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-rw-r--r--libcrystfel/src/hdf5-file.c11
-rw-r--r--libcrystfel/src/hdf5-file.h2
-rw-r--r--src/indexamajig.c6
-rw-r--r--src/process_image.c2
-rw-r--r--src/process_image.h2
5 files changed, 12 insertions, 11 deletions
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 923d27ca..0d041e01 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -380,10 +380,9 @@ static int read_hdf5_data_into_buffer(struct hdfile *f, char *path, int line,
int get_peaks(struct image *image, struct hdfile *f, const char *p,
- int cxidb_format, struct filename_plus_event *fpe)
+ int cxi_format, struct filename_plus_event *fpe)
{
-
- if ( cxidb_format ) {
+ if ( cxi_format ) {
char *path_n;
char *path_x;
@@ -404,10 +403,12 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p,
path_y=malloc((strlen(p)+strlen("/peakYPosRaw")+1)*sizeof(char));
path_i=malloc((strlen(p)+strlen("/peakIntensity")+1)*sizeof(char));
- if ( fpe != NULL && fpe->ev != NULL && fpe->ev->dim_entries != NULL ) {
+ if ( (fpe != NULL) && (fpe->ev != NULL)
+ && (fpe->ev->dim_entries != NULL) )
+ {
line = fpe->ev->dim_entries[0];
} else {
- ERROR("CXIDB peak list format selected,"
+ ERROR("CXI format peak list format selected,"
"but file has no event structure");
free(path_n);
free(path_x);
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
index 93ef1d95..84b20798 100644
--- a/libcrystfel/src/hdf5-file.h
+++ b/libcrystfel/src/hdf5-file.h
@@ -80,7 +80,7 @@ extern int hdfile_is_scalar(struct hdfile *f, const char *name, int verbose);
char *hdfile_get_string_value(struct hdfile *f, const char *name,
struct event* ev);
extern int get_peaks(struct image *image, struct hdfile *f, const char *p,
- int cxidb_format, struct filename_plus_event *fpe);
+ int cxi_format, struct filename_plus_event *fpe);
extern double get_value(struct hdfile *f, const char *name);
extern double get_ev_based_value(struct hdfile *f, const char *name,
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 6aeaaad5..e3daa1c9 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -99,7 +99,7 @@ static void show_help(const char *s)
" hdf5 : Get from a table in HDF5 file.\n"
" --hdf5-peaks=<p> Find peaks table in HDF5 file here.\n"
" Default: /processing/hitfinder/peakinfo\n"
-" --cxidb-hdf5-peaks Peaks in the HDF5 file are in CXIDB format.\n"
+" --cxi-hdf5-peaks Peaks in the HDF5 file are in CXI file format.\n"
" Only used in conjunction with the --hdf5-peaks,\n"
" ignored otherwise."
" --integration=<meth> Perform final pattern integration using <meth>.\n"
@@ -219,7 +219,7 @@ int main(int argc, char *argv[])
iargs.beam = &beam;
iargs.element = NULL;
iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
- iargs.cxidb_hdf5_peaks = 0;
+ iargs.cxi_hdf5_peaks = 0;
iargs.copyme = NULL;
iargs.pk_inn = -1.0;
iargs.pk_mid = -1.0;
@@ -269,7 +269,7 @@ int main(int argc, char *argv[])
{"no-use-saturated", 0, &iargs.use_saturated, 0},
{"no-revalidate", 0, &iargs.no_revalidate, 1},
{"check-hdf5-snr", 0, &iargs.check_hdf5_snr, 1},
- {"cxidb-hdf5-peaks", 0, &iargs.cxidb_hdf5_peaks, 1},
+ {"cxi-hdf5-peaks", 0, &iargs.cxi_hdf5_peaks, 1},
/* Long-only options which don't actually do anything */
{"no-sat-corr", 0, &iargs.satcorr, 0},
diff --git a/src/process_image.c b/src/process_image.c
index 57bc9e3c..6ccd0c9a 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -180,7 +180,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Get peaks from HDF5 */
if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path,
- iargs->cxidb_hdf5_peaks, pargs->filename_p_e) ) {
+ iargs->cxi_hdf5_peaks, pargs->filename_p_e) ) {
ERROR("Failed to get peaks from HDF5 file.\n");
}
if ( !iargs->no_revalidate ) {
diff --git a/src/process_image.h b/src/process_image.h
index 891553e6..8dba8a85 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -64,7 +64,7 @@ struct index_args
struct beam_params *beam;
char *element;
char *hdf5_peak_path;
- int cxidb_hdf5_peaks;
+ int cxi_hdf5_peaks;
float pk_inn;
float pk_mid;
float pk_out;