Move the "indexed reflection array" thing to where it can't do any harm

11 files changed, 19 insertions, 1320 deletions

diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 576044a6..141842ff 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -1,22 +1,22 @@
 lib_LTLIBRARIES        = libcrystfel.la
+
 libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/thread-pool.c src/image.c src/hdf5-file.c \
                          src/beam-parameters.c src/geometry.c src/statistics.c \
                          src/symmetry.c src/stream.c src/peaks.c \
-                         src/reflist-utils.c src/filters.c src/diffraction.c \
-                         src/diffraction-gpu.c src/cl-utils.c src/render.c \
-                         src/index.c src/dirax.c src/mosflm.c src/reax.c
+                         src/reflist-utils.c src/filters.c src/cl-utils.c \
+                         src/render.c src/index.c src/dirax.c src/mosflm.c \
+                         src/reax.c
 
 libcrystfel_la_includedir=$(includedir)/crystfel/
-libcrystfel_la_include_HEADERS = src/beam-parameters.h src/diffraction-gpu.h \
-                                 src/hdf5-file.h src/reflist.h src/symmetry.h \
-                                 src/cell.h src/diffraction.h src/image.h \
+
+libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
+                                 src/reflist.h src/symmetry.h src/cell.h \
                                  src/reflist-utils.h src/thread-pool.h \
-                                 src/cl-utils.h src/filters.h src/list_tmp.h \
+                                 src/cl-utils.h src/filters.h \
                                  src/statistics.h src/utils.h src/detector.h \
                                  src/geometry.h src/peaks.h src/stream.h \
-                                 src/render.h src/index.h \
-                                 ../data/defs.h
+                                 src/render.h src/index.h src/image.h
 
 INCLUDES = "-I$(top_srcdir)/data"
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib
diff --git a/libcrystfel/Makefile.in b/libcrystfel/Makefile.in
index a0b527e4..8992f9ed 100644
--- a/libcrystfel/Makefile.in
+++ b/libcrystfel/Makefile.in
@@ -88,9 +88,9 @@ am_libcrystfel_la_OBJECTS = src/reflist.lo src/utils.lo src/cell.lo \
 	src/detector.lo src/thread-pool.lo src/image.lo \
 	src/hdf5-file.lo src/beam-parameters.lo src/geometry.lo \
 	src/statistics.lo src/symmetry.lo src/stream.lo src/peaks.lo \
-	src/reflist-utils.lo src/filters.lo src/diffraction.lo \
-	src/diffraction-gpu.lo src/cl-utils.lo src/render.lo \
-	src/index.lo src/dirax.lo src/mosflm.lo src/reax.lo
+	src/reflist-utils.lo src/filters.lo src/cl-utils.lo \
+	src/render.lo src/index.lo src/dirax.lo src/mosflm.lo \
+	src/reax.lo
 libcrystfel_la_OBJECTS = $(am_libcrystfel_la_OBJECTS)
 AM_V_lt = $(am__v_lt_$(V))
 am__v_lt_ = $(am__v_lt_$(AM_DEFAULT_VERBOSITY))
@@ -351,20 +351,18 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/thread-pool.c src/image.c src/hdf5-file.c \
                          src/beam-parameters.c src/geometry.c src/statistics.c \
                          src/symmetry.c src/stream.c src/peaks.c \
-                         src/reflist-utils.c src/filters.c src/diffraction.c \
-                         src/diffraction-gpu.c src/cl-utils.c src/render.c \
-                         src/index.c src/dirax.c src/mosflm.c src/reax.c
+                         src/reflist-utils.c src/filters.c src/cl-utils.c \
+                         src/render.c src/index.c src/dirax.c src/mosflm.c \
+                         src/reax.c
 
 libcrystfel_la_includedir = $(includedir)/crystfel/
-libcrystfel_la_include_HEADERS = src/beam-parameters.h src/diffraction-gpu.h \
-                                 src/hdf5-file.h src/reflist.h src/symmetry.h \
-                                 src/cell.h src/diffraction.h src/image.h \
+libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
+                                 src/reflist.h src/symmetry.h src/cell.h \
                                  src/reflist-utils.h src/thread-pool.h \
-                                 src/cl-utils.h src/filters.h src/list_tmp.h \
+                                 src/cl-utils.h src/filters.h \
                                  src/statistics.h src/utils.h src/detector.h \
                                  src/geometry.h src/peaks.h src/stream.h \
-                                 src/render.h src/index.h \
-                                 ../data/defs.h
+                                 src/render.h src/index.h src/image.h
 
 INCLUDES = "-I$(top_srcdir)/data"
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib \
@@ -457,9 +455,6 @@ src/peaks.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/reflist-utils.lo: src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/filters.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
-src/diffraction.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
-src/diffraction-gpu.lo: src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
 src/cl-utils.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/render.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/index.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
@@ -479,10 +474,6 @@ mostlyclean-compile:
 	-rm -f src/cl-utils.lo
 	-rm -f src/detector.$(OBJEXT)
 	-rm -f src/detector.lo
-	-rm -f src/diffraction-gpu.$(OBJEXT)
-	-rm -f src/diffraction-gpu.lo
-	-rm -f src/diffraction.$(OBJEXT)
-	-rm -f src/diffraction.lo
 	-rm -f src/dirax.$(OBJEXT)
 	-rm -f src/dirax.lo
 	-rm -f src/filters.$(OBJEXT)
@@ -525,8 +516,6 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cell.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cl-utils.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/detector.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction-gpu.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/dirax.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/filters.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/geometry.Plo@am__quote@
diff --git a/libcrystfel/src/diffraction-gpu.c b/libcrystfel/src/diffraction-gpu.c
deleted file mode 100644
index 605b1514..00000000
--- a/libcrystfel/src/diffraction-gpu.c
+++ /dev/null
@@ -1,529 +0,0 @@
-/*
- * diffraction-gpu.c
- *
- * Calculate diffraction patterns by Fourier methods (GPU version)
- *
- * (c) 2006-2011 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdlib.h>
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
-#include <complex.h>
-
-#ifdef HAVE_CL_CL_H
-#include <CL/cl.h>
-#else
-#include <cl.h>
-#endif
-
-#include "image.h"
-#include "utils.h"
-#include "cell.h"
-#include "diffraction.h"
-#include "cl-utils.h"
-#include "beam-parameters.h"
-
-
-#define SAMPLING (4)
-#define BWSAMPLING (10)
-#define DIVSAMPLING (1)
-#define SINC_LUT_ELEMENTS (4096)
-
-
-struct gpu_context
-{
-	cl_context ctx;
-	cl_command_queue cq;
-	cl_program prog;
-	cl_kernel kern;
-	cl_mem intensities;
-	cl_mem flags;
-
-	/* Array of sinc LUTs */
-	cl_mem *sinc_luts;
-	cl_float **sinc_lut_ptrs;
-	int max_sinc_lut;  /* Number of LUTs, i.e. one greater than the maximum
-	                    * index.  This equals the highest allowable "n". */
-};
-
-
-static void check_sinc_lut(struct gpu_context *gctx, int n)
-{
-	cl_int err;
-	cl_image_format fmt;
-	int i;
-
-	if ( n > gctx->max_sinc_lut ) {
-
-		gctx->sinc_luts = realloc(gctx->sinc_luts,
-		                          n*sizeof(*gctx->sinc_luts));
-		gctx->sinc_lut_ptrs = realloc(gctx->sinc_lut_ptrs,
-		                              n*sizeof(*gctx->sinc_lut_ptrs));
-
-		for ( i=gctx->max_sinc_lut; i<n; i++ ) {
-			gctx->sinc_lut_ptrs[i] = NULL;
-		}
-
-		gctx->max_sinc_lut = n;
-	}
-
-	if ( gctx->sinc_lut_ptrs[n-1] != NULL ) return;
-
-	/* Create a new sinc LUT */
-	gctx->sinc_lut_ptrs[n-1] = malloc(SINC_LUT_ELEMENTS*sizeof(cl_float));
-	gctx->sinc_lut_ptrs[n-1][0] = n;
-	if ( n == 1 ) {
-		for ( i=1; i<SINC_LUT_ELEMENTS; i++ ) {
-			gctx->sinc_lut_ptrs[n-1][i] = 1.0;
-		}
-	} else {
-		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));
-			gctx->sinc_lut_ptrs[n-1][i] = val;
-		}
-	}
-
-	fmt.image_channel_order = CL_INTENSITY;
-	fmt.image_channel_data_type = CL_FLOAT;
-
-	gctx->sinc_luts[n-1] = clCreateImage2D(gctx->ctx,
-	                                CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR,
-	                                &fmt, SINC_LUT_ELEMENTS, 1, 0,
-	                                gctx->sinc_lut_ptrs[n-1], &err);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't create LUT for %i\n", n);
-		return;
-	}
-}
-
-
-static int set_arg_float(struct gpu_context *gctx, int idx, float val)
-{
-	cl_int err;
-	err = clSetKernelArg(gctx->kern, idx, sizeof(cl_float), &val);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't set kernel argument %i: %s\n",
-		      idx, clError(err));
-		return 1;
-	}
-
-	return 0;
-}
-
-
-static int set_arg_int(struct gpu_context *gctx, int idx, int val)
-{
-	cl_int err;
-
-	err = clSetKernelArg(gctx->kern, idx, sizeof(cl_int), &val);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't set kernel argument %i: %s\n",
-		      idx, clError(err));
-		return 1;
-	}
-
-	return 0;
-}
-
-
-static int set_arg_mem(struct gpu_context *gctx, int idx, cl_mem val)
-{
-	cl_int err;
-
-	err = clSetKernelArg(gctx->kern, idx, sizeof(cl_mem), &val);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't set kernel argument %i: %s\n",
-		      idx, clError(err));
-		return 1;
-	}
-
-	return 0;
-}
-
-
-void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
-                         int na, int nb, int nc, UnitCell *ucell)
-{
-	cl_int err;
-	double ax, ay, az;
-	double bx, by, bz;
-	double cx, cy, cz;
-	float klow, khigh;
-	int i;
-	cl_float16 cell;
-	cl_int4 ncells;
-	const int sampling = SAMPLING;
-	cl_float bwstep;
-	int n_inf = 0;
-	int n_neg = 0;
-	cl_float divxlow, divxstep;
-	cl_float divylow, divystep;
-	int n_nan = 0;
-	int sprod;
-
-	if ( gctx == NULL ) {
-		ERROR("GPU setup failed.\n");
-		return;
-	}
-
-	cell_get_cartesian(ucell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-	cell.s[0] = ax;  cell.s[1] = ay;  cell.s[2] = az;
-	cell.s[3] = bx;  cell.s[4] = by;  cell.s[5] = bz;
-	cell.s[6] = cx;  cell.s[7] = cy;  cell.s[8] = cz;
-
-	/* Calculate wavelength */
-	klow = 1.0/(image->lambda*(1.0 + image->beam->bandwidth/2.0));
-	khigh = 1.0/(image->lambda*(1.0 - image->beam->bandwidth/2.0));
-	bwstep = (khigh-klow) / BWSAMPLING;
-
-	/* Calculate divergence stuff */
-	divxlow = -image->beam->divergence/2.0;
-	divylow = -image->beam->divergence/2.0;
-	divxstep = image->beam->divergence / DIVSAMPLING;
-	divystep = image->beam->divergence / DIVSAMPLING;
-
-	ncells.s[0] = na;
-	ncells.s[1] = nb;
-	ncells.s[2] = nc;
-	ncells.s[3] = 0;  /* unused */
-
-	/* Ensure all required LUTs are available */
-	check_sinc_lut(gctx, na);
-	check_sinc_lut(gctx, nb);
-	check_sinc_lut(gctx, nc);
-
-	if ( set_arg_float(gctx, 2, klow) ) return;
-	if ( set_arg_mem(gctx, 9, gctx->intensities) ) return;
-	if ( set_arg_int(gctx, 12, sampling) ) return;
-	if ( set_arg_float(gctx, 14, bwstep) ) return;
-	if ( set_arg_mem(gctx, 15, gctx->sinc_luts[na-1]) ) return;
-	if ( set_arg_mem(gctx, 16, gctx->sinc_luts[nb-1]) ) return;
-	if ( set_arg_mem(gctx, 17, gctx->sinc_luts[nc-1]) ) return;
-	if ( set_arg_mem(gctx, 18, gctx->flags) ) return;
-	if ( set_arg_float(gctx, 23, divxlow) ) return;
-	if ( set_arg_float(gctx, 24, divxstep) ) return;
-	if ( set_arg_int(gctx, 25, DIVSAMPLING) ) return;
-	if ( set_arg_float(gctx, 26, divylow) ) return;
-	if ( set_arg_float(gctx, 27, divystep) ) return;
-	if ( set_arg_int(gctx, 28, DIVSAMPLING) ) return;
-
-	/* Unit cell */
-	err = clSetKernelArg(gctx->kern, 8, sizeof(cl_float16), &cell);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't set unit cell: %s\n", clError(err));
-		return;
-	}
-
-	/* Local memory for reduction */
-	sprod = BWSAMPLING*SAMPLING*SAMPLING*DIVSAMPLING*DIVSAMPLING;
-	err = clSetKernelArg(gctx->kern, 13, sprod*sizeof(cl_float), NULL);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't set local memory: %s\n", clError(err));
-		return;
-	}
-
-	/* Allocate memory for the result */
-	image->data = calloc(image->width * image->height, sizeof(float));
-	image->twotheta = calloc(image->width * image->height, sizeof(double));
-
-	/* Iterate over panels */
-	for ( i=0; i<image->det->n_panels; i++ ) {
-
-		size_t dims[3];
-		size_t ldims[3] = {SAMPLING, SAMPLING,
-		                   BWSAMPLING * DIVSAMPLING * DIVSAMPLING};
-		struct panel *p;
-		cl_mem tt;
-		size_t tt_size;
-		cl_mem diff;
-		size_t diff_size;
-		float *diff_ptr;
-		float *tt_ptr;
-		int pan_width, pan_height;
-		int fs, ss;
-
-		p = &image->det->panels[i];
-
-		pan_width = 1 + p->max_fs - p->min_fs;
-		pan_height = 1 + p->max_ss - p->min_ss;
-
-		/* Buffer for the results of this panel */
-		diff_size = pan_width * pan_height * sizeof(cl_float);
-		diff = clCreateBuffer(gctx->ctx, CL_MEM_WRITE_ONLY,
-	                              diff_size, NULL, &err);
-		if ( err != CL_SUCCESS ) {
-			ERROR("Couldn't allocate diffraction memory\n");
-			return;
-		}
-		tt_size = pan_width * pan_height * sizeof(cl_float);
-		tt = clCreateBuffer(gctx->ctx, CL_MEM_WRITE_ONLY, tt_size,
-			            NULL, &err);
-		if ( err != CL_SUCCESS ) {
-			ERROR("Couldn't allocate twotheta memory\n");
-			return;
-		}
-
-		if ( set_arg_mem(gctx, 0, diff) ) return;
-		if ( set_arg_mem(gctx, 1, tt) ) return;
-		if ( set_arg_int(gctx, 3, pan_width) ) return;
-		if ( set_arg_float(gctx, 4, p->cnx) ) return;
-		if ( set_arg_float(gctx, 5, p->cny) ) return;
-		if ( set_arg_float(gctx, 6, p->res) ) return;
-		if ( set_arg_float(gctx, 7, p->clen) ) return;
-		if ( set_arg_int(gctx, 10, p->min_fs) ) return;
-		if ( set_arg_int(gctx, 11, p->min_ss) ) return;
-		if ( set_arg_float(gctx, 19, p->fsx) ) return;
-		if ( set_arg_float(gctx, 20, p->fsy) ) return;
-		if ( set_arg_float(gctx, 21, p->ssx) ) return;
-		if ( set_arg_float(gctx, 22, p->ssy) ) return;
-
-		dims[0] = pan_width * SAMPLING;
-		dims[1] = pan_height * SAMPLING;
-		dims[2] = BWSAMPLING * DIVSAMPLING * DIVSAMPLING;
-
-		err = clEnqueueNDRangeKernel(gctx->cq, gctx->kern, 3, NULL,
-		                             dims, ldims, 0, NULL, NULL);
-		if ( err != CL_SUCCESS ) {
-			ERROR("Couldn't enqueue diffraction kernel: %s\n",
-			      clError(err));
-			return;
-		}
-
-		clFinish(gctx->cq);
-
-		diff_ptr = clEnqueueMapBuffer(gctx->cq, diff, CL_TRUE,
-		                              CL_MAP_READ, 0, diff_size,
-		                              0, NULL, NULL, &err);
-		if ( err != CL_SUCCESS ) {
-			ERROR("Couldn't map diffraction buffer: %s\n",
-			      clError(err));
-			return;
-		}
-		tt_ptr = clEnqueueMapBuffer(gctx->cq, tt, CL_TRUE, CL_MAP_READ,
-		                            0, tt_size, 0, NULL, NULL, &err);
-		if ( err != CL_SUCCESS ) {
-			ERROR("Couldn't map tt buffer\n");
-			return;
-		}
-
-		for ( fs=0; fs<pan_width; fs++ ) {
-		for ( ss=0; ss<pan_height; ss++ ) {
-
-			float val, tt;
-			int tfs, tss;
-
-			val = diff_ptr[fs + pan_width*ss];
-			if ( isinf(val) ) n_inf++;
-			if ( val < 0.0 ) n_neg++;
-			if ( isnan(val) ) n_nan++;
-			tt = tt_ptr[fs + pan_width*ss];
-
-			tfs = p->min_fs + fs;
-			tss = p->min_ss + ss;
-			image->data[tfs + image->width*tss] = val;
-			image->twotheta[tfs + image->width*tss] = tt;
-
-		}
-		}
-
-		clEnqueueUnmapMemObject(gctx->cq, diff, diff_ptr,
-		                        0, NULL, NULL);
-		clEnqueueUnmapMemObject(gctx->cq, tt, tt_ptr,
-		                        0, NULL, NULL);
-
-		clReleaseMemObject(diff);
-		clReleaseMemObject(tt);
-
-	}
-
-
-	if ( n_neg + n_inf + n_nan ) {
-		ERROR("WARNING: The GPU calculation produced %i negative"
-		      " values, %i infinities and %i NaNs.\n",
-		      n_neg, n_inf, n_nan);
-	}
-
-}
-
-
-/* Setup the OpenCL stuff, create buffers, load the structure factor table */
-struct gpu_context *setup_gpu(int no_sfac,
-                              const double *intensities, unsigned char *flags,
-                              const char *sym, int dev_num)
-{
-	struct gpu_context *gctx;
-	cl_uint nplat;
-	cl_platform_id platforms[8];
-	cl_context_properties prop[3];
-	cl_int err;
-	cl_device_id dev;
-	size_t intensities_size;
-	float *intensities_ptr;
-	size_t flags_size;
-	float *flags_ptr;
-	size_t maxwgsize;
-	int i;
-	char cflags[512] = "";
-
-	STATUS("Setting up GPU...\n");
-
-	err = clGetPlatformIDs(8, platforms, &nplat);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't get platform IDs: %i\n", err);
-		return NULL;
-	}
-	if ( nplat == 0 ) {
-		ERROR("Couldn't find at least one platform!\n");
-		return NULL;
-	}
-	prop[0] = CL_CONTEXT_PLATFORM;
-	prop[1] = (cl_context_properties)platforms[0];
-	prop[2] = 0;
-
-	gctx = malloc(sizeof(*gctx));
-	gctx->ctx = clCreateContextFromType(prop, CL_DEVICE_TYPE_GPU,
-	                                    NULL, NULL, &err);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't create OpenCL context: %i\n", err);
-		free(gctx);
-		return NULL;
-	}
-
-	dev = get_cl_dev(gctx->ctx, dev_num);
-
-	gctx->cq = clCreateCommandQueue(gctx->ctx, dev, 0, &err);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't create OpenCL command queue\n");
-		free(gctx);
-		return NULL;
-	}
-
-	/* Create a single-precision version of the scattering factors */
-	intensities_size = IDIM*IDIM*IDIM*sizeof(cl_float);
-	intensities_ptr = malloc(intensities_size);
-	if ( intensities != NULL ) {
-		for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
-			intensities_ptr[i] = intensities[i];
-		}
-	} else {
-		for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
-			intensities_ptr[i] = 1e5;
-		}
-		strncat(cflags, "-DFLAT_INTENSITIES ", 511-strlen(cflags));
-	}
-	gctx->intensities = clCreateBuffer(gctx->ctx,
-	                             CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR,
-	                             intensities_size, intensities_ptr, &err);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't allocate intensities memory\n");
-		free(gctx);
-		return NULL;
-	}
-	free(intensities_ptr);
-
-	if ( sym != NULL ) {
-		if ( strcmp(sym, "1") == 0 ) {
-			strncat(cflags, "-DPG1 ", 511-strlen(cflags));
-		} else if ( strcmp(sym, "-1") == 0 ) {
-			strncat(cflags, "-DPG1BAR ", 511-strlen(cflags));
-		} else if ( strcmp(sym, "6/mmm") == 0 ) {
-			strncat(cflags, "-DPG6MMM ", 511-strlen(cflags));
-		} else if ( strcmp(sym, "6") == 0 ) {
-			strncat(cflags, "-DPG6 ", 511-strlen(cflags));
-		} else if ( strcmp(sym, "6/m") == 0 ) {
-			strncat(cflags, "-DPG6M ", 511-strlen(cflags));
-		} else {
-			ERROR("Sorry!  Point group '%s' is not currently"
-			      " supported on the GPU."
-			      " I'm using '1' instead.\n", sym);
-			strncat(cflags, "-DPG1 ", 511-strlen(cflags));
-		}
-	} else {
-		if ( intensities != NULL ) {
-			ERROR("You gave me an intensities file but no point"
-			      " group.  I'm assuming '1'.\n");
-			strncat(cflags, "-DPG1 ", 511-strlen(cflags));
-		}
-	}
-
-	/* Create a flag array */
-	flags_size = IDIM*IDIM*IDIM*sizeof(cl_float);
-	flags_ptr = malloc(flags_size);
-	if ( flags != NULL ) {
-		for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
-			flags_ptr[i] = flags[i];
-		}
-	} else {
-		for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
-			flags_ptr[i] = 1.0;
-		}
-	}
-	gctx->flags = clCreateBuffer(gctx->ctx,
-	                             CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR,
-	                             flags_size, flags_ptr, &err);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't allocate flag buffer\n");
-		free(gctx);
-		return NULL;
-	}
-	free(flags_ptr);
-
-	gctx->prog = load_program(DATADIR"/crystfel/diffraction.cl", gctx->ctx,
-	                          dev, &err, cflags);
-	if ( err != CL_SUCCESS ) {
-		free(gctx);
-		return NULL;
-	}
-
-	gctx->kern = clCreateKernel(gctx->prog, "diffraction", &err);
-	if ( err != CL_SUCCESS ) {
-		ERROR("Couldn't create kernel\n");
-		free(gctx);
-		return NULL;
-	}
-
-	gctx->max_sinc_lut = 0;
-	gctx->sinc_lut_ptrs = NULL;
-	gctx->sinc_luts = NULL;
-
-	clGetDeviceInfo(dev, CL_DEVICE_MAX_WORK_GROUP_SIZE,
-	                sizeof(size_t), &maxwgsize, NULL);
-	STATUS("Maximum work group size = %lli\n", (long long int)maxwgsize);
-
-	return gctx;
-}
-
-
-void cleanup_gpu(struct gpu_context *gctx)
-{
-	int i;
-
-	clReleaseProgram(gctx->prog);
-	clReleaseMemObject(gctx->intensities);
-
-	/* Release LUTs */
-	for ( i=1; i<=gctx->max_sinc_lut; i++ ) {
-		if ( gctx->sinc_lut_ptrs[i-1] != NULL ) {
-			clReleaseMemObject(gctx->sinc_luts[i-1]);
-			free(gctx->sinc_lut_ptrs[i-1]);
-		}
-	}
-
-	free(gctx->sinc_luts);
-	free(gctx->sinc_lut_ptrs);
-
-	clReleaseCommandQueue(gctx->cq);
-	clReleaseContext(gctx->ctx);
-	free(gctx);
-}
diff --git a/libcrystfel/src/diffraction-gpu.h b/libcrystfel/src/diffraction-gpu.h
deleted file mode 100644
index a3bde4e1..00000000
--- a/libcrystfel/src/diffraction-gpu.h
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * diffraction-gpu.h
- *
- * Calculate diffraction patterns by Fourier methods (GPU version)
- *
- * (c) 2006-2011 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#ifndef DIFFRACTION_GPU_H
-#define DIFFRACTION_GPU_H
-
-#include "image.h"
-#include "cell.h"
-
-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);
-extern struct gpu_context *setup_gpu(int no_sfac,
-                                     const double *intensities,
-                                     const unsigned char *flags,
-                                     const char *sym, int dev_num);
-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)
-{
-	/* Do nothing */
-	ERROR("This copy of CrystFEL was not compiled with OpenCL support.\n");
-}
-
-static struct gpu_context *setup_gpu(int no_sfac,
-                                     const double *intensities,
-                                     const unsigned char *flags,
-                                     const char *sym, int dev_num)
-{
-	return NULL;
-}
-
-static void cleanup_gpu(struct gpu_context *gctx)
-{
-}
-
-#endif
-
-#endif	/* DIFFRACTION_GPU_H */
diff --git a/libcrystfel/src/diffraction.c b/libcrystfel/src/diffraction.c
deleted file mode 100644
index 9532a6ce..00000000
--- a/libcrystfel/src/diffraction.c
+++ /dev/null
@@ -1,463 +0,0 @@
-/*
- * diffraction.c
- *
- * Calculate diffraction patterns by Fourier methods
- *
- * (c) 2006-2011 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#include <stdlib.h>
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
-#include <complex.h>
-#include <assert.h>
-#include <fenv.h>
-
-#include "image.h"
-#include "utils.h"
-#include "cell.h"
-#include "diffraction.h"
-#include "beam-parameters.h"
-#include "symmetry.h"
-
-
-#define SAMPLING (4)
-#define BWSAMPLING (10)
-#define DIVSAMPLING (1)
-#define SINC_LUT_ELEMENTS (4096)
-
-
-static double *get_sinc_lut(int n)
-{
-	int i;
-	double *lut;
-
-	lut = malloc(SINC_LUT_ELEMENTS*sizeof(double));
-	lut[0] = n;
-	if ( n == 1 ) {
-		for ( i=1; i<SINC_LUT_ELEMENTS; i++ ) {
-			lut[i] = 1.0;
-		}
-	} else {
-		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));
-			lut[i] = val;
-		}
-	}
-
-	return lut;
-}
-
-
-static double interpolate_lut(double *lut, double val)
-{
-	double i, pos, f;
-	unsigned int low, high;
-
-	pos = SINC_LUT_ELEMENTS * modf(fabs(val), &i);
-	low = (int)pos;  /* Discard fractional part */
-	high = low + 1;
-	f = modf(pos, &i);  /* Fraction */
-	if ( high == SINC_LUT_ELEMENTS ) high = 0;
-
-	return (1.0-f)*lut[low] + f*lut[high];
-}
-
-
-static double lattice_factor(struct rvec q, double ax, double ay, double az,
-                                            double bx, double by, double bz,
-                                            double cx, double cy, double cz,
-                                            double *lut_a, double *lut_b,
-                                            double *lut_c)
-{
-	struct rvec Udotq;
-	double f1, f2, f3;
-
-	Udotq.u = ax*q.u + ay*q.v + az*q.w;
-	Udotq.v = bx*q.u + by*q.v + bz*q.w;
-	Udotq.w = cx*q.u + cy*q.v + cz*q.w;
-
-	f1 = interpolate_lut(lut_a, Udotq.u);
-	f2 = interpolate_lut(lut_b, Udotq.v);
-	f3 = interpolate_lut(lut_c, Udotq.w);
-
-	return f1 * f2 * f3;
-}
-
-
-static double sym_lookup_intensity(const double *intensities,
-                                   const unsigned char *flags,
-                                   const SymOpList *sym,
-                                   signed int h, signed int k, signed int l)
-{
-	int i;
-	double ret = 0.0;
-
-	for ( i=0; i<num_equivs(sym, NULL); i++ ) {
-
-		signed int he;
-		signed int ke;
-		signed int le;
-		double f, val;
-
-		get_equiv(sym, NULL, i, h, k, l, &he, &ke, &le);
-
-		f = (double)lookup_flag(flags, he, ke, le);
-		val = lookup_intensity(intensities, he, ke, le);
-
-		ret += f*val;
-
-	}
-
-	return ret;
-}
-
-
-static double sym_lookup_phase(const double *phases,
-                               const unsigned char *flags, const SymOpList *sym,
-                               signed int h, signed int k, signed int l)
-{
-	int i;
-	double ret = 0.0;
-
-	for ( i=0; i<num_equivs(sym, NULL); i++ ) {
-
-		signed int he;
-		signed int ke;
-		signed int le;
-		double f, val;
-
-		get_equiv(sym, NULL, i, h, k, l, &he, &ke, &le);
-
-		f = (double)lookup_flag(flags, he, ke, le);
-		val = lookup_phase(phases, he, ke, le);
-
-		ret += f*val;
-
-	}
-
-	return ret;
-}
-
-
-static double interpolate_linear(const double *ref, const unsigned char *flags,
-                                 const SymOpList *sym, float hd,
-                                 signed int k, signed int l)
-{
-	signed int h;
-	double val1, val2;
-	float f;
-
-	h = (signed int)hd;
-	if ( hd < 0.0 ) h -= 1;
-	f = hd - (float)h;
-	assert(f >= 0.0);
-
-	val1 = sym_lookup_intensity(ref, flags, sym, h, k, l);
-	val2 = sym_lookup_intensity(ref, flags, sym, h+1, k, l);
-
-	val1 = val1;
-	val2 = val2;
-
-	return (1.0-f)*val1 + f*val2;
-}
-
-
-static double interpolate_bilinear(const double *ref,
-                                   const unsigned char *flags,
-                                   const SymOpList *sym,
-                                   float hd, float kd, signed int l)
-{
-	signed int k;
-	double val1, val2;
-	float f;
-
-	k = (signed int)kd;
-	if ( kd < 0.0 ) k -= 1;
-	f = kd - (float)k;
-	assert(f >= 0.0);
-
-	val1 = interpolate_linear(ref, flags, sym, hd, k, l);
-	val2 = interpolate_linear(ref, flags, sym, hd, k+1, l);
-
-	return (1.0-f)*val1 + f*val2;
-}
-
-
-static double interpolate_intensity(const double *ref,
-                                    const unsigned char *flags,
-                                    const SymOpList *sym,
-                                    float hd, float kd, float ld)
-{
-	signed int l;
-	double val1, val2;
-	float f;
-
-	l = (signed int)ld;
-	if ( ld < 0.0 ) l -= 1;
-	f = ld - (float)l;
-	assert(f >= 0.0);
-
-	val1 = interpolate_bilinear(ref, flags, sym, hd, kd, l);
-	val2 = interpolate_bilinear(ref, flags, sym, hd, kd, l+1);
-
-	return (1.0-f)*val1 + f*val2;
-}
-
-
-static double complex interpolate_phased_linear(const double *ref,
-                                                const double *phases,
-                                                const unsigned char *flags,
-                                                const SymOpList *sym,
-                                                float hd,
-                                                signed int k, signed int l)
-{
-	signed int h;
-	double val1, val2;
-	float f;
-	double ph1, ph2;
-	double re1, re2, im1, im2;
-	double re, im;
-
-	h = (signed int)hd;
-	if ( hd < 0.0 ) h -= 1;
-	f = hd - (float)h;
-	assert(f >= 0.0);
-
-	val1 = sym_lookup_intensity(ref, flags, sym, h, k, l);
-	val2 = sym_lookup_intensity(ref, flags, sym, h+1, k, l);
-	ph1 = sym_lookup_phase(phases, flags, sym, h, k, l);
-	ph2 = sym_lookup_phase(phases, flags, sym, h+1, k, l);
-
-	val1 = val1;
-	val2 = val2;
-
-	/* Calculate real and imaginary parts */
-	re1 = val1 * cos(ph1);
-	im1 = val1 * sin(ph1);
-	re2 = val2 * cos(ph2);
-	im2 = val2 * sin(ph2);
-
-	re = (1.0-f)*re1 + f*re2;
-	im = (1.0-f)*im1 + f*im2;
-
-	return re + im*I;
-}
-
-
-static double complex interpolate_phased_bilinear(const double *ref,
-                                                  const double *phases,
-                                                  const unsigned char *flags,
-                                                  const SymOpList *sym,
-                                                  float hd, float kd,
-                                                  signed int l)
-{
-	signed int k;
-	double complex val1, val2;
-	float f;
-
-	k = (signed int)kd;
-	if ( kd < 0.0 ) k -= 1;
-	f = kd - (float)k;
-	assert(f >= 0.0);
-
-	val1 = interpolate_phased_linear(ref, phases, flags, sym, hd, k, l);
-	val2 = interpolate_phased_linear(ref, phases, flags, sym, hd, k+1, l);
-
-	return (1.0-f)*val1 + f*val2;
-}
-
-
-static double interpolate_phased_intensity(const double *ref,
-                                           const double *phases,
-                                           const unsigned char *flags,
-                                           const SymOpList *sym,
-                                           float hd, float kd, float ld)
-{
-	signed int l;
-	double complex val1, val2;
-	float f;
-
-	l = (signed int)ld;
-	if ( ld < 0.0 ) l -= 1;
-	f = ld - (float)l;
-	assert(f >= 0.0);
-
-	val1 = interpolate_phased_bilinear(ref, phases, flags, sym,
-	                                   hd, kd, l);
-	val2 = interpolate_phased_bilinear(ref, phases, flags, sym,
-	                                   hd, kd, l+1);
-
-	return cabs((1.0-f)*val1 + f*val2);
-}
-
-
-/* Look up the structure factor for the nearest Bragg condition */
-static double molecule_factor(const double *intensities, const double *phases,
-                              const unsigned char *flags, struct rvec q,
-                              double ax, double ay, double az,
-                              double bx, double by, double bz,
-                              double cx, double cy, double cz,
-                              GradientMethod m, const SymOpList *sym)
-{
-	float hd, kd, ld;
-	signed int h, k, l;
-	double r;
-
-	hd = q.u * ax + q.v * ay + q.w * az;
-	kd = q.u * bx + q.v * by + q.w * bz;
-	ld = q.u * cx + q.v * cy + q.w * cz;
-
-	/* No flags -> flat intensity distribution */
-	if ( flags == NULL ) return 1.0e5;
-
-	switch ( m ) {
-	case GRADIENT_MOSAIC :
-		fesetround(1);  /* Round to nearest */
-		h = (signed int)rint(hd);
-		k = (signed int)rint(kd);
-		l = (signed int)rint(ld);
-		if ( abs(h) > INDMAX ) r = 0.0;
-		else if ( abs(k) > INDMAX ) r = 0.0;
-		else if ( abs(l) > INDMAX ) r = 0.0;
-		else r = sym_lookup_intensity(intensities, flags, sym, h, k, l);
-		break;
-	case GRADIENT_INTERPOLATE :
-		r = interpolate_intensity(intensities, flags, sym, hd, kd, ld);
-		break;
-	case GRADIENT_PHASED :
-		r = interpolate_phased_intensity(intensities, phases, flags,
-		                                 sym, hd, kd, ld);
-		break;
-	default:
-		ERROR("This gradient method not implemented yet.\n");
-		exit(1);
-	}
-
-	return r;
-}
-
-
-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)
-{
-	unsigned int fs, ss;
-	double ax, ay, az;
-	double bx, by, bz;
-	double cx, cy, cz;
-	float klow, khigh, bwstep;
-	double *lut_a;
-	double *lut_b;
-	double *lut_c;
-	double divxlow, divylow, divxstep, divystep;
-
-	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-
-	/* Allocate (and zero) the "diffraction array" */
-	image->data = calloc(image->width * image->height, sizeof(float));
-
-	/* Needed later for Lorentz calculation */
-	image->twotheta = malloc(image->width * image->height * sizeof(double));
-
-	klow = 1.0/(image->lambda*(1.0 + image->beam->bandwidth/2.0));
-	khigh = 1.0/(image->lambda*(1.0 - image->beam->bandwidth/2.0));
-	bwstep = (khigh-klow) / BWSAMPLING;
-
-	divxlow = -image->beam->divergence/2.0;
-	divylow = -image->beam->divergence/2.0;
-	divxstep = image->beam->divergence / DIVSAMPLING;
-	divystep = image->beam->divergence / DIVSAMPLING;
-
-	lut_a = get_sinc_lut(na);
-	lut_b = get_sinc_lut(nb);
-	lut_c = get_sinc_lut(nc);
-
-	for ( fs=0; fs<image->width; fs++ ) {
-	for ( ss=0; ss<image->height; ss++ ) {
-
-		int fs_step, ss_step, kstep;
-		int divxval, divyval;
-		int idx = fs + image->width*ss;
-
-		for ( fs_step=0; fs_step<SAMPLING; fs_step++ ) {
-		for ( ss_step=0; ss_step<SAMPLING; ss_step++ ) {
-		for ( kstep=0; kstep<BWSAMPLING; kstep++ ) {
-		for ( divxval=0; divxval<DIVSAMPLING; divxval++ ) {
-		for ( divyval=0; divyval<DIVSAMPLING; divyval++ ) {
-
-			double k;
-			double intensity;
-			double f_lattice, I_lattice;
-			double I_molecule;
-			struct rvec q, qn;
-			double twotheta;
-			const double dfs = (double)fs
-			                    + ((double)fs_step / SAMPLING);
-			const double dss = (double)ss
-			                    + ((double)ss_step / SAMPLING);
-
-			double xdiv = divxlow + divxstep*(double)divxval;
-			double ydiv = divylow + divystep*(double)divyval;
-
-			/* Calculate k this time round */
-			k = klow + (double)kstep * bwstep;
-
-			qn = get_q(image, dfs, dss, &twotheta, k);
-
-			/* x divergence */
-			q.u =  qn.u*cos(xdiv) +qn.w*sin(xdiv);
-			q.v =  qn.v;
-			q.w = -qn.u*sin(xdiv) +qn.w*cos(xdiv);
-
-			qn = q;
-
-			/* y divergence */
-			q.v =  qn.v*cos(ydiv) +qn.w*sin(ydiv);
-			q.w = -qn.v*sin(ydiv) +qn.w*cos(ydiv);
-
-			f_lattice = lattice_factor(q, ax, ay, az,
-			                              bx, by, bz,
-			                              cx, cy, cz,
-			                              lut_a, lut_b, lut_c);
-
-			I_molecule = molecule_factor(intensities,
-			                             phases, flags, q,
-			                             ax,ay,az,bx,by,bz,cx,cy,cz,
-			                             m, sym);
-
-			I_lattice = pow(f_lattice, 2.0);
-			intensity = I_lattice * I_molecule;
-
-			image->data[idx] += intensity;
-
-			if ( fs_step + ss_step + kstep == 0 ) {
-				image->twotheta[idx] = twotheta;
-			}
-
-		}
-		}
-		}
-		}
-		}
-
-		image->data[idx] /= (SAMPLING*SAMPLING*BWSAMPLING
-		                     *DIVSAMPLING*DIVSAMPLING);
-
-
-	}
-	progress_bar(fs, image->width-1, "Calculating diffraction");
-	}
-
-	free(lut_a);
-	free(lut_b);
-	free(lut_c);
-}
diff --git a/libcrystfel/src/diffraction.h b/libcrystfel/src/diffraction.h
deleted file mode 100644
index f71d3cce..00000000
--- a/libcrystfel/src/diffraction.h
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * diffraction.h
- *
- * Calculate diffraction patterns by Fourier methods
- *
- * (c) 2006-2011 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#ifndef DIFFRACTION_H
-#define DIFFRACTION_H
-
-#include "image.h"
-#include "cell.h"
-#include "symmetry.h"
-
-typedef enum {
-	GRADIENT_MOSAIC,
-	GRADIENT_INTERPOLATE,
-	GRADIENT_PHASED
-} GradientMethod;
-
-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);
-
-#endif	/* DIFFRACTION_H */
diff --git a/libcrystfel/src/list_tmp.h b/libcrystfel/src/list_tmp.h
deleted file mode 100644
index a524b2f9..00000000
--- a/libcrystfel/src/list_tmp.h
+++ /dev/null
@@ -1,106 +0,0 @@
-/*
- * Template for creating indexed 3D lists of a given type, usually indexed
- * as signed h,k,l values where -INDMAX<={h,k,l}<=+INDMAX.
- *
- * These are used, for example, for:
- *  - a list of 'double complex' values for storing structure factors,
- *  - a list of 'double' values for storing reflection intensities,
- *  - a list of 'unsigned int' values for counts of some sort.
- *
- * When LABEL and TYPE are #defined appropriately, including this header
- * defines functions such as:
- *  - new_list_<LABEL>(), for creating a new list of the given type,
- *  - set_<LABEL>(), for setting a value in a list,
- *  - lookup_<LABEL>(), for retrieving values from a list,
- * ..and so on.
- *
- * See src/utils.h for more information.
- *
- */
-
-#include <stdio.h>
-
-#define ERROR_T(...) fprintf(stderr, __VA_ARGS__)
-
-static inline void LABEL(integrate)(TYPE *ref, signed int h,
-                                    signed int k, signed int l,
-                                    TYPE i)
-{
-	int idx;
-
-	if ( (abs(h) > INDMAX) || (abs(k) > INDMAX) || (abs(l) > INDMAX) ) {
-		ERROR_T("\nReflection %i %i %i is out of range!\n", h, k, l);
-		ERROR_T("You need to re-configure INDMAX and re-run.\n");
-		exit(1);
-	}
-
-	if ( h < 0 ) h += IDIM;
-	if ( k < 0 ) k += IDIM;
-	if ( l < 0 ) l += IDIM;
-
-	idx = h + (IDIM*k) + (IDIM*IDIM*l);
-	ref[idx] += i;
-}
-
-
-static inline void LABEL(set)(TYPE *ref, signed int h,
-                              signed int k, signed int l,
-                              TYPE i)
-{
-	int idx;
-
-	if ( (abs(h) > INDMAX) || (abs(k) > INDMAX) || (abs(l) > INDMAX) ) {
-		ERROR_T("\nReflection %i %i %i is out of range!\n", h, k, l);
-		ERROR_T("You need to re-configure INDMAX and re-run.\n");
-		exit(1);
-	}
-
-	if ( h < 0 ) h += IDIM;
-	if ( k < 0 ) k += IDIM;
-	if ( l < 0 ) l += IDIM;
-
-	idx = h + (IDIM*k) + (IDIM*IDIM*l);
-	ref[idx] = i;
-}
-
-
-static inline TYPE LABEL(lookup)(const TYPE *ref, signed int h,
-                                 signed int k, signed int l)
-{
-	int idx;
-
-	if ( (abs(h) > INDMAX) || (abs(k) > INDMAX) || (abs(l) > INDMAX) ) {
-		ERROR_T("\nReflection %i %i %i is out of range!\n", h, k, l);
-		ERROR_T("You need to re-configure INDMAX and re-run.\n");
-		exit(1);
-	}
-
-	if ( h < 0 ) h += IDIM;
-	if ( k < 0 ) k += IDIM;
-	if ( l < 0 ) l += IDIM;
-
-	idx = h + (IDIM*k) + (IDIM*IDIM*l);
-	return ref[idx];
-}
-
-
-static inline TYPE *LABEL(new_list)(void)
-{
-	TYPE *r;
-	size_t r_size;
-	r_size = IDIM*IDIM*IDIM*sizeof(TYPE);
-	r = malloc(r_size);
-	memset(r, 0, r_size);
-	return r;
-}
-
-
-static inline void LABEL(zero_list)(TYPE *ref)
-{
-	memset(ref, 0, IDIM*IDIM*IDIM*sizeof(TYPE));
-}
-
-
-#undef LABEL
-#undef TYPE
-#undef ERROR_T
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index ad524c61..854db1d1 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -29,7 +29,6 @@
 #include "peaks.h"
 #include "detector.h"
 #include "filters.h"
-#include "diffraction.h"
 #include "reflist-utils.h"
 #include "beam-parameters.h"
 
diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index b64e9979..6e2f9c4a 100644
--- a/libcrystfel/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
@@ -34,76 +34,6 @@
  **/
 
 
-double *intensities_from_list(RefList *list)
-{
-	Reflection *refl;
-	RefListIterator *iter;
-	double *out = new_list_intensity();
-
-	for ( refl = first_refl(list, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) ) {
-
-		signed int h, k, l;
-		double intensity = get_intensity(refl);
-
-		get_indices(refl, &h, &k, &l);
-
-		set_intensity(out, h, k, l, intensity);
-
-	}
-
-	return out;
-}
-
-
-double *phases_from_list(RefList *list)
-{
-	Reflection *refl;
-	RefListIterator *iter;
-	double *out = new_list_phase();
-
-	for ( refl = first_refl(list, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) ) {
-
-		signed int h, k, l;
-		double phase = get_phase(refl, NULL);
-
-		get_indices(refl, &h, &k, &l);
-
-		set_phase(out, h, k, l, phase);
-
-	}
-
-	return out;
-
-}
-
-
-unsigned char *flags_from_list(RefList *list)
-{
-	Reflection *refl;
-	RefListIterator *iter;
-	unsigned char *out = new_list_flag();
-
-	for ( refl = first_refl(list, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) ) {
-
-		signed int h, k, l;
-
-		get_indices(refl, &h, &k, &l);
-
-		set_flag(out, h, k, l, 1);
-
-	}
-
-	return out;
-
-}
-
-
 int check_list_symmetry(RefList *list, const SymOpList *sym)
 {
 	Reflection *refl;
diff --git a/libcrystfel/src/reflist-utils.h b/libcrystfel/src/reflist-utils.h
index d14e5f8e..c451954b 100644
--- a/libcrystfel/src/reflist-utils.h
+++ b/libcrystfel/src/reflist-utils.h
@@ -33,10 +33,6 @@ extern RefList *read_reflections_from_file(FILE *fh);
 
 extern RefList *read_reflections(const char *filename);
 
-extern double *intensities_from_list(RefList *list);
-extern double *phases_from_list(RefList *list);
-extern unsigned char *flags_from_list(RefList *list);
-
 extern int check_list_symmetry(RefList *list, const SymOpList *sym);
 extern int find_equiv_in_list(RefList *list, signed int h, signed int k,
                               signed int l, const SymOpList *sym, signed int *hu,
diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h
index 1179a57f..7b8d8fa8 100644
--- a/libcrystfel/src/utils.h
+++ b/libcrystfel/src/utils.h
@@ -175,32 +175,6 @@ static inline int within_tolerance(double a, double b, double percent)
 
 #define UNUSED __attribute__((unused))
 
-/* -------------------- Indexed lists for specified types ------------------- */
-
-#include "defs.h"
-
-#define LIST_SIZE (IDIM*IDIM*IDIM)
-
-/* Create functions for storing reflection intensities indexed as h,k,l */
-#define LABEL(x) x##_intensity
-#define TYPE double
-#include "list_tmp.h"
-
-/* CAs above, but for phase values */
-#define LABEL(x) x##_phase
-#define TYPE double
-#include "list_tmp.h"
-
-/* As above, but for (unsigned) integer counts */
-#define LABEL(x) x##_count
-#define TYPE unsigned int
-#include "list_tmp.h"
-
-/* As above, but for simple flags */
-#define LABEL(x) x##_flag
-#define TYPE unsigned char
-#include "list_tmp.h"
-
 
 /* ------------------------------ Message macros ---------------------------- */