From 89b372a8d17f3e9d5f8a4fef36cbc5aba033e639 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 5 Apr 2012 15:06:17 +0200
Subject: Fix iteration bounds for peak integration

---
 libcrystfel/src/peaks.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 829a35ab..2ab45e53 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -185,8 +185,8 @@ static int integrate_peak(struct image *image, int cfs, int css,
 	out_lim_sq = pow(ir_out, 2.0);
 
 	/* Estimate the background */
-	for ( fs=-ir_out; fs<+ir_out; fs++ ) {
-	for ( ss=-ir_out; ss<+ir_out; ss++ ) {
+	for ( fs=-ir_out; fs<=+ir_out; fs++ ) {
+	for ( ss=-ir_out; ss<=+ir_out; ss++ ) {
 
 		double val;
 		uint16_t flags;
@@ -234,8 +234,8 @@ static int integrate_peak(struct image *image, int cfs, int css,
 	pk_total = 0.0;
 	pk_counts = 0;
 	fsct = 0.0;  ssct = 0.0;
-	for ( fs=-ir_inn; fs<+ir_inn; fs++ ) {
-	for ( ss=-ir_inn; ss<+ir_inn; ss++ ) {
+	for ( fs=-ir_inn; fs<=+ir_inn; fs++ ) {
+	for ( ss=-ir_inn; ss<=+ir_inn; ss++ ) {
 
 		double val;
 		uint16_t flags;
-- 
cgit v1.2.3


From f556bc88774d44206990557303881e3b3c320248 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Mon, 2 Apr 2012 19:29:48 +0200
Subject: Improved spot prediction

---
 libcrystfel/src/geometry.c | 83 +++++++++++++++++-----------------------------
 1 file changed, 30 insertions(+), 53 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 218c0fee..0f6e4809 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -99,29 +99,6 @@ static signed int locate_peak(double x, double y, double z, double k,
 }
 
 
-static double excitation_error(double xl, double yl, double zl,
-                               double ds, double k, double divergence,
-                               double tt)
-{
-	double al;
-	double r;
-	double delta;
-
-	al = M_PI_2 - asin(-zl/ds);
-
-	r = ( ds * sin(al) / sin(tt) ) - k;
-
-	delta = sqrt(2.0 * pow(ds, 2.0) * (1.0-cos(divergence)));
-	if ( divergence > 0.0 ) {
-		r += delta;
-	} else {
-		r -= delta;
-	}
-
-	return r;
-}
-
-
 static double partiality(double r1, double r2, double r)
 {
 	double q1, q2;
@@ -146,46 +123,44 @@ static Reflection *check_reflection(struct image *image,
                                     double csx, double csy, double csz)
 {
 	const int output = 0;
-	double xl, yl, zl;
-	double ds, ds_sq;
+	double xl, yl, zl, tl;
 	double rlow, rhigh;     /* "Excitation error" */
 	signed int p;           /* Panel number */
 	double xda, yda;        /* Position on detector */
 	int close, inside;
 	double part;            /* Partiality */
-	int clamp_low = 0;
-	int clamp_high = 0;
-	double bandwidth = image->bw;
-	double divergence = image->div;
-	double lambda = image->lambda;
-	double klow, kcen, khigh;    /* Wavenumber */
+	int clamp_low, clamp_high;
+	double klow, khigh;    /* Wavenumber */
 	Reflection *refl;
-	double tt, psi;
+	double cet, cez;
 
 	/* "low" gives the largest Ewald sphere,
 	 * "high" gives the smallest Ewald sphere. */
-	klow = 1.0/(lambda - lambda*bandwidth/2.0);
-	kcen = 1.0/lambda;
-	khigh = 1.0/(lambda + lambda*bandwidth/2.0);
+	klow = 1.0/(image->lambda - image->lambda*image->bw/2.0);
+	khigh = 1.0/(image->lambda + image->lambda*image->bw/2.0);
 
 	/* Get the coordinates of the reciprocal lattice point */
 	xl = h*asx + k*bsx + l*csx;
 	yl = h*asy + k*bsy + l*csy;
 	zl = h*asz + k*bsz + l*csz;
 
-	ds_sq = modulus_squared(xl, yl, zl);  /* d*^2 */
-	ds = sqrt(ds_sq);
+	/* If the point is looking "backscattery", reject it straight away */
+	if ( zl < -khigh/2.0 ) return NULL;
 
-	/* Simple (fast) check to reject reflection if it's "in front" */
-	psi = atan2(zl, sqrt(xl*xl + yl*yl));
-	if ( psi - atan2(image->profile_radius, ds) > divergence ) return NULL;
+	tl = sqrt(xl*xl + yl*yl);
 
-	tt = angle_between(0.0, 0.0, 1.0,  xl, yl, zl+kcen);
-	if ( tt > deg2rad(90.0) ) return NULL;
+	cet = -sin(image->div/2.0) * khigh;
+	cez = -cos(image->div/2.0) * khigh;
+	rhigh = khigh - distance(cet, cez, tl, zl);  /* Loss of precision */
 
-	/* Calculate excitation errors */
-	rlow = excitation_error(xl, yl, zl, ds, klow, -divergence/2.0, tt);
-	rhigh = excitation_error(xl, yl, zl, ds, khigh, +divergence/2.0, tt);
+	cet =  sin(image->div/2.0) * klow;
+	cez = -cos(image->div/2.0) * klow;
+	rlow = klow - distance(cet, cez, tl, zl);  /* Loss of precision */
+
+	if ( rlow < rhigh ) {
+		STATUS("%i %i %i\n", h, k, l);
+		return NULL;
+	}
 
 	/* Is the reciprocal lattice point close to either extreme of
 	 * the sphere, maybe just outside the "Ewald volume"? */
@@ -204,7 +179,13 @@ static Reflection *check_reflection(struct image *image,
 
 	/* If the "lower" Ewald sphere is a long way away, use the
 	 * position at which the Ewald sphere would just touch the
-	 * reflection. */
+	 * reflection.
+	 *
+	 * The six possible combinations of clamp_{low,high} (including
+	 * zero) correspond to the six situations in Table 3 of Rossmann
+	 * et al. (1979).
+	 */
+	clamp_low = 0;  clamp_high = 0;
 	if ( rlow < -image->profile_radius ) {
 		rlow = -image->profile_radius;
 		clamp_low = -1;
@@ -213,7 +194,6 @@ static Reflection *check_reflection(struct image *image,
 		rlow = +image->profile_radius;
 		clamp_low = +1;
 	}
-	/* Likewise the "higher" Ewald sphere */
 	if ( rhigh < -image->profile_radius ) {
 		rhigh = -image->profile_radius;
 		clamp_high = -1;
@@ -222,16 +202,13 @@ static Reflection *check_reflection(struct image *image,
 		rhigh = +image->profile_radius;
 		clamp_high = +1;
 	}
-	assert(clamp_low <= clamp_high);
-	/* The six possible combinations of clamp_{low,high} (including
-	 * zero) correspond to the six situations in Table 3 of Rossmann
-	 * et al. (1979). */
+	assert(clamp_low >= clamp_high);
 
 	/* Calculate partiality */
 	part = partiality(rlow, rhigh, image->profile_radius);
 
 	/* Locate peak on detector. */
-	p = locate_peak(xl, yl, zl, kcen, image->det, &xda, &yda);
+	p = locate_peak(xl, yl, zl, 1.0/image->lambda, image->det, &xda, &yda);
 	if ( p == -1 ) return NULL;
 
 	/* Add peak to list */
@@ -276,7 +253,7 @@ RefList *find_intersections(struct image *image, UnitCell *cell)
 
 	/* We add a horrific 20% fudge factor because bandwidth, divergence
 	 * and so on mean reflections appear beyond the largest q */
-	mres = 1.2 * largest_q(image);
+	mres = largest_q(image);
 
 	hmax = mres / modulus(asx, asy, asz);
 	kmax = mres / modulus(bsx, bsy, bsz);
-- 
cgit v1.2.3


From 6a694000083fd5d6e0ecb48212cf25396854c60e Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 3 Apr 2012 15:16:04 +0200
Subject: Fix partiality calculation

---
 libcrystfel/src/geometry.c | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 0f6e4809..a62820b4 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -99,20 +99,20 @@ static signed int locate_peak(double x, double y, double z, double k,
 }
 
 
-static double partiality(double r1, double r2, double r)
+static double partiality(double rlow, double rhigh, double r)
 {
-	double q1, q2;
-	double p1, p2;
+	double qlow, qhigh;
+	double plow, phigh;
 
 	/* Calculate degrees of penetration */
-	q1 = (r1 + r)/(2.0*r);
-	q2 = (r2 + r)/(2.0*r);
+	qlow  = (rlow + r)/(2.0*r);
+	qhigh = (rhigh + r)/(2.0*r);
 
 	/* Convert to partiality */
-	p1 = 3.0*pow(q1,2.0) - 2.0*pow(q1,3.0);
-	p2 = 3.0*pow(q2,2.0) - 2.0*pow(q2,3.0);
+	plow  = 3.0*pow(qlow,2.0)  - 2.0*pow(qlow,3.0);
+	phigh = 3.0*pow(qhigh,2.0) - 2.0*pow(qhigh,3.0);
 
-	return p2 - p1;
+	return plow - phigh;
 }
 
 
-- 
cgit v1.2.3


From 0b63042eb2ba93cb7706d1501f4237fe30b0ef2c Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 3 Apr 2012 15:21:24 +0200
Subject: Remove old comment

---
 libcrystfel/src/geometry.c | 2 --
 1 file changed, 2 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index a62820b4..92a0ab9a 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -251,8 +251,6 @@ RefList *find_intersections(struct image *image, UnitCell *cell)
 	                          &bsx, &bsy, &bsz,
 	                          &csx, &csy, &csz);
 
-	/* We add a horrific 20% fudge factor because bandwidth, divergence
-	 * and so on mean reflections appear beyond the largest q */
 	mres = largest_q(image);
 
 	hmax = mres / modulus(asx, asy, asz);
-- 
cgit v1.2.3


From cac83d4925f3543b4dfc4ce881824fea225cef7e Mon Sep 17 00:00:00 2001
From: Thomas White <taw@bitwiz.org.uk>
Date: Tue, 10 Apr 2012 12:04:19 +0100
Subject: Fix maximum index calculation

---
 libcrystfel/src/geometry.c | 45 +++++++++++++++++++++++++++------------------
 1 file changed, 27 insertions(+), 18 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 92a0ab9a..6b01c51c 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -118,12 +118,10 @@ static double partiality(double rlow, double rhigh, double r)
 
 static Reflection *check_reflection(struct image *image,
                                     signed int h, signed int k, signed int l,
-                                    double asx, double asy, double asz,
-                                    double bsx, double bsy, double bsz,
-                                    double csx, double csy, double csz)
+                                    double xl, double yl, double zl)
 {
 	const int output = 0;
-	double xl, yl, zl, tl;
+	double tl;
 	double rlow, rhigh;     /* "Excitation error" */
 	signed int p;           /* Panel number */
 	double xda, yda;        /* Position on detector */
@@ -139,10 +137,6 @@ static Reflection *check_reflection(struct image *image,
 	klow = 1.0/(image->lambda - image->lambda*image->bw/2.0);
 	khigh = 1.0/(image->lambda + image->lambda*image->bw/2.0);
 
-	/* Get the coordinates of the reciprocal lattice point */
-	xl = h*asx + k*bsx + l*csx;
-	yl = h*asy + k*bsy + l*csy;
-	zl = h*asz + k*bsz + l*csz;
 
 	/* If the point is looking "backscattery", reject it straight away */
 	if ( zl < -khigh/2.0 ) return NULL;
@@ -229,6 +223,9 @@ static Reflection *check_reflection(struct image *image,
 
 RefList *find_intersections(struct image *image, UnitCell *cell)
 {
+	double ax, ay, az;
+	double bx, by, bz;
+	double cx, cy, cz;
 	double asx, asy, asz;
 	double bsx, bsy, bsz;
 	double csx, csy, csz;
@@ -247,15 +244,13 @@ RefList *find_intersections(struct image *image, UnitCell *cell)
 		return NULL;
 	}
 
-	cell_get_reciprocal(cell, &asx, &asy, &asz,
-	                          &bsx, &bsy, &bsz,
-	                          &csx, &csy, &csz);
+	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
 
 	mres = largest_q(image);
 
-	hmax = mres / modulus(asx, asy, asz);
-	kmax = mres / modulus(bsx, bsy, bsz);
-	lmax = mres / modulus(csx, csy, csz);
+	hmax = mres * modulus(ax, ay, az);
+	kmax = mres * modulus(bx, by, bz);
+	lmax = mres * modulus(cx, cy, cz);
 
 	if ( (hmax >= 256) || (kmax >= 256) || (lmax >= 256) ) {
 		ERROR("Unit cell is stupidly large.\n");
@@ -265,14 +260,23 @@ RefList *find_intersections(struct image *image, UnitCell *cell)
 		if ( lmax >= 256 ) lmax = 255;
 	}
 
+	cell_get_reciprocal(cell, &asx, &asy, &asz,
+	                          &bsx, &bsy, &bsz,
+	                          &csx, &csy, &csz);
+
 	for ( h=-hmax; h<=hmax; h++ ) {
 	for ( k=-kmax; k<=kmax; k++ ) {
 	for ( l=-lmax; l<=lmax; l++ ) {
 
 		Reflection *refl;
+		double xl, yl, zl;
 
-		refl = check_reflection(image, h, k, l,
-		                        asx,asy,asz,bsx,bsy,bsz,csx,csy,csz);
+		/* Get the coordinates of the reciprocal lattice point */
+		xl = h*asx + k*bsx + l*csx;
+		yl = h*asy + k*bsy + l*csy;
+		zl = h*asz + k*bsz + l*csz;
+
+		refl = check_reflection(image, h, k, l, xl, yl, zl);
 
 		if ( refl != NULL ) {
 			add_refl_to_list(refl, reflections);
@@ -308,13 +312,18 @@ void update_partialities(struct image *image)
 	{
 		Reflection *vals;
 		double r1, r2, p, x, y;
+		double xl, yl, zl;
 		signed int h, k, l;
 		int clamp1, clamp2;
 
 		get_symmetric_indices(refl, &h, &k, &l);
 
-		vals = check_reflection(image, h, k, l,
-		                        asx,asy,asz,bsx,bsy,bsz,csx,csy,csz);
+		/* Get the coordinates of the reciprocal lattice point */
+		xl = h*asx + k*bsx + l*csx;
+		yl = h*asy + k*bsy + l*csy;
+		zl = h*asz + k*bsz + l*csz;
+
+		vals = check_reflection(image, h, k, l, xl, yl, zl);
 
 		if ( vals == NULL ) {
 			set_redundancy(refl, 0);
-- 
cgit v1.2.3


From 605ed411cc56da3bbf6d33a441c3d16adcfeb3a1 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 19 Apr 2012 12:10:13 +0200
Subject: Simplify prediction criterion

---
 libcrystfel/src/geometry.c | 23 ++++++-----------------
 1 file changed, 6 insertions(+), 17 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 6b01c51c..e416a883 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -125,15 +125,15 @@ static Reflection *check_reflection(struct image *image,
 	double rlow, rhigh;     /* "Excitation error" */
 	signed int p;           /* Panel number */
 	double xda, yda;        /* Position on detector */
-	int close, inside;
 	double part;            /* Partiality */
 	int clamp_low, clamp_high;
 	double klow, khigh;    /* Wavenumber */
 	Reflection *refl;
 	double cet, cez;
 
-	/* "low" gives the largest Ewald sphere,
-	 * "high" gives the smallest Ewald sphere. */
+	/* "low" gives the largest Ewald sphere (wavelength short => k large)
+	 * "high" gives the smallest Ewald sphere (wavelength long => k small)
+	 */
 	klow = 1.0/(image->lambda - image->lambda*image->bw/2.0);
 	khigh = 1.0/(image->lambda + image->lambda*image->bw/2.0);
 
@@ -156,20 +156,9 @@ static Reflection *check_reflection(struct image *image,
 		return NULL;
 	}
 
-	/* Is the reciprocal lattice point close to either extreme of
-	 * the sphere, maybe just outside the "Ewald volume"? */
-	close = (fabs(rlow) < image->profile_radius)
-	     || (fabs(rhigh) < image->profile_radius);
-
-	/* Is the reciprocal lattice point somewhere between the
-	 * extremes of the sphere, i.e. inside the "Ewald volume"? */
-	inside = signbit(rlow) ^ signbit(rhigh);
-
-	/* Can't be both inside and close */
-	if ( inside ) close = 0;
-
-	/* Neither?  Skip it. */
-	if ( !(close || inside) ) return NULL;
+	if ( (signbit(rlow) == signbit(rhigh))
+	     && (fabs(rlow) > image->profile_radius)
+	     && (fabs(rhigh) > image->profile_radius) ) return NULL;
 
 	/* If the "lower" Ewald sphere is a long way away, use the
 	 * position at which the Ewald sphere would just touch the
-- 
cgit v1.2.3


From 83e8ae45888b8edbe6112d9bcceea3352c422255 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 19 Apr 2012 12:15:05 +0200
Subject: Remove check for rlow > rhigh

I'm happy that there are no gremlins here, now.  This happens only for 000,
where rlow and rhigh both go to zero.  It doesn't make sense to have a special
check for the condition.
---
 libcrystfel/src/geometry.c | 5 -----
 1 file changed, 5 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index e416a883..f46cea25 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -151,11 +151,6 @@ static Reflection *check_reflection(struct image *image,
 	cez = -cos(image->div/2.0) * klow;
 	rlow = klow - distance(cet, cez, tl, zl);  /* Loss of precision */
 
-	if ( rlow < rhigh ) {
-		STATUS("%i %i %i\n", h, k, l);
-		return NULL;
-	}
-
 	if ( (signbit(rlow) == signbit(rhigh))
 	     && (fabs(rlow) > image->profile_radius)
 	     && (fabs(rhigh) > image->profile_radius) ) return NULL;
-- 
cgit v1.2.3


From 7f221c3bfbc5ad41016a451c778f7b8710be03ef Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 19 Apr 2012 16:49:20 +0200
Subject: Formatting

---
 libcrystfel/src/geometry.c | 1 -
 1 file changed, 1 deletion(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index f46cea25..24669aef 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -137,7 +137,6 @@ static Reflection *check_reflection(struct image *image,
 	klow = 1.0/(image->lambda - image->lambda*image->bw/2.0);
 	khigh = 1.0/(image->lambda + image->lambda*image->bw/2.0);
 
-
 	/* If the point is looking "backscattery", reject it straight away */
 	if ( zl < -khigh/2.0 ) return NULL;
 
-- 
cgit v1.2.3


From d7ff5c5ab2ffdaa2808d5e336603804450ca15b0 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 26 Apr 2012 13:58:38 +0200
Subject: Remove PEAK_CLOSE (not used for anything)

---
 libcrystfel/src/peaks.c | 4 ----
 1 file changed, 4 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 2ab45e53..88477190 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -52,10 +52,6 @@
 #include "beam-parameters.h"
 
 
-/* How close a peak must be to an indexed position to be considered "close"
- * for the purposes of double hit detection and sanity checking. */
-#define PEAK_CLOSE (30.0)
-
 /* How close a peak must be to an indexed position to be considered "close"
  * for the purposes of integration. */
 #define PEAK_REALLY_CLOSE (10.0)
-- 
cgit v1.2.3


From cfbbdae0ff6b0823fd9de0971f51b9fd939db5b6 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 26 Apr 2012 14:08:12 +0200
Subject: indexamajig: Make --no-closer-peak the default

---
 libcrystfel/src/peaks.c | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 88477190..cddb6069 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -52,10 +52,6 @@
 #include "beam-parameters.h"
 
 
-/* How close a peak must be to an indexed position to be considered "close"
- * for the purposes of integration. */
-#define PEAK_REALLY_CLOSE (10.0)
-
 /* Degree of polarisation of X-ray beam */
 #define POL (1.0)
 
@@ -640,7 +636,9 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
 			} else {
 				f = NULL;
 			}
-			if ( (f != NULL) && (d < PEAK_REALLY_CLOSE) ) {
+
+			/* FIXME: Horrible hardcoded value */
+			if ( (f != NULL) && (d < 10.0) ) {
 
 				pfs = f->fs;
 				pss = f->ss;
-- 
cgit v1.2.3


From d6c040ed981827f072e3e22501620a65a4418acd Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 26 Apr 2012 14:10:20 +0200
Subject: Single point of truth for indices when sorting reflections

---
 libcrystfel/src/peaks.c | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index cddb6069..4b146eb6 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -534,9 +534,6 @@ int peak_sanity_check(struct image *image)
 
 struct integr_ind
 {
-	signed int h;
-	signed int k;
-	signed int l;
 	double res;
 	Reflection *refl;
 };
@@ -578,9 +575,6 @@ static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
 		get_indices(refl, &h, &k, &l);
 		res = resolution(cell, h, k, l);
 
-		il[i].h = h;
-		il[i].k = k;
-		il[i].l = l;
 		il[i].res = res;
 		il[i].refl = refl;
 
@@ -620,10 +614,12 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
 		double pfs, pss;
 		int r;
 		Reflection *refl;
+		signed int h, k, l;
 
 		refl = il[i].refl;
 
 		get_detector_pos(refl, &pfs, &pss);
+		get_indices(refl, &h, &k, &l);
 
 		/* Is there a really close feature which was detected? */
 		if ( use_closer ) {
-- 
cgit v1.2.3


From 23295e405b524d86475e22eb21a56fd1ada3e530 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 26 Apr 2012 14:51:58 +0200
Subject: Update the peak coordinates when doing --closer-peak

This should make it much more obvious (via check-near-bragg) when the peak positions are wrong.
---
 libcrystfel/src/peaks.c | 6 ++++++
 1 file changed, 6 insertions(+)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 4b146eb6..78a68185 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -636,9 +636,15 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
 			/* FIXME: Horrible hardcoded value */
 			if ( (f != NULL) && (d < 10.0) ) {
 
+				double exe;
+
+				exe = get_excitation_error(refl);
+
 				pfs = f->fs;
 				pss = f->ss;
 
+				set_detector_pos(refl, exe, pfs, pss);
+
 			}
 
 		}
-- 
cgit v1.2.3