indexamajig: Add --median-filter

3 files changed, 21 insertions, 8 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index 9b868b9f..27ec31fc 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -111,6 +111,10 @@ static void show_help(const char *s)
 "                         pixels in each 3x3 region to zero if any of them\n"
 "                         have negative values.  Intensity measurement will\n"
 "                         be performed on the image as it was before this.\n"
+"    --median-filter=<n> Apply a median filter to the image data.  Intensity\n"
+"                         measurement will be performed on the image as it\n"
+"                         was before this.  The side length of the median\n"
+"                         filter box will be <n>.  Default: 0 (no filter).\n"
 "    --no-sat-corr       Don't correct values of saturated peaks using a\n"
 "                         table included in the HDF5 file.\n"
 "    --threshold=<n>     Only accept peaks above <n> ADU.  Default: 800.\n"
@@ -183,6 +187,7 @@ int main(int argc, char *argv[])
 	iargs.cell = NULL;
 	iargs.cmfilter = 0;
 	iargs.noisefilter = 0;
+	iargs.median_filter = 0;
 	iargs.satcorr = 1;
 	iargs.closer = 0;
 	iargs.bgsub = 1;
@@ -266,6 +271,7 @@ int main(int argc, char *argv[])
 		{"min-integration-snr",1, NULL,               12},
 		{"tolerance",          1, NULL,               13},
 		{"int-radius",         1, NULL,               14},
+		{"median-filter",      1, NULL,               15},
 
 		{0, 0, NULL, 0}
 	};
@@ -386,6 +392,10 @@ int main(int argc, char *argv[])
 			intrad = strdup(optarg);
 			break;
 
+			case 15 :
+			iargs.median_filter = atoi(optarg);
+			break;
+
 			case 0 :
 			break;
 
diff --git a/src/process_image.c b/src/process_image.c
index 010054c8..a8eeb663 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -136,23 +136,25 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	if ( iargs->cmfilter ) filter_cm(&image);
 
-	/* Take snapshot of image after CM subtraction but before
-	 * the aggressive noise filter. */
+	/* Take snapshot of image after CM subtraction but before applying
+	 * horrible noise filters to it */
 	data_size = image.width * image.height * sizeof(float);
 	data_for_measurement = malloc(data_size);
+	memcpy(data_for_measurement, image.data, data_size);
+
+	if ( iargs->median_filter > 0 ) {
+		filter_median(&image, iargs->median_filter);
+	}
 
 	if ( iargs->noisefilter ) {
-		filter_noise(&image, data_for_measurement);
-	} else {
-		memcpy(data_for_measurement, image.data, data_size);
+		filter_noise(&image);
 	}
 
 	switch ( iargs->peaks ) {
 
 		case PEAK_HDF5:
-		// Get peaks from HDF5
-		if (get_peaks(&image, hdfile,
-			iargs->hdf5_peak_path)) {
+		/* Get peaks from HDF5 */
+		if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) {
 			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 f2f034d9..5fe11e33 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -46,6 +46,7 @@ struct index_args
 	UnitCell *cell;
 	int cmfilter;
 	int noisefilter;
+	int median_filter;
 	int satcorr;
 	int closer;
 	int bgsub;