From 50af164e6151c69de0f93428bd83cdb60d2e9d27 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Mon, 11 Aug 2014 11:58:19 +0200
Subject: Add scsphere partiality model

---
 libcrystfel/src/geometry.c | 19 +++++++++++++------
 libcrystfel/src/geometry.h |  2 ++
 src/partialator.c          |  2 ++
 3 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 3586ed0b..21f81915 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -105,7 +105,7 @@ static signed int locate_peak(double x, double y, double z, double k,
 
 static double partiality(PartialityModel pmodel,
                          double rlow, double rmid, double rhigh,
-                         double r)
+                         double r, double D)
 {
 	double qlow, qhigh;
 	double plow, phigh;
@@ -135,6 +135,11 @@ static double partiality(PartialityModel pmodel,
 		case PMODEL_THIN:
 		return 1.0 - (rmid*rmid)/(r*r);
 
+		case PMODEL_SCSPHERE:
+		plow  = 3.0*qlow*qlow  - 2.0*qlow*qlow*qlow;
+		phigh = 3.0*qhigh*qhigh - 2.0*qhigh*qhigh*qhigh;
+		return 4.0*(plow-phigh)*r / (3.0*D);
+
 	}
 }
 
@@ -153,7 +158,7 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
 	Reflection *refl;
 	double cet, cez;  /* Centre of Ewald sphere */
 	double pr;
-	double L;
+	double L, D;
 	double del;
 
 	/* Don't predict 000 */
@@ -197,10 +202,10 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
 	/* Conditions for reflection to be excited at all */
 	switch ( pmodel ) {
 
-		default:
 		case PMODEL_UNITY:  /* PMODEL_UNITY shouldn't end up here */
 		case PMODEL_SPHERE:
 		case PMODEL_GAUSSIAN:
+		case PMODEL_SCSPHERE:
 		if ( (signbit(rlow) == signbit(rhigh))
 		     && (fabs(rlow) > pr)
 		     && (fabs(rhigh) > pr) ) return NULL;
@@ -212,19 +217,21 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
 
 	}
 
+	D = rlow - rhigh;
+
 	/* Lorentz factor is determined direction from the r values, before
 	 * clamping.  The multiplication by 0.01e9 to make the
 	 * correction factor vaguely near 1. */
 	switch ( pmodel ) {
 
-		default:
 		case PMODEL_SPHERE:
 		case PMODEL_GAUSSIAN:
-		L = LORENTZ_SCALE / (rlow - rhigh);
+		L = LORENTZ_SCALE / D;
 		break;
 
 		case PMODEL_UNITY:  /* PMODEL_UNITY shouldn't end up here */
 		case PMODEL_THIN:
+		case PMODEL_SCSPHERE:
 		L = 1.0;
 		break;
 
@@ -257,7 +264,7 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst,
 	}
 
 	/* Calculate partiality */
-	part = partiality(pmodel, rlow, rmid, rhigh, pr);
+	part = partiality(pmodel, rlow, rmid, rhigh, pr, D);
 
 	/* Add peak to list */
 	refl = reflection_new(h, k, l);
diff --git a/libcrystfel/src/geometry.h b/libcrystfel/src/geometry.h
index 8041936a..d8d226f0 100644
--- a/libcrystfel/src/geometry.h
+++ b/libcrystfel/src/geometry.h
@@ -51,6 +51,7 @@ extern "C" {
  * @PMODEL_UNITY : Set all all partialities and Lorentz factors to 1.
  * @PMODEL_GAUSSIAN : Gaussian profiles in 3D
  * @PMODEL_THIN : Thin Ewald sphere intersecting sphere
+ * @PMODEL_SCSPHERE : Sphere model with source coverage factor included
  *
  * A %PartialityModel describes a geometrical model which can be used to
  * calculate spot partialities and Lorentz correction factors.
@@ -61,6 +62,7 @@ typedef enum {
 	PMODEL_UNITY,
 	PMODEL_GAUSSIAN,
 	PMODEL_THIN,
+	PMODEL_SCSPHERE,
 
 } PartialityModel;
 
diff --git a/src/partialator.c b/src/partialator.c
index e5083611..0d532997 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -350,6 +350,8 @@ int main(int argc, char *argv[])
 			pmodel = PMODEL_GAUSSIAN;
 		} else if ( strcmp(pmodel_str, "thin") == 0 ) {
 			pmodel = PMODEL_THIN;
+		} else if ( strcmp(pmodel_str, "scsphere") == 0 ) {
+			pmodel = PMODEL_SCSPHERE;
 		} else {
 			ERROR("Unknown partiality model '%s'.\n", pmodel_str);
 			return 1;
-- 
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