From d1d8e9d2f7bdb13977181145519f71fa23c3cb73 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Sat, 23 Nov 2013 03:42:33 -0800
Subject: indexamajig: Add --int-diag=implausible

---
 doc/man/indexamajig.1         |  2 +-
 libcrystfel/src/integration.c | 18 ++++++++++++------
 libcrystfel/src/integration.h |  3 ++-
 src/indexamajig.c             |  4 ++++
 4 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 25bc1cd6..cb24e916 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, \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.
+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, \fBimplausible\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.  \fBimplausible\fR means to show peaks with intensities which are negative my more than 5 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 3111d345..83cf8d0e 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1299,6 +1299,13 @@ static int get_int_diag(struct intcontext *ic, Reflection *refl)
 		return i < -3.0*sigi;
 	}
 
+	if ( ic->int_diag == INTDIAG_IMPLAUSIBLE ) {
+		double i, sigi;
+		i = get_intensity(refl);
+		sigi = get_esd_intensity(refl);
+		return i < -5.0*sigi;
+	}
+
 	if ( ic->int_diag == INTDIAG_INDICES ) {
 		signed int h, k, l;
 		get_indices(refl, &h, &k, &l);
@@ -1565,12 +1572,6 @@ static void integrate_rings_once(Reflection *refl, struct image *image,
 
 	sigma = sqrt(sig2_poisson + bx->m*sig2_bg);
 
-	if ( intensity < -5.0*sigma ) {
-		delete_box(ic, bx);
-		ic->n_implausible++;
-		return;
-	}
-
 	/* Record intensity and set redundancy to 1 */
 	bx->intensity = intensity;
 	set_intensity(refl, intensity);
@@ -1587,6 +1588,11 @@ static void integrate_rings_once(Reflection *refl, struct image *image,
 	set_detector_pos(refl, 0.0, pfs, pss);
 
 	if ( get_int_diag(ic, refl) ) show_peak_box(ic, bx);
+
+	if ( intensity < -5.0*sigma ) {
+		ic->n_implausible++;
+		set_redundancy(refl, 0);
+	}
 }
 
 
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index 38cb8163..ec674128 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -40,7 +40,8 @@ typedef enum {
 	INTDIAG_RANDOM,
 	INTDIAG_ALL,
 	INTDIAG_INDICES,
-	INTDIAG_NEGATIVE
+	INTDIAG_NEGATIVE,
+	INTDIAG_IMPLAUSIBLE
 
 } IntDiag;
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index b769d303..7aeccd53 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -552,6 +552,10 @@ int main(int argc, char *argv[])
 			iargs.int_diag = INTDIAG_NEGATIVE;
 		}
 
+		if ( strcmp(int_diag, "implausible") == 0 ) {
+			iargs.int_diag = INTDIAG_IMPLAUSIBLE;
+		}
+
 		r = sscanf(int_diag, "%i,%i,%i", &h, &k, &l);
 		if ( r == 3 ) {
 			iargs.int_diag = INTDIAG_INDICES;
-- 
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