indexamajig: Get rid of --min-integration-snr

This functionality belongs in process_hkl.

5 files changed, 6 insertions, 26 deletions

diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 315c8a33..e874d5c6 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1394,7 +1394,7 @@ static void estimate_resolution(RefList *reflections, Crystal *cr,
 
 
 static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
-                             struct image *image,  double min_snr,
+                             struct image *image,
                              double ir_inn, double ir_mid, double ir_out)
 {
 	RefList *reflections;
@@ -1498,7 +1498,7 @@ static void integrate_box(struct intcontext *ic, struct peak_box *bx,
 
 
 static void integrate_rings(IntegrationMethod meth, Crystal *cr,
-                            struct image *image, double min_snr,
+                            struct image *image,
                             double ir_inn, double ir_mid, double ir_out)
 {
 	RefList *list;
@@ -1542,7 +1542,7 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
 		                      * in overall data block */
 		int cfs, css;  /* Corner coordinates */
 		double intensity;
-		double sigma, snr;
+		double sigma;
 		int saturated;
 		double one_over_d;
 		int r;
@@ -1597,14 +1597,7 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
 
 		integrate_box(&ic, bx, &intensity, &sigma);
 
-		/* I/sigma(I) cutoff
-		 * Rejects reflections below --min-integration-snr, or if the
-		 * SNR is clearly silly.  Silly indicates that the intensity
-		 * was zero. */
-		snr = fabs(intensity)/sigma;
-		if ( (isnan(snr) || (snr < min_snr)) ) continue;
-
-		/* Record intensity and set redundancy to 1 on success */
+		/* Record intensity and set redundancy to 1 */
 		set_intensity(refl, intensity);
 		set_esd_intensity(refl, sigma);
 		set_redundancy(refl, 1);
@@ -1623,7 +1616,6 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
 
 
 void integrate_all(struct image *image, IntegrationMethod meth,
-                   int use_closer, double min_snr,
                    double ir_inn, double ir_mid, double ir_out,
                    int integrate_saturated)
 {
@@ -1638,12 +1630,12 @@ void integrate_all(struct image *image, IntegrationMethod meth,
 
 			case INTEGRATION_RINGS :
 			integrate_rings(meth, image->crystals[i], image,
-			                min_snr, ir_inn, ir_mid, ir_out);
+			                ir_inn, ir_mid, ir_out);
 			return;
 
 			case INTEGRATION_PROF2D :
 			integrate_prof2d(meth, image->crystals[i], image,
-			                 min_snr, ir_inn, ir_mid, ir_out);
+			                ir_inn, ir_mid, ir_out);
 			return;
 
 			default :
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index 913297fa..8edcb91f 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -68,7 +68,6 @@ typedef enum {
 extern IntegrationMethod integration_method(const char *t, int *err);
 
 extern void integrate_all(struct image *image, IntegrationMethod meth,
-	                  int use_closer, double min_snr,
 	                  double ir_inn, double ir_mid, double ir_out,
 	                  int integrate_saturated);
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 84a372cb..dc244866 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -121,8 +121,6 @@ static void show_help(const char *s)
 "                         Default: 100,000.\n"
 "    --min-snr=<n>       Minimum signal-to-noise ratio for peaks.\n"
 "                         Default: 5.\n"
-"    --min-integration-snr=<n> Minimum signal-to-noise ratio for peaks\n"
-"                         during integration. Default: -infinity.\n"
 "    --int-radius=<r>    Set the integration radii.  Default: 4,5,7.\n"
 "-e, --image=<element>   Use this image from the HDF5 file.\n"
 "                          Example: /data/data0.\n"
@@ -191,7 +189,6 @@ int main(int argc, char *argv[])
 	iargs.threshold = 800.0;
 	iargs.min_gradient = 100000.0;
 	iargs.min_snr = 5.0;
-	iargs.min_int_snr = -INFINITY;
 	iargs.det = NULL;
 	iargs.peaks = PEAK_ZAEF;
 	iargs.beam = NULL;
@@ -255,7 +252,6 @@ int main(int argc, char *argv[])
 		{"hdf5-peaks",         1, NULL,                9},
 		{"copy-hdf5-field",    1, NULL,               10},
 		{"min-snr",            1, NULL,               11},
-		{"min-integration-snr",1, NULL,               12},
 		{"tolerance",          1, NULL,               13},
 		{"int-radius",         1, NULL,               14},
 		{"median-filter",      1, NULL,               15},
@@ -368,10 +364,6 @@ int main(int argc, char *argv[])
 			iargs.min_snr = strtof(optarg, NULL);
 			break;
 
-			case 12 :
-			iargs.min_int_snr = strtof(optarg, NULL);
-			break;
-
 			case 13 :
 			toler = strdup(optarg);
 			break;
diff --git a/src/process_image.c b/src/process_image.c
index f432f8eb..6bddae50 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -174,8 +174,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	/* Integrate all the crystals at once - need all the crystals so that
 	 * overlaps can be detected. */
 	integrate_all(&image, iargs->int_meth,
-	                      iargs->closer,
-	                      iargs->min_int_snr,
 	                      iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
 	                      iargs->integrate_saturated);
 
diff --git a/src/process_image.h b/src/process_image.h
index 03041562..ac197927 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -55,7 +55,6 @@ struct index_args
 	float threshold;
 	float min_gradient;
 	float min_snr;
-	double min_int_snr;
 	struct detector *det;
 	IndexingMethod *indm;
 	IndexingPrivate **ipriv;