indexamajig: Add --no-non-hits-in-stream

4 files changed, 22 insertions, 1 deletions

diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 5855c866..eaf812d6 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -233,6 +233,16 @@ these.  The defaults are probably not appropriate for your situation.
 The default is \fB--int-radius=4,5,7\fR.
 
 .PD 0
+.IP \fB--min-peaks=\fIn\fR
+.PD
+Do not try to index frames with fewer than \fIn\fR peaks.  These frames will still be described in the output stream.  To exclude them, use \fB--no-non-hits-in-stream\fR.
+
+.PD 0
+.IP \fB--no-non-hits-in-stream\fR
+.PD
+Completely exclude 'non-hit' frames in the stream.  When this option is given, frames with fewer than the number of peaks given to \fB--min-peaks\fR will not have chunks written to the stream at all.
+
+.PD 0
 .IP \fB--basename\fR
 .PD
 Remove the directory parts of the filenames taken from the input file.  If \fB--prefix\fR or \fB-x\fR is also given, the directory parts of the filename will be removed \fIbefore\fR adding the prefix.
diff --git a/src/indexamajig.c b/src/indexamajig.c
index fec7fc39..ce87fde6 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -160,6 +160,8 @@ static void show_help(const char *s)
 "                            validity.\n"
 "     --no-peaks-in-stream  Do not record peak search results in the stream.\n"
 "     --no-refls-in-stream  Do not record integrated reflections in the stream.\n"
+"     --no-non-hits-in-stream  Do not include non-hit frames in the stream.\n"
+"                               (see --min-peaks)\n"
 "     --int-diag=<cond>     Show debugging information about reflections.\n"
 "     --no-refine           Skip the prediction refinement step.\n"
 "     --profile             Show timing data for performance monitoring.\n"
@@ -257,6 +259,7 @@ int main(int argc, char *argv[])
 	iargs.no_revalidate = 0;
 	iargs.stream_peaks = 1;
 	iargs.stream_refls = 1;
+	iargs.stream_nonhits = 1;
 	iargs.int_diag = INTDIAG_NONE;
 	iargs.copyme = new_imagefile_field_list();
 	iargs.min_peaks = 0;
@@ -295,6 +298,7 @@ int main(int argc, char *argv[])
 		{"basename",           0, &config_basename,          1},
 		{"no-peaks-in-stream", 0, &iargs.stream_peaks,       0},
 		{"no-refls-in-stream", 0, &iargs.stream_refls,       0},
+		{"no-non-hits-in-stream", 0, &iargs.stream_nonhits,  0},
 		{"integrate-saturated",0, &integrate_saturated,      1},
 		{"no-use-saturated",   0, &iargs.use_saturated,      0},
 		{"no-revalidate",      0, &iargs.no_revalidate,      1},
diff --git a/src/process_image.c b/src/process_image.c
index f735cb00..498b3398 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -257,7 +257,12 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 			return;
 		}
 		free(rn);
-		goto streamwrite;
+
+		if ( iargs->stream_nonhits ) {
+			goto streamwrite;
+		} else {
+			goto out;
+		}
 	}
 
 	/* Index the pattern */
@@ -323,6 +328,7 @@ streamwrite:
 		       get_event_string(image.event));
 	}
 
+out:
 	/* Count crystals which are still good */
 	time_accounts_set(taccs, TACC_TOTALS);
 	sb_shared->pings[cookie]++;
diff --git a/src/process_image.h b/src/process_image.h
index a668f1ba..ec51c188 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -87,6 +87,7 @@ struct index_args
 	int no_revalidate;
 	int stream_peaks;
 	int stream_refls;
+	int stream_nonhits;
 	IntegrationMethod int_meth;
 	IntDiag int_diag;
 	signed int int_diag_h;