Add --int-diag=negative

4 files changed, 17 insertions, 13 deletions

diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 351a2e45..25bc1cd6 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -330,7 +330,7 @@ Do not record integrated reflections in the stream.  The resulting output won't
 .PD 0
 .IP \fB--int-diag=\fIcondition\fR\fR
 .PD
-Show detailed information about reflection integration when \fIcondition\fR is met.  The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, or \fBrandom\fR.  The default is \fB--int-diag=none\fR, and \fBrandom\fR means to show information about a random 1% of the peaks.
+Show detailed information about reflection integration when \fIcondition\fR is met.  The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR or \fBnegative\fR.  \fBrandom\fR means to show information about a random 1% of the peaks.  \fBnegative\fR means to show peaks with intensities which are negative my more than 3 sigma.  The default is \fB--int-diag=none\fR.
 
 .SH BUGS
 ReAx indexing is experimental.  It works very nicely for some people, and crashes for others.  In a future version, it will be improved and fully supported.
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 63495c43..3746d3a8 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -223,8 +223,6 @@ struct peak_box
 	int rp;   /* Reference profile number */
 
 	Reflection *refl;
-
-	int verbose;
 };
 
 
@@ -598,7 +596,6 @@ static struct peak_box *add_box(struct intcontext *ic)
 	ic->boxes[idx].J = 0.0;
 	ic->boxes[idx].rp = -1;
 	ic->boxes[idx].refl = NULL;
-	ic->boxes[idx].verbose = 0;
 
 	ic->boxes[idx].bgm = gsl_matrix_calloc(3, 3);
 	if ( ic->boxes[idx].bgm == NULL ) {
@@ -1295,6 +1292,13 @@ static int get_int_diag(struct intcontext *ic, Reflection *refl)
 		return random() < RAND_MAX/100;
 	}
 
+	if ( ic->int_diag == INTDIAG_NEGATIVE ) {
+		double i, sigi;
+		i = get_intensity(refl);
+		sigi = get_esd_intensity(refl);
+		return i < -3.0*sigi;
+	}
+
 	if ( ic->int_diag == INTDIAG_INDICES ) {
 		signed int h, k, l;
 		get_indices(refl, &h, &k, &l);
@@ -1349,7 +1353,6 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
 	      refl = next_refl(refl, iter) )
 	{
 		double pfs, pss;
-		signed int h, k, l;
 		struct peak_box *bx;
 		int pn;
 		struct panel *p;
@@ -1384,9 +1387,6 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
 		bx->p = p;
 		bx->pn = pn;
 
-		get_indices(refl, &h, &k, &l);
-		bx->verbose = get_int_diag(&ic, refl);
-
 		/* Which reference profile? */
 		bx->rp = 0;//bx->pn;
 
@@ -1462,7 +1462,7 @@ static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
 			pss += bx->offs_ss;
 			set_detector_pos(bx->refl, 0.0, pfs, pss);
 
-			if ( bx->verbose ) show_peak_box(&ic, bx);
+			if ( get_int_diag(&ic, refl) ) show_peak_box(&ic, bx);
 
 		}
 
@@ -1520,8 +1520,6 @@ static void integrate_rings_once(Reflection *refl, struct image *image,
 	bx->css = css;
 	bx->p = p;
 	bx->pn = pn;
-	get_indices(refl, &h, &k, &l);
-	bx->verbose = get_int_diag(ic, refl);
 
 	if ( ic->meth & INTEGRATION_CENTER ) {
 		r = center_and_check_box(ic, bx, &saturated);
@@ -1579,6 +1577,7 @@ static void integrate_rings_once(Reflection *refl, struct image *image,
 	set_esd_intensity(refl, sigma);
 	set_redundancy(refl, 1);
 
+	get_indices(refl, &h, &k, &l);
 	one_over_d = resolution(cell, h, k, l);
 	if ( one_over_d > ic->limit ) ic->limit = one_over_d;
 
@@ -1587,7 +1586,7 @@ static void integrate_rings_once(Reflection *refl, struct image *image,
 	pss += bx->offs_ss;
 	set_detector_pos(refl, 0.0, pfs, pss);
 
-	if ( bx->verbose ) show_peak_box(ic, bx);
+	if ( get_int_diag(ic, refl) ) show_peak_box(ic, bx);
 }
 
 
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index 68ce91ec..38cb8163 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -39,7 +39,8 @@ typedef enum {
 	INTDIAG_NONE,
 	INTDIAG_RANDOM,
 	INTDIAG_ALL,
-	INTDIAG_INDICES
+	INTDIAG_INDICES,
+	INTDIAG_NEGATIVE
 
 } IntDiag;
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index c450fd83..b769d303 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -548,6 +548,10 @@ int main(int argc, char *argv[])
 			iargs.int_diag = INTDIAG_ALL;
 		}
 
+		if ( strcmp(int_diag, "negative") == 0 ) {
+			iargs.int_diag = INTDIAG_NEGATIVE;
+		}
+
 		r = sscanf(int_diag, "%i,%i,%i", &h, &k, &l);
 		if ( r == 3 ) {
 			iargs.int_diag = INTDIAG_INDICES;