indexamajig: --peaks=cxi instead of --peaks=hdf5 --cxi-hdf5-peaks

3 files changed, 18 insertions, 10 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index 4f28aec5..627dfa67 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -97,11 +97,9 @@ static void show_help(const char *s)
 "                           zaef  : Use Zaefferer (2000) gradient detection.\n"
 "                                    This is the default method.\n"
 "                           hdf5  : Get from a table in HDF5 file.\n"
+"                           cxi   : Get from CXI format HDF5 file.\n"
 "     --hdf5-peaks=<p>     Find peaks table in HDF5 file here.\n"
 "                           Default: /processing/hitfinder/peakinfo\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"
 "\n\n"
 "For more control over the process, you might need:\n\n"
@@ -219,7 +217,6 @@ int main(int argc, char *argv[])
 	iargs.peaks = PEAK_ZAEF;
 	iargs.beam = &beam;
 	iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
-	iargs.cxi_hdf5_peaks = 0;
 	iargs.copyme = NULL;
 	iargs.pk_inn = -1.0;
 	iargs.pk_mid = -1.0;
@@ -271,7 +268,6 @@ 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},
-		{"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},
@@ -513,6 +509,8 @@ int main(int argc, char *argv[])
 		iargs.peaks = PEAK_ZAEF;
 	} else if ( strcmp(speaks, "hdf5") == 0 ) {
 		iargs.peaks = PEAK_HDF5;
+	} else if ( strcmp(speaks, "cxi") == 0 ) {
+		iargs.peaks = PEAK_CXI;
 	} else {
 		ERROR("Unrecognised peak detection method '%s'\n", speaks);
 		return 1;
diff --git a/src/process_image.c b/src/process_image.c
index d5133a0c..847cc9f4 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -225,10 +225,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	switch ( iargs->peaks ) {
 
 		case PEAK_HDF5:
-		/* Get peaks from HDF5 */
-
-		if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path,
-		               iargs->cxi_hdf5_peaks, pargs->filename_p_e) ) {
+		if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) {
 			ERROR("Failed to get peaks from HDF5 file.\n");
 		}
 		if ( !iargs->no_revalidate ) {
@@ -239,6 +236,19 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		}
 		break;
 
+		case PEAK_CXI:
+		if ( get_peaks_cxi(&image, hdfile, iargs->hdf5_peak_path,
+		                   pargs->filename_p_e) ) {
+			ERROR("Failed to get peaks from CXI file.\n");
+		}
+		if ( !iargs->no_revalidate ) {
+			validate_peaks(&image, iargs->min_snr,
+				       iargs->pk_inn, iargs->pk_mid,
+		                       iargs->pk_out, iargs->use_saturated,
+				       iargs->check_hdf5_snr);
+		}
+		break;
+
 		case PEAK_ZAEF:
 		search_peaks(&image, iargs->threshold,
 		             iargs->min_gradient, iargs->min_snr,
diff --git a/src/process_image.h b/src/process_image.h
index 53e2c66a..68254485 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -41,6 +41,7 @@
 enum {
 	PEAK_ZAEF,
 	PEAK_HDF5,
+	PEAK_CXI,
 };
 
 
@@ -63,7 +64,6 @@ struct index_args
 	float tols[4];
 	struct beam_params *beam;
 	char *hdf5_peak_path;
-	int cxi_hdf5_peaks;
 	float pk_inn;
 	float pk_mid;
 	float pk_out;