, int no_index)
g_io_add_watch(image->dirax, G_IO_IN | G_IO_HUP,
(GIOFunc)dirax_readable, image);
- ml = g_main_loop_new(NULL, FALSE);
- g_main_loop_run(ml);
+ image->dirax_ml = g_main_loop_new(NULL, FALSE);
+ g_main_loop_run(image->dirax_ml);
return;
}
diff --git a/src/dirax.h b/src/dirax.h
index f4b82ba5..4ebad677 100644
--- a/src/dirax.h
+++ b/src/dirax.h
@@ -18,7 +18,7 @@
#endif
-extern void index_pattern(struct image *image, int no_index);
+extern void index_pattern(struct image *image, int no_index, int dump_peaks);
#endif /* DIRAX_H */
diff --git a/src/displaywindow.c b/src/displaywindow.c
index 9a65fb16..008aa19f 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -415,13 +415,21 @@ static void load_features_from_file(struct image *image, const char *filename)
do {
char line[1024];
- int x, y;
- int r;
+ int x, y, r, d;
+ float df;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
+ /* Try long format (output of pattern_sim --near-bragg) */
+ r = sscanf(line, "%i %i %i %f (at %i,%i)",
+ &d, &d, &d, &df, &x, &y);
+ if ( r == 6 ) {
+ image_add_feature(image->features, x, y, image, 1.0);
+ continue;
+ }
+
r = sscanf(line, "%i %i", &x, &y);
if ( r != 2 ) continue;
diff --git a/src/image.h b/src/image.h
index 1dcfdc3b..9649fe8e 100644
--- a/src/image.h
+++ b/src/image.h
@@ -94,8 +94,6 @@ struct image {
ImageFeatureList *features; /* "Experimental" features */
ImageFeatureList *rflist; /* "Predicted" features */
- UnitCell *cell;
-
/* DirAx auto-indexing low-level stuff */
GIOChannel *dirax;
int dirax_pty;
@@ -103,6 +101,7 @@ struct image {
char *dirax_rbuffer;
int dirax_rbufpos;
int dirax_rbuflen;
+ GMainLoop *dirax_ml;
/* DirAx auto-indexing high-level stuff */
int dirax_step;
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 1ff6d2e6..41cf5b22 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -24,6 +24,8 @@
#include "utils.h"
#include "hdf5-file.h"
#include "dirax.h"
+#include "intensities.h"
+#include "ewald.h"
static void show_help(const char *s)
@@ -195,12 +197,14 @@ int main(int argc, char *argv[])
int n_images;
int n_hits;
int config_noindex = 0;
+ int config_dumpfound = 0;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"no-index", 0, &config_noindex, 1},
+ {"dump-found-peaks", 0, &config_dumpfound, 1},
{0, 0, NULL, 0}
};
@@ -257,6 +261,7 @@ int main(int argc, char *argv[])
chomp(line);
image.features = NULL;
+ image.molecule = NULL;
STATUS("Processing '%s'\n", line);
@@ -272,7 +277,18 @@ int main(int argc, char *argv[])
fom = image_fom(&image);
if ( fom > 0 ) {
- index_pattern(&image, config_noindex);
+ /* Calculate orientation matrix (by magic) */
+ index_pattern(&image, config_noindex, config_dumpfound);
+
+ /* View head-on (unit cell is tilted) */
+ image.orientation.x = 0.0;
+ image.orientation.y = 0.0;
+ image.orientation.z = 0.0;
+ image.orientation.w = 1.0;
+ get_ewald(&image);
+
+ /* Read h,k,l,I */
+ output_intensities(&image);
n_hits++;