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-rw-r--r--src/calibrate_detector.c3
-rw-r--r--src/cubeit.c3
-rw-r--r--src/hdf5-file.c7
-rw-r--r--src/hdf5-file.h3
-rw-r--r--src/index.c6
-rw-r--r--src/index.h3
-rw-r--r--src/indexamajig.c34
-rw-r--r--src/powder_plot.c2
-rw-r--r--src/reintegrate.c3
-rw-r--r--src/render.c3
-rw-r--r--src/templates.c5
-rw-r--r--src/templates.h3
12 files changed, 57 insertions, 18 deletions
diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
index 5ca468c6..b20b1619 100644
--- a/src/calibrate_detector.c
+++ b/src/calibrate_detector.c
@@ -189,7 +189,8 @@ static void add_image(void *args, int cookie)
return;
}
- hdf5_read(hdfile, &image, 1);
+ /* FIXME: Nominal photon energy */
+ hdf5_read(hdfile, &image, 1, 2000.0);
if ( pargs->config_cmfilter ) {
filter_cm(&image);
diff --git a/src/cubeit.c b/src/cubeit.c
index ad78704e..b613a3fa 100644
--- a/src/cubeit.c
+++ b/src/cubeit.c
@@ -237,7 +237,8 @@ static void sum_image(void *pg, int cookie)
return;
}
- hdf5_read(hdfile, &image, 1);
+ /* FIXME: Nominal photon energy */
+ hdf5_read(hdfile, &image, 1, 2000.0);
cell_get_cartesian(apargs->cell, &ax, &ay, &az, &bx, &by,
&bz, &cx, &cy, &cz);
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index bcd51f99..a24a663a 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -390,7 +390,8 @@ static void debodge_saturation(struct hdfile *f, struct image *image)
}
-int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
+int hdf5_read(struct hdfile *f, struct image *image, int satcorr,
+ double nominal_photon_energy)
{
herr_t r;
float *buf;
@@ -432,8 +433,8 @@ int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
/* Read wavelength from file */
image->lambda = get_wavelength(f);
if ( image->lambda < 0.0 ) {
- ERROR("Couldn't read wavelength - using 2 keV.\n");
- image->lambda = ph_en_to_lambda(eV_to_J(2000.0));
+ ERROR("Couldn't read wavelength - using nominal value.\n");
+ image->lambda = ph_en_to_lambda(eV_to_J(nominal_photon_energy));
}
image->f0 = get_f0(f);
diff --git a/src/hdf5-file.h b/src/hdf5-file.h
index 145c9cac..4f849638 100644
--- a/src/hdf5-file.h
+++ b/src/hdf5-file.h
@@ -27,7 +27,8 @@ struct hdfile;
extern int hdf5_write(const char *filename, const void *data,
int width, int height, int type);
-extern int hdf5_read(struct hdfile *f, struct image *image, int satcorr);
+extern int hdf5_read(struct hdfile *f, struct image *image, int satcorr,
+ double nominal_photon_energy);
extern struct hdfile *hdfile_open(const char *filename);
extern int hdfile_set_image(struct hdfile *f, const char *path);
diff --git a/src/index.c b/src/index.c
index 97cf3887..0c656042 100644
--- a/src/index.c
+++ b/src/index.c
@@ -42,7 +42,8 @@ static IndexingPrivate *indexing_private(IndexingMethod indm)
IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
- const char *filename, struct detector *det)
+ const char *filename, struct detector *det,
+ double nominal_photon_energy)
{
switch ( indm ) {
case INDEXING_NONE :
@@ -50,7 +51,8 @@ IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
case INDEXING_DIRAX :
return indexing_private(indm);
case INDEXING_TEMPLATE :
- return generate_templates(cell, filename, det);
+ return generate_templates(cell, filename, det,
+ nominal_photon_energy);
}
return 0;
}
diff --git a/src/index.h b/src/index.h
index 259d3eb6..0b740995 100644
--- a/src/index.h
+++ b/src/index.h
@@ -33,7 +33,8 @@ typedef struct _indexingprivate IndexingPrivate;
extern IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
const char *filename,
- struct detector *det);
+ struct detector *det,
+ double nominal_photon_energy);
extern void map_all_peaks(struct image *image);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 54d5e630..348e3e8b 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -36,6 +36,7 @@
#include "filters.h"
#include "reflections.h"
#include "thread-pool.h"
+#include "beam-parameters.h"
enum {
@@ -71,6 +72,7 @@ struct static_index_args
const double *intensities;
struct gpu_context *gctx;
int peaks;
+ double nominal_photon_energy;
/* Output stream */
pthread_mutex_t *output_mutex; /* Protects the output stream */
@@ -120,6 +122,9 @@ static void show_help(const char *s)
" dirax : invoke DirAx\n"
" template : index by template matching\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
+" -b, --beam=<file> Get beam parameters from file (provides nominal\n"
+" wavelength value if no per-shot value is found in\n"
+" the HDF5 files.\n"
" -p, --pdb=<file> PDB file from which to get the unit cell to match.\n"
" Default: 'molecule.pdb'.\n"
" -x, --prefix=<p> Prefix filenames from input file with <p>.\n"
@@ -340,7 +345,8 @@ static void process_image(void *pp, int cookie)
return;
}
- hdf5_read(hdfile, &image, pargs->static_args.config_satcorr);
+ hdf5_read(hdfile, &image, pargs->static_args.config_satcorr,
+ pargs->static_args.nominal_photon_energy);
if ( config_cmfilter ) {
filter_cm(&image);
@@ -531,6 +537,8 @@ int main(int argc, char *argv[])
char prepare_filename[1024];
IndexingPrivate *ipriv;
struct queue_args qargs;
+ struct beam_params *beam = NULL;
+ double nominal_photon_energy;
/* Long options */
const struct option longopts[] = {
@@ -545,6 +553,7 @@ int main(int argc, char *argv[])
{"write-drx", 0, &config_writedrx, 1},
{"indexing", 1, NULL, 'z'},
{"geometry", 1, NULL, 'g'},
+ {"beam", 1, NULL, 'b'},
{"simulate", 0, &config_simulate, 1},
{"filter-cm", 0, &config_cmfilter, 1},
{"filter-noise", 0, &config_noisefilter, 1},
@@ -566,7 +575,7 @@ int main(int argc, char *argv[])
};
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:",
+ while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:",
longopts, NULL)) != -1) {
switch (c) {
@@ -610,6 +619,15 @@ int main(int argc, char *argv[])
threshold = strtof(optarg, NULL);
break;
+ case 'b' :
+ beam = get_beam_parameters(optarg);
+ if ( beam == NULL ) {
+ ERROR("Failed to load beam parameters"
+ " from '%s'\n", optarg);
+ return 1;
+ }
+ break;
+
case 2 :
speaks = strdup(optarg);
break;
@@ -742,6 +760,14 @@ int main(int argc, char *argv[])
fprintf(ofh, "\n");
fflush(ofh);
+ if ( beam != NULL ) {
+ nominal_photon_energy = beam->photon_energy;
+ } else {
+ STATUS("No beam parameters file was given, so I'm taking the"
+ " nominal photon energy to be 2 keV.\n");
+ nominal_photon_energy = 2000.0;
+ }
+
/* Get first filename and use it to set up the indexing */
if ( fh != stdin ) {
rval = fgets(prepare_line, 1023, fh);
@@ -758,7 +784,8 @@ int main(int argc, char *argv[])
STATUS("Stuff might break.\n");
prepare_filename[0] = '\0';
}
- ipriv = prepare_indexing(indm, cell, prepare_filename, det);
+ ipriv = prepare_indexing(indm, cell, prepare_filename, det,
+ nominal_photon_energy);
if ( ipriv == NULL ) {
ERROR("Failed to prepare indexing.\n");
return 1;
@@ -792,6 +819,7 @@ int main(int argc, char *argv[])
qargs.static_args.peaks = peaks;
qargs.static_args.output_mutex = &output_mutex;
qargs.static_args.ofh = ofh;
+ qargs.static_args.nominal_photon_energy = nominal_photon_energy;
qargs.fh = fh;
qargs.prefix = prefix;
diff --git a/src/powder_plot.c b/src/powder_plot.c
index d9049cc3..f8038274 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -102,7 +102,7 @@ int main(int argc, char *argv[])
hdfile = hdfile_open(filename);
hdfile_set_image(hdfile, "/data/data");
- hdf5_read(hdfile, &image, 1);
+ hdf5_read(hdfile, &image, 1, 2000.0);
for ( x=0; x<image.width; x++ ) {
for ( y=0; y<image.height; y++ ) {
diff --git a/src/reintegrate.c b/src/reintegrate.c
index c9de3338..220cad26 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -129,7 +129,8 @@ static void process_image(void *pg, int cookie)
return;
}
- hdf5_read(hdfile, &image, pargs->config_satcorr);
+ /* FIXME: Nominal photon energy */
+ hdf5_read(hdfile, &image, pargs->config_satcorr, 2000.0);
map_all_peaks(&image);
diff --git a/src/render.c b/src/render.c
index 7b694a25..128ede3a 100644
--- a/src/render.c
+++ b/src/render.c
@@ -78,7 +78,8 @@ float *render_get_image_binned(DisplayWindow *dw, int binning, float *max)
image->features = NULL;
image->data = NULL;
- hdf5_read(dw->hdfile, image, 1);
+ /* We don't care about the photon energy here */
+ hdf5_read(dw->hdfile, image, 1, 0.0);
dw->image_dirty = 0;
if ( dw->cmfilter ) filter_cm(image);
if ( dw->noisefilter ) filter_noise(image, NULL);
diff --git a/src/templates.c b/src/templates.c
index 105fa755..e9bd7b72 100644
--- a/src/templates.c
+++ b/src/templates.c
@@ -109,7 +109,8 @@ UnitCell *rotate_cell(UnitCell *in, double omega, double phi, double rot)
/* Generate templates for the given cell using a representative image */
IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
- struct detector *det)
+ struct detector *det,
+ double nominal_photon_energy)
{
struct _indexingprivate_template *priv;
const char *holo;
@@ -129,7 +130,7 @@ IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
ERROR("Couldn't select path\n");
return NULL;
}
- hdf5_read(hdfile, &image, 0);
+ hdf5_read(hdfile, &image, 0, nominal_photon_energy);
hdfile_close(hdfile);
image.det = det;
diff --git a/src/templates.h b/src/templates.h
index 50aa7443..33e6c75e 100644
--- a/src/templates.h
+++ b/src/templates.h
@@ -22,7 +22,8 @@
#include "cell.h"
extern IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
- struct detector *det);
+ struct detector *det,
+ double nominal_photon_energy);
extern void match_templates(struct image *image, IndexingPrivate *ipriv);
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-30 15:50:25 +0000