pattern_sim: Add --no-fringes

7 files changed, 46 insertions, 24 deletions

diff --git a/doc/man/pattern_sim.1 b/doc/man/pattern_sim.1
index 2ce1f9f0..e71413db 100644
--- a/doc/man/pattern_sim.1
+++ b/doc/man/pattern_sim.1
@@ -1,7 +1,8 @@
 .\"
 .\" pattern_sim man page
 .\"
-.\" Copyright © 2012 Thomas White <taw@physics.org>
+.\" Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+.\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
 .\"
@@ -137,6 +138,11 @@ Use \fItype\fR of spectrum.  \fItype\fR can be one of \fBtophat\fR or \fBsase\fR
 .PD
 Add \fIn\fR photons of Poisson-distributed background uniformly over the detector surface.
 
+.PD 0
+.IP \fB--no-fringes\fR
+.PD
+Suppress the subsidiary maxima of the shape transforms by setting I_latt(q) to zero beyond the first minimum of the function.
+
 
 .SH REFLECTION LISTS
 
@@ -206,7 +212,7 @@ This page was written by Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 pattern_sim, and this manual, are part of CrystFEL.
 .P
diff --git a/src/diffraction-gpu.c b/src/diffraction-gpu.c
index b5bd2e88..8b165856 100644
--- a/src/diffraction-gpu.c
+++ b/src/diffraction-gpu.c
@@ -73,7 +73,7 @@ struct gpu_context
 };
 
 
-static void check_sinc_lut(struct gpu_context *gctx, int n)
+static void check_sinc_lut(struct gpu_context *gctx, int n, int no_fringes)
 {
 	cl_int err;
 	cl_image_format fmt;
@@ -106,7 +106,11 @@ static void check_sinc_lut(struct gpu_context *gctx, int n)
 		for ( i=1; i<SINC_LUT_ELEMENTS; i++ ) {
 			double x, val;
 			x = (double)i/SINC_LUT_ELEMENTS;
-			val = fabs(sin(M_PI*n*x)/sin(M_PI*x));
+			if ( no_fringes && (x > 1.0/n) && (1.0-x > 1.0/n) ) {
+				val = 0.0;
+			} else {
+				val = fabs(sin(M_PI*n*x)/sin(M_PI*x));
+			}
 			gctx->sinc_lut_ptrs[n-1][i] = val;
 		}
 	}
@@ -278,7 +282,8 @@ static void do_panels(struct gpu_context *gctx, struct image *image,
 
 
 void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
-                         int na, int nb, int nc, UnitCell *ucell)
+                         int na, int nb, int nc, UnitCell *ucell,
+                         int no_fringes)
 {
 	double ax, ay, az;
 	double bx, by, bz;
@@ -297,9 +302,9 @@ void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
 	}
 
 	/* Ensure all required LUTs are available */
-	check_sinc_lut(gctx, na);
-	check_sinc_lut(gctx, nb);
-	check_sinc_lut(gctx, nc);
+	check_sinc_lut(gctx, na, no_fringes);
+	check_sinc_lut(gctx, nb, no_fringes);
+	check_sinc_lut(gctx, nc, no_fringes);
 
 	/* Unit cell */
 	cell_get_cartesian(ucell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
diff --git a/src/diffraction-gpu.h b/src/diffraction-gpu.h
index 349a6bff..e7ae23fd 100644
--- a/src/diffraction-gpu.h
+++ b/src/diffraction-gpu.h
@@ -3,11 +3,11 @@
  *
  * Calculate diffraction patterns by Fourier methods (GPU version)
  *
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2012 Thomas White <taw@physics.org>
+ *   2010-2014 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -41,7 +41,8 @@ struct gpu_context;
 #if HAVE_OPENCL
 
 extern void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
-                                int na, int nb, int nc, UnitCell *ucell);
+                                int na, int nb, int nc, UnitCell *ucell,
+                                int no_fringes);
 extern struct gpu_context *setup_gpu(int no_sfac,
                                      const double *intensities,
                                      const unsigned char *flags,
@@ -51,7 +52,8 @@ extern void cleanup_gpu(struct gpu_context *gctx);
 #else
 
 static void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
-                                int na, int nb, int nc, UnitCell *ucell)
+                                int na, int nb, int nc, UnitCell *ucell,
+                                int no_fringes)
 {
 	/* Do nothing */
 	ERROR("This copy of CrystFEL was not compiled with OpenCL support.\n");
diff --git a/src/diffraction.c b/src/diffraction.c
index 0fa9f79b..6383a8b4 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -49,7 +49,7 @@
 #define SINC_LUT_ELEMENTS (4096)
 
 
-static double *get_sinc_lut(int n)
+static double *get_sinc_lut(int n, int no_fringes)
 {
 	int i;
 	double *lut;
@@ -64,7 +64,11 @@ static double *get_sinc_lut(int n)
 		for ( i=1; i<SINC_LUT_ELEMENTS; i++ ) {
 			double x, val;
 			x = (double)i/SINC_LUT_ELEMENTS;
-			val = fabs(sin(M_PI*n*x)/sin(M_PI*x));
+			if ( no_fringes && (x > 1.0/n) && (1.0-x > 1.0/n) ) {
+				val = 0.0;
+			} else {
+				val = fabs(sin(M_PI*n*x)/sin(M_PI*x));
+			}
 			lut[i] = val;
 		}
 	}
@@ -665,7 +669,7 @@ struct sample *generate_twocolour(struct image *image)
 void get_diffraction(struct image *image, int na, int nb, int nc,
                      const double *intensities, const double *phases,
                      const unsigned char *flags, UnitCell *cell,
-                     GradientMethod m, const SymOpList *sym)
+                     GradientMethod m, const SymOpList *sym, int no_fringes)
 {
 	double ax, ay, az;
 	double bx, by, bz;
@@ -683,9 +687,9 @@ void get_diffraction(struct image *image, int na, int nb, int nc,
 	/* Needed later for Lorentz calculation */
 	image->twotheta = malloc(image->width * image->height * sizeof(double));
 
-	lut_a = get_sinc_lut(na);
-	lut_b = get_sinc_lut(nb);
-	lut_c = get_sinc_lut(nc);
+	lut_a = get_sinc_lut(na, no_fringes);
+	lut_b = get_sinc_lut(nb, no_fringes);
+	lut_c = get_sinc_lut(nc, no_fringes);
 
 	for ( i=0; i<image->nsamples; i++ ) {
 
diff --git a/src/diffraction.h b/src/diffraction.h
index e397bd3a..28f3ec0a 100644
--- a/src/diffraction.h
+++ b/src/diffraction.h
@@ -51,7 +51,8 @@ typedef enum {
 extern void get_diffraction(struct image *image, int na, int nb, int nc,
                             const double *intensities, const double *phases,
                             const unsigned char *flags, UnitCell *cell,
-                            GradientMethod m, const SymOpList *sym);
+                            GradientMethod m, const SymOpList *sym,
+                            int no_fringes);
 
 extern struct sample *generate_tophat(struct image *image);
 
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index a747cd72..b8cc1c68 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -92,6 +92,7 @@ static void show_help(const char *s)
 " -x, --spectrum=<type>     Type of spectrum to simulate.\n"
 "     --background=<N>      Add N photons of Poisson background (default 0).\n"
 "     --template=<file>     Take orientations from stream <file>.\n"
+"     --no-fringes          Exclude the side maxima of Bragg peaks.\n"
 );
 }
 
@@ -255,6 +256,7 @@ int main(int argc, char *argv[])
 	int background = 0;
 	char *template_file = NULL;
 	Stream *st = NULL;
+	int no_fringes = 0;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -276,6 +278,7 @@ int main(int argc, char *argv[])
 		{"type-spectrum",      1, NULL,               'x'},
 		{"spectrum",           1, NULL,               'x'},
 		{"really-random",      0, &config_random,      1},
+		{"no-fringes",         0, &no_fringes,         1},
 		{"gpu-dev",            1, NULL,                2},
 		{"min-size",           1, NULL,                3},
 		{"max-size",           1, NULL,                4},
@@ -693,10 +696,11 @@ int main(int argc, char *argv[])
 				                 intensities, flags, sym_str,
 				                 gpu_dev);
 			}
-			get_diffraction_gpu(gctx, &image, na, nb, nc, cell);
+			get_diffraction_gpu(gctx, &image, na, nb, nc, cell,
+			                    no_fringes);
 		} else {
 			get_diffraction(&image, na, nb, nc, intensities, phases,
-			                flags, cell, grad, sym);
+			                flags, cell, grad, sym, no_fringes);
 		}
 		if ( image.data == NULL ) {
 			ERROR("Diffraction calculation failed.\n");
diff --git a/tests/gpu_sim_check.c b/tests/gpu_sim_check.c
index d2475213..0419d945 100644
--- a/tests/gpu_sim_check.c
+++ b/tests/gpu_sim_check.c
@@ -166,7 +166,7 @@ int main(int argc, char *argv[])
 	gpu_image.spectrum = generate_tophat(&gpu_image);
 
 	start = get_hires_seconds();
-	get_diffraction_gpu(gctx, &gpu_image, 8, 8, 8, cell);
+	get_diffraction_gpu(gctx, &gpu_image, 8, 8, 8, cell, 1);
 	end = get_hires_seconds();
 	gpu_time = end - start;
 
@@ -174,7 +174,7 @@ int main(int argc, char *argv[])
 
 	start = get_hires_seconds();
 	get_diffraction(&cpu_image, 8, 8, 8, NULL, NULL, NULL, cell,
-	                GRADIENT_MOSAIC, sym);
+	                GRADIENT_MOSAIC, sym, 1);
 	end = get_hires_seconds();
 	cpu_time = end - start;