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-rw-r--r--libcrystfel/src/detector.c38
-rw-r--r--libcrystfel/src/detector.h3
-rw-r--r--libcrystfel/src/hdf5-file.c46
-rw-r--r--libcrystfel/src/image.c53
4 files changed, 100 insertions, 40 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index b2e3cc58..e3b351ff 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -528,37 +528,15 @@ int panel_number(struct detector *det, struct panel *p)
}
-void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev)
+void adjust_centering_for_rail(struct panel *p)
{
- int i;
-
- for ( i=0; i<det->n_panels; i++ ) {
-
- double offs;
- struct panel *p = &det->panels[i];
+ double offs;
- if ( p->clen_from != NULL ) {
-
- double val;
- int r;
-
- r = hdfile_get_value(f, p->clen_from, ev, &val,
- H5T_NATIVE_DOUBLE);
- if ( r ) {
- ERROR("Failed to read '%s'\n", p->clen_from);
- } else {
- p->clen = val * 1.0e-3;
- }
-
- }
-
- /* Offset in +z direction from calibrated clen to actual */
- offs = p->clen - p->clen_for_centering;
- p->cnx += p->rail_x * offs;
- p->cny += p->rail_y * offs;
- p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs;
-
- }
+ /* Offset in +z direction from calibrated clen to actual */
+ offs = p->clen - p->clen_for_centering;
+ p->cnx += p->rail_x * offs;
+ p->cny += p->rail_y * offs;
+ p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs;
}
@@ -1076,10 +1054,8 @@ static void parse_toplevel(struct detector *det, struct beam_params *beam,
} else if ( strcmp(key, "photon_energy") == 0 ) {
if ( beam != NULL ) {
-
double v;
char *end;
-
v = strtod(val, &end);
if ( (val[0] != '\0') && (end[0] == '\0') ) {
beam->photon_energy = v;
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 04e3c1ec..e9dd1154 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -224,9 +224,8 @@ extern void get_pixel_extents(struct detector *det,
double *min_x, double *min_y,
double *max_x, double *max_y);
-extern void fill_in_values(struct detector *det, struct hdfile *f,
- struct event* ev);
extern void fill_in_adu(struct image *image);
+extern void adjust_centering_for_rail(struct panel *p);
extern int panel_is_in_rigid_group(const struct rigid_group *rg,
struct panel *p);
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 9a52fd4d..dc86d641 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -1390,8 +1390,10 @@ int hdfile_get_value(struct hdfile *f, const char *name,
}
-void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
- struct event *ev, struct image *image)
+static void hdfile_fill_in_beam_parameters(struct beam_params *beam,
+ struct hdfile *f,
+ struct event *ev,
+ struct image *image)
{
double eV;
@@ -1404,8 +1406,8 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
int r;
- r = hdfile_get_value(f, beam->photon_energy_from, ev, &eV,
- H5T_NATIVE_DOUBLE);
+ r = hdfile_get_value(f, beam->photon_energy_from,
+ ev, &eV, H5T_NATIVE_DOUBLE);
if ( r ) {
ERROR("Failed to read '%s'\n",
beam->photon_energy_from);
@@ -1417,6 +1419,36 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
}
+static void hdfile_fill_in_clen(struct detector *det, struct hdfile *f,
+ struct event *ev)
+{
+ int i;
+
+ for ( i=0; i<det->n_panels; i++ ) {
+
+ struct panel *p = &det->panels[i];
+
+ if ( p->clen_from != NULL ) {
+
+ double val;
+ int r;
+
+ r = hdfile_get_value(f, p->clen_from, ev, &val,
+ H5T_NATIVE_DOUBLE);
+ if ( r ) {
+ ERROR("Failed to read '%s'\n", p->clen_from);
+ } else {
+ p->clen = val * 1.0e-3;
+ }
+
+ }
+
+ adjust_centering_for_rail(p);
+
+ }
+}
+
+
int hdf5_read(struct hdfile *f, struct image *image, const char *element,
int satcorr)
{
@@ -1481,7 +1513,7 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element,
if ( image->beam != NULL ) {
- fill_in_beam_parameters(image->beam, f, NULL, image);
+ hdfile_fill_in_beam_parameters(image->beam, f, NULL, image);
if ( image->lambda > 1000 ) {
/* Error message covers a silly value in the beam file
@@ -1885,13 +1917,13 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev,
H5Dclose(f->dh);
f->data_open = 0;
- fill_in_values(image->det, f, ev);
+ hdfile_fill_in_clen(image->det, f, ev);
if ( satcorr ) debodge_saturation(f, image);
if ( image->beam != NULL ) {
- fill_in_beam_parameters(image->beam, f, ev, image);
+ hdfile_fill_in_beam_parameters(image->beam, f, ev, image);
if ( (image->lambda > 1.0) || (image->lambda < 1e-20) ) {
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index a8c278fc..849d95bf 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -521,6 +521,48 @@ static int unpack_panels(struct image *image, signed int *data, int data_width)
}
+static void cbf_fill_in_beam_parameters(struct beam_params *beam,
+ struct imagefile *f,
+ struct image *image)
+{
+ double eV;
+
+ if ( beam->photon_energy_from == NULL ) {
+
+ /* Explicit value given */
+ eV = beam->photon_energy;
+
+ } else {
+
+ ERROR("Can't get photon energy from CBF yet.\n");
+ eV = 0.0;
+
+ }
+
+ image->lambda = ph_en_to_lambda(eV_to_J(eV))*beam->photon_energy_scale;
+}
+
+
+static void cbf_fill_in_clen(struct detector *det, struct imagefile *f)
+{
+ int i;
+
+ for ( i=0; i<det->n_panels; i++ ) {
+
+ struct panel *p = &det->panels[i];
+
+ if ( p->clen_from != NULL ) {
+
+ ERROR("Can't get clen from CBF yet.\n");
+
+ }
+
+ adjust_centering_for_rail(p);
+
+ }
+}
+
+
static int read_cbf(struct imagefile *f, struct image *image)
{
cbf_handle cbfh;
@@ -617,6 +659,17 @@ static int read_cbf(struct imagefile *f, struct image *image)
unpack_panels(image, data, dimfast);
free(data);
+ if ( image->beam != NULL ) {
+ cbf_fill_in_beam_parameters(image->beam, f, image);
+ if ( image->lambda > 1000 ) {
+ ERROR("WARNING: Missing or nonsensical wavelength "
+ "(%e m) for %s.\n",
+ image->lambda, image->filename);
+ }
+ }
+ cbf_fill_in_clen(image->det, f);
+ fill_in_adu(image);
+
cbf_free_handle(cbfh);
return 0;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 18:15:17 +0000