3 files changed, 50 insertions, 13 deletions

diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 1b7001a6..afa4edca 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -331,7 +331,7 @@ static void show_peak_box(struct intcontext *ic, struct peak_box *bx,
 }
 
 
-static void fit_bg(struct intcontext *ic, struct peak_box *bx)
+static void fit_gradient_bg(struct intcontext *ic, struct peak_box *bx)
 {
 	int p, q;
 	gsl_vector *v;
@@ -369,6 +369,33 @@ static void fit_bg(struct intcontext *ic, struct peak_box *bx)
 }
 
 
+static void fit_bg(struct intcontext *ic, struct peak_box *bx)
+{
+	int p, q;
+	double tbg = 0.0;
+	int n = 0;
+
+	if ( ic->meth & INTEGRATION_GRADIENTBG ) {
+		fit_gradient_bg(ic, bx);
+		return;
+	}
+
+	/* else do a flat background */
+	for ( p=0; p<ic->w; p++ ) {
+	for ( q=0; q<ic->w; q++ ) {
+		if ( bx->bm[p + ic->w*q] == BM_BG ) {
+			tbg += boxi(ic, bx, p, q);
+			n++;
+		}
+	}
+	}
+
+	bx->a = 0.0;
+	bx->b = 0.0;
+	bx->c = tbg / n;
+}
+
+
 static void zero_profiles(struct intcontext *ic)
 {
 	int i;
@@ -1113,7 +1140,9 @@ static double peak_height(struct intcontext *ic, struct peak_box *bx)
 
 static int bg_ok(struct intcontext *ic, struct peak_box *bx)
 {
-	double max_grad = (peak_height(ic, bx) - bg_under_peak(ic, bx)) / 10.0;
+	double max_grad;
+
+	max_grad = fabs((peak_height(ic, bx) - bg_under_peak(ic, bx))) / 10.0;
 
 	if ( (fabs(bx->a) > max_grad) || (fabs(bx->b) > max_grad) ) {
 		return 0;
@@ -1717,32 +1746,38 @@ IntegrationMethod integration_method(const char *str, int *err)
 
 	for ( i=0; i<n; i++ ) {
 
-		if ( strcmp(methods[i], "rings") == 0) {
+		if ( strcmp(methods[i], "rings") == 0 ) {
 			meth = INTEGRATION_DEFAULTS_RINGS;
 
-		} else if ( strcmp(methods[i], "prof2d") == 0) {
+		} else if ( strcmp(methods[i], "prof2d") == 0 ) {
 			meth = INTEGRATION_DEFAULTS_PROF2D;
 
-		} else if ( strcmp(methods[i], "none") == 0) {
+		} else if ( strcmp(methods[i], "none") == 0 ) {
 			return INTEGRATION_NONE;
 
-		} else if ( strcmp(methods[i], "sat") == 0) {
+		} else if ( strcmp(methods[i], "sat") == 0 ) {
 			meth |= INTEGRATION_SATURATED;
 
-		} else if ( strcmp(methods[i], "nosat") == 0) {
+		} else if ( strcmp(methods[i], "nosat") == 0 ) {
 			meth &= ~INTEGRATION_SATURATED;
 
-		} else if ( strcmp(methods[i], "cen") == 0) {
+		} else if ( strcmp(methods[i], "cen") == 0 ) {
 			meth |= INTEGRATION_CENTER;
 
-		} else if ( strcmp(methods[i], "rescut") == 0) {
+		} else if ( strcmp(methods[i], "nocen") == 0 ) {
+			meth &= ~INTEGRATION_CENTER;
+
+		} else if ( strcmp(methods[i], "rescut") == 0 ) {
 			meth |= INTEGRATION_RESCUT;
 
-		} else if ( strcmp(methods[i], "norescut") == 0) {
+		} else if ( strcmp(methods[i], "norescut") == 0 ) {
 			meth &= ~INTEGRATION_RESCUT;
 
-		} else if ( strcmp(methods[i], "nocen") == 0) {
-			meth &= ~INTEGRATION_CENTER;
+		} else if ( strcmp(methods[i], "grad") == 0 ) {
+			meth |= INTEGRATION_GRADIENTBG;
+
+		} else if ( strcmp(methods[i], "nograd") == 0 ) {
+			meth &= ~INTEGRATION_GRADIENTBG;
 
 		} else {
 			ERROR("Bad integration method: '%s'\n", str);
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index a012fc14..2dd6139a 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -75,6 +75,7 @@ typedef enum {
  * @INTEGRATION_SATURATED: Integrate saturated reflections
  * @INTEGRATION_CENTER: Center the peak in the box prior to integration
  * @INTEGRATION_RESCUT: Stop integrating at the diffraction limit of the crystal
+ * @INTEGRATION_GRADIENTBG: Fit a gradient to the background
  *
  * An enumeration of all the available integration methods.
  **/
@@ -91,6 +92,7 @@ typedef enum {
 	INTEGRATION_SATURATED = 256,
 	INTEGRATION_CENTER = 512,
 	INTEGRATION_RESCUT = 1024,
+	INTEGRATION_GRADIENTBG = 2048,
 
 } IntegrationMethod;
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 164fa071..7fe66805 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -235,7 +235,7 @@ int main(int argc, char *argv[])
 	}
 	iargs.indm = NULL;  /* No default */
 	iargs.ipriv = NULL;  /* No default */
-	iargs.int_meth = integration_method("rings-nocen", NULL);
+	iargs.int_meth = integration_method("rings-nocen-nosat-grad", NULL);
 	iargs.push_res = 0.0;
 	iargs.highres = +INFINITY;
 	iargs.fix_profile_r = -1.0;