Move a load more stuff into libcrystfel

25 files changed, 136 insertions, 209 deletions

diff --git a/Makefile.am b/Makefile.am
index 28eb179e..b119e288 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -30,58 +30,41 @@ AM_CPPFLAGS += -I$(top_srcdir)/lib
 LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
 LDADD += $(top_builddir)/libcrystfel/libcrystfel.la
 
-src_partial_sim_SOURCES = src/partial_sim.c src/reflist-utils.c src/symmetry.c \
-                          src/geometry.c src/peaks.c src/stream.c
+src_partial_sim_SOURCES = src/partial_sim.c
 
-src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c src/peaks.c \
-                          src/reflist-utils.c src/symmetry.c
+src_pattern_sim_SOURCES = src/pattern_sim.c
 if HAVE_OPENCL
-src_pattern_sim_SOURCES += src/diffraction-gpu.c src/cl-utils.c
-
 TESTS += tests/gpu_sim_check
 noinst_PROGRAMS += tests/gpu_sim_check
 
-tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c  src/diffraction.c \
-                              src/diffraction-gpu.c src/cl-utils.c \
-                              src/symmetry.c
+tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c
 endif
 
-src_process_hkl_SOURCES = src/process_hkl.c src/statistics.c src/symmetry.c \
-                          src/stream.c src/reflist-utils.c
+src_process_hkl_SOURCES = src/process_hkl.c
 
-src_indexamajig_SOURCES = src/indexamajig.c src/peaks.c src/index.c \
-                          src/filters.c src/diffraction.c src/dirax.c \
-                          src/mosflm.c src/reflist-utils.c src/symmetry.c \
-                          src/geometry.c src/stream.c src/reax.c
+src_indexamajig_SOURCES = src/indexamajig.c src/index.c src/dirax.c \
+                          src/mosflm.c src/reax.c
 
 if BUILD_HDFSEE
-src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c src/filters.c
+src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c
 endif
 
-src_get_hkl_SOURCES = src/get_hkl.c src/reflist-utils.c src/symmetry.c
+src_get_hkl_SOURCES = src/get_hkl.c
 
-src_compare_hkl_SOURCES = src/compare_hkl.c  src/reflist-utils.c \
-                          src/statistics.c src/symmetry.c
+src_compare_hkl_SOURCES = src/compare_hkl.c
 
-src_check_hkl_SOURCES = src/check_hkl.c src/reflist-utils.c src/statistics.c \
-                        src/symmetry.c
+src_check_hkl_SOURCES = src/check_hkl.c
 
-src_powder_plot_SOURCES = src/powder_plot.c src/reflist-utils.c src/stream.c \
-                          src/symmetry.c
+src_powder_plot_SOURCES = src/powder_plot.c
 
-src_render_hkl_SOURCES = src/render_hkl.c src/reflist-utils.c src/povray.c \
-                         src/symmetry.c src/render.c src/filters.c
+src_render_hkl_SOURCES = src/render_hkl.c src/povray.c src/render.c
 
-src_sum_stack_SOURCES = src/sum_stack.c src/filters.c src/peaks.c
+src_sum_stack_SOURCES = src/sum_stack.c
 
-src_calibrate_detector_SOURCES = src/calibrate_detector.c src/stream.c \
-                                 src/reflist-utils.c src/symmetry.c \
-                                 src/peaks.c
+src_calibrate_detector_SOURCES = src/calibrate_detector.c
 
-src_partialator_SOURCES = src/partialator.c src/peaks.c src/geometry.c \
-                          src/reflist-utils.c src/stream.c \
-                          src/symmetry.c \
-                          src/post-refinement.c src/hrs-scaling.c
+src_partialator_SOURCES = src/partialator.c src/post-refinement.c \
+                          src/hrs-scaling.c
 
 if HAVE_CAIRO
 src_partialator_SOURCES += src/scaling-report.c
@@ -89,25 +72,20 @@ endif
 
 tests_list_check_SOURCES = tests/list_check.c
 
-tests_integration_check_SOURCES = tests/integration_check.c src/peaks.c
+tests_integration_check_SOURCES = tests/integration_check.c
 
-tests_symmetry_check_SOURCES = tests/symmetry_check.c src/symmetry.c
+tests_symmetry_check_SOURCES = tests/symmetry_check.c
 
 
-tests_pr_gradient_check_SOURCES = tests/pr_gradient_check.c src/peaks.c \
-                                  src/symmetry.c src/post-refinement.c \
-                                  src/geometry.c
+tests_pr_gradient_check_SOURCES = tests/pr_gradient_check.c \
+                                  src/post-refinement.c
 
 INCLUDES = -I$(top_srcdir)/libcrystfel/src -I$(top_srcdir)/data
 
-EXTRA_DIST += src/diffraction.h src/reflist-utils.h \
-              src/statistics.h src/dw-hdfsee.h \
-              src/render.h src/hdfsee.h src/dirax.h src/mosflm.h src/peaks.h \
-              src/index.h src/filters.h src/diffraction-gpu.h src/cl-utils.h \
-              src/symmetry.h src/povray.h src/index-priv.h src/geometry.h \
-              src/render_hkl.h src/stream.h \
-              src/post-refinement.h src/hrs-scaling.h \
-              src/reflist.h src/scaling-report.h src/reax.h
+EXTRA_DIST += src/dw-hdfsee.h src/render.h src/hdfsee.h src/dirax.h \
+              src/mosflm.h src/index.h src/povray.h src/index-priv.h \
+              src/render_hkl.h src/post-refinement.h src/hrs-scaling.h \
+              src/scaling-report.h src/reax.h
 
 crystfeldir = $(datadir)/crystfel
 crystfel_DATA = data/diffraction.cl data/defs.h data/hdfsee.ui
diff --git a/Makefile.in b/Makefile.in
index 12969762..e054cd4b 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -52,10 +52,9 @@ TESTS = tests/list_check$(EXEEXT) tests/first_merge_check \
 	tests/pr_gradient_check$(EXEEXT) tests/symmetry_check$(EXEEXT) \
 	$(am__EXEEXT_2)
 @BUILD_HDFSEE_TRUE@am__append_1 = src/hdfsee
-@HAVE_OPENCL_TRUE@am__append_2 = src/diffraction-gpu.c src/cl-utils.c
+@HAVE_OPENCL_TRUE@am__append_2 = tests/gpu_sim_check
 @HAVE_OPENCL_TRUE@am__append_3 = tests/gpu_sim_check
-@HAVE_OPENCL_TRUE@am__append_4 = tests/gpu_sim_check
-@HAVE_CAIRO_TRUE@am__append_5 = src/scaling-report.c
+@HAVE_CAIRO_TRUE@am__append_4 = src/scaling-report.c
 subdir = .
 DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
 	$(srcdir)/Makefile.in $(srcdir)/config.h.in \
@@ -92,9 +91,7 @@ am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(man1dir)" \
 @HAVE_OPENCL_TRUE@am__EXEEXT_2 = tests/gpu_sim_check$(EXEEXT)
 PROGRAMS = $(bin_PROGRAMS) $(noinst_PROGRAMS)
 am__dirstamp = $(am__leading_dot)dirstamp
-am_src_calibrate_detector_OBJECTS = src/calibrate_detector.$(OBJEXT) \
-	src/stream.$(OBJEXT) src/reflist-utils.$(OBJEXT) \
-	src/symmetry.$(OBJEXT) src/peaks.$(OBJEXT)
+am_src_calibrate_detector_OBJECTS = src/calibrate_detector.$(OBJEXT)
 src_calibrate_detector_OBJECTS = $(am_src_calibrate_detector_OBJECTS)
 src_calibrate_detector_LDADD = $(LDADD)
 src_calibrate_detector_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
@@ -102,122 +99,87 @@ src_calibrate_detector_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 AM_V_lt = $(am__v_lt_$(V))
 am__v_lt_ = $(am__v_lt_$(AM_DEFAULT_VERBOSITY))
 am__v_lt_0 = --silent
-am_src_check_hkl_OBJECTS = src/check_hkl.$(OBJEXT) \
-	src/reflist-utils.$(OBJEXT) src/statistics.$(OBJEXT) \
-	src/symmetry.$(OBJEXT)
+am_src_check_hkl_OBJECTS = src/check_hkl.$(OBJEXT)
 src_check_hkl_OBJECTS = $(am_src_check_hkl_OBJECTS)
 src_check_hkl_LDADD = $(LDADD)
 src_check_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am_src_compare_hkl_OBJECTS = src/compare_hkl.$(OBJEXT) \
-	src/reflist-utils.$(OBJEXT) src/statistics.$(OBJEXT) \
-	src/symmetry.$(OBJEXT)
+am_src_compare_hkl_OBJECTS = src/compare_hkl.$(OBJEXT)
 src_compare_hkl_OBJECTS = $(am_src_compare_hkl_OBJECTS)
 src_compare_hkl_LDADD = $(LDADD)
 src_compare_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am_src_get_hkl_OBJECTS = src/get_hkl.$(OBJEXT) \
-	src/reflist-utils.$(OBJEXT) src/symmetry.$(OBJEXT)
+am_src_get_hkl_OBJECTS = src/get_hkl.$(OBJEXT)
 src_get_hkl_OBJECTS = $(am_src_get_hkl_OBJECTS)
 src_get_hkl_LDADD = $(LDADD)
 src_get_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
 am__src_hdfsee_SOURCES_DIST = src/hdfsee.c src/dw-hdfsee.c \
-	src/render.c src/filters.c
+	src/render.c
 @BUILD_HDFSEE_TRUE@am_src_hdfsee_OBJECTS = src/hdfsee.$(OBJEXT) \
 @BUILD_HDFSEE_TRUE@	src/dw-hdfsee.$(OBJEXT) \
-@BUILD_HDFSEE_TRUE@	src/render.$(OBJEXT) src/filters.$(OBJEXT)
+@BUILD_HDFSEE_TRUE@	src/render.$(OBJEXT)
 src_hdfsee_OBJECTS = $(am_src_hdfsee_OBJECTS)
 src_hdfsee_LDADD = $(LDADD)
 src_hdfsee_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
 am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT) \
-	src/peaks.$(OBJEXT) src/index.$(OBJEXT) src/filters.$(OBJEXT) \
-	src/diffraction.$(OBJEXT) src/dirax.$(OBJEXT) \
-	src/mosflm.$(OBJEXT) src/reflist-utils.$(OBJEXT) \
-	src/symmetry.$(OBJEXT) src/geometry.$(OBJEXT) \
-	src/stream.$(OBJEXT) src/reax.$(OBJEXT)
+	src/index.$(OBJEXT) src/dirax.$(OBJEXT) src/mosflm.$(OBJEXT) \
+	src/reax.$(OBJEXT)
 src_indexamajig_OBJECTS = $(am_src_indexamajig_OBJECTS)
 src_indexamajig_LDADD = $(LDADD)
 src_indexamajig_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am_src_partial_sim_OBJECTS = src/partial_sim.$(OBJEXT) \
-	src/reflist-utils.$(OBJEXT) src/symmetry.$(OBJEXT) \
-	src/geometry.$(OBJEXT) src/peaks.$(OBJEXT) \
-	src/stream.$(OBJEXT)
+am_src_partial_sim_OBJECTS = src/partial_sim.$(OBJEXT)
 src_partial_sim_OBJECTS = $(am_src_partial_sim_OBJECTS)
 src_partial_sim_LDADD = $(LDADD)
 src_partial_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am__src_partialator_SOURCES_DIST = src/partialator.c src/peaks.c \
-	src/geometry.c src/reflist-utils.c src/stream.c src/symmetry.c \
+am__src_partialator_SOURCES_DIST = src/partialator.c \
 	src/post-refinement.c src/hrs-scaling.c src/scaling-report.c
 @HAVE_CAIRO_TRUE@am__objects_1 = src/scaling-report.$(OBJEXT)
 am_src_partialator_OBJECTS = src/partialator.$(OBJEXT) \
-	src/peaks.$(OBJEXT) src/geometry.$(OBJEXT) \
-	src/reflist-utils.$(OBJEXT) src/stream.$(OBJEXT) \
-	src/symmetry.$(OBJEXT) src/post-refinement.$(OBJEXT) \
-	src/hrs-scaling.$(OBJEXT) $(am__objects_1)
+	src/post-refinement.$(OBJEXT) src/hrs-scaling.$(OBJEXT) \
+	$(am__objects_1)
 src_partialator_OBJECTS = $(am_src_partialator_OBJECTS)
 src_partialator_LDADD = $(LDADD)
 src_partialator_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am__src_pattern_sim_SOURCES_DIST = src/pattern_sim.c src/diffraction.c \
-	src/peaks.c src/reflist-utils.c src/symmetry.c \
-	src/diffraction-gpu.c src/cl-utils.c
-@HAVE_OPENCL_TRUE@am__objects_2 = src/diffraction-gpu.$(OBJEXT) \
-@HAVE_OPENCL_TRUE@	src/cl-utils.$(OBJEXT)
-am_src_pattern_sim_OBJECTS = src/pattern_sim.$(OBJEXT) \
-	src/diffraction.$(OBJEXT) src/peaks.$(OBJEXT) \
-	src/reflist-utils.$(OBJEXT) src/symmetry.$(OBJEXT) \
-	$(am__objects_2)
+am_src_pattern_sim_OBJECTS = src/pattern_sim.$(OBJEXT)
 src_pattern_sim_OBJECTS = $(am_src_pattern_sim_OBJECTS)
 src_pattern_sim_LDADD = $(LDADD)
 src_pattern_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am_src_powder_plot_OBJECTS = src/powder_plot.$(OBJEXT) \
-	src/reflist-utils.$(OBJEXT) src/stream.$(OBJEXT) \
-	src/symmetry.$(OBJEXT)
+am_src_powder_plot_OBJECTS = src/powder_plot.$(OBJEXT)
 src_powder_plot_OBJECTS = $(am_src_powder_plot_OBJECTS)
 src_powder_plot_LDADD = $(LDADD)
 src_powder_plot_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am_src_process_hkl_OBJECTS = src/process_hkl.$(OBJEXT) \
-	src/statistics.$(OBJEXT) src/symmetry.$(OBJEXT) \
-	src/stream.$(OBJEXT) src/reflist-utils.$(OBJEXT)
+am_src_process_hkl_OBJECTS = src/process_hkl.$(OBJEXT)
 src_process_hkl_OBJECTS = $(am_src_process_hkl_OBJECTS)
 src_process_hkl_LDADD = $(LDADD)
 src_process_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
 am_src_render_hkl_OBJECTS = src/render_hkl.$(OBJEXT) \
-	src/reflist-utils.$(OBJEXT) src/povray.$(OBJEXT) \
-	src/symmetry.$(OBJEXT) src/render.$(OBJEXT) \
-	src/filters.$(OBJEXT)
+	src/povray.$(OBJEXT) src/render.$(OBJEXT)
 src_render_hkl_OBJECTS = $(am_src_render_hkl_OBJECTS)
 src_render_hkl_LDADD = $(LDADD)
 src_render_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am_src_sum_stack_OBJECTS = src/sum_stack.$(OBJEXT) \
-	src/filters.$(OBJEXT) src/peaks.$(OBJEXT)
+am_src_sum_stack_OBJECTS = src/sum_stack.$(OBJEXT)
 src_sum_stack_OBJECTS = $(am_src_sum_stack_OBJECTS)
 src_sum_stack_LDADD = $(LDADD)
 src_sum_stack_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am__tests_gpu_sim_check_SOURCES_DIST = tests/gpu_sim_check.c \
-	src/diffraction.c src/diffraction-gpu.c src/cl-utils.c \
-	src/symmetry.c
+am__tests_gpu_sim_check_SOURCES_DIST = tests/gpu_sim_check.c
 @HAVE_OPENCL_TRUE@am_tests_gpu_sim_check_OBJECTS =  \
-@HAVE_OPENCL_TRUE@	tests/gpu_sim_check.$(OBJEXT) \
-@HAVE_OPENCL_TRUE@	src/diffraction.$(OBJEXT) \
-@HAVE_OPENCL_TRUE@	src/diffraction-gpu.$(OBJEXT) \
-@HAVE_OPENCL_TRUE@	src/cl-utils.$(OBJEXT) \
-@HAVE_OPENCL_TRUE@	src/symmetry.$(OBJEXT)
+@HAVE_OPENCL_TRUE@	tests/gpu_sim_check.$(OBJEXT)
 tests_gpu_sim_check_OBJECTS = $(am_tests_gpu_sim_check_OBJECTS)
 tests_gpu_sim_check_LDADD = $(LDADD)
 tests_gpu_sim_check_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
 am_tests_integration_check_OBJECTS =  \
-	tests/integration_check.$(OBJEXT) src/peaks.$(OBJEXT)
+	tests/integration_check.$(OBJEXT)
 tests_integration_check_OBJECTS =  \
 	$(am_tests_integration_check_OBJECTS)
 tests_integration_check_LDADD = $(LDADD)
@@ -229,16 +191,14 @@ tests_list_check_LDADD = $(LDADD)
 tests_list_check_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
 am_tests_pr_gradient_check_OBJECTS =  \
-	tests/pr_gradient_check.$(OBJEXT) src/peaks.$(OBJEXT) \
-	src/symmetry.$(OBJEXT) src/post-refinement.$(OBJEXT) \
-	src/geometry.$(OBJEXT)
+	tests/pr_gradient_check.$(OBJEXT) \
+	src/post-refinement.$(OBJEXT)
 tests_pr_gradient_check_OBJECTS =  \
 	$(am_tests_pr_gradient_check_OBJECTS)
 tests_pr_gradient_check_LDADD = $(LDADD)
 tests_pr_gradient_check_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am_tests_symmetry_check_OBJECTS = tests/symmetry_check.$(OBJEXT) \
-	src/symmetry.$(OBJEXT)
+am_tests_symmetry_check_OBJECTS = tests/symmetry_check.$(OBJEXT)
 tests_symmetry_check_OBJECTS = $(am_tests_symmetry_check_OBJECTS)
 tests_symmetry_check_LDADD = $(LDADD)
 tests_symmetry_check_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
@@ -283,10 +243,9 @@ DIST_SOURCES = $(src_calibrate_detector_SOURCES) \
 	$(src_check_hkl_SOURCES) $(src_compare_hkl_SOURCES) \
 	$(src_get_hkl_SOURCES) $(am__src_hdfsee_SOURCES_DIST) \
 	$(src_indexamajig_SOURCES) $(src_partial_sim_SOURCES) \
-	$(am__src_partialator_SOURCES_DIST) \
-	$(am__src_pattern_sim_SOURCES_DIST) $(src_powder_plot_SOURCES) \
-	$(src_process_hkl_SOURCES) $(src_render_hkl_SOURCES) \
-	$(src_sum_stack_SOURCES) \
+	$(am__src_partialator_SOURCES_DIST) $(src_pattern_sim_SOURCES) \
+	$(src_powder_plot_SOURCES) $(src_process_hkl_SOURCES) \
+	$(src_render_hkl_SOURCES) $(src_sum_stack_SOURCES) \
 	$(am__tests_gpu_sim_check_SOURCES_DIST) \
 	$(tests_integration_check_SOURCES) $(tests_list_check_SOURCES) \
 	$(tests_pr_gradient_check_SOURCES) \
@@ -592,13 +551,10 @@ EXTRA_DIST = configure m4/gnulib-cache.m4 tests/first_merge_check \
 	tests/second_merge_check tests/third_merge_check \
 	tests/fourth_merge_check tests/first_merge_check.hkl \
 	tests/third_merge_check.hkl tests/fourth_merge_check.hkl \
-	src/diffraction.h src/reflist-utils.h src/statistics.h \
 	src/dw-hdfsee.h src/render.h src/hdfsee.h src/dirax.h \
-	src/mosflm.h src/peaks.h src/index.h src/filters.h \
-	src/diffraction-gpu.h src/cl-utils.h src/symmetry.h \
-	src/povray.h src/index-priv.h src/geometry.h src/render_hkl.h \
-	src/stream.h src/post-refinement.h src/hrs-scaling.h \
-	src/reflist.h src/scaling-report.h src/reax.h $(crystfel_DATA) \
+	src/mosflm.h src/index.h src/povray.h src/index-priv.h \
+	src/render_hkl.h src/post-refinement.h src/hrs-scaling.h \
+	src/scaling-report.h src/reax.h $(crystfel_DATA) \
 	doc/twin-calculator.pdf doc/examples/lcls-dec.geom \
 	doc/examples/lcls-june-r0013-r0128.geom \
 	doc/examples/lcls-xpp-estimate.geom doc/examples/simple.geom \
@@ -619,51 +575,28 @@ AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib \
 	-I$(top_srcdir)/lib
 LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@ \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-src_partial_sim_SOURCES = src/partial_sim.c src/reflist-utils.c src/symmetry.c \
-                          src/geometry.c src/peaks.c src/stream.c
-
-src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
-	src/peaks.c src/reflist-utils.c src/symmetry.c $(am__append_2)
-@HAVE_OPENCL_TRUE@tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c  src/diffraction.c \
-@HAVE_OPENCL_TRUE@                              src/diffraction-gpu.c src/cl-utils.c \
-@HAVE_OPENCL_TRUE@                              src/symmetry.c
-
-src_process_hkl_SOURCES = src/process_hkl.c src/statistics.c src/symmetry.c \
-                          src/stream.c src/reflist-utils.c
-
-src_indexamajig_SOURCES = src/indexamajig.c src/peaks.c src/index.c \
-                          src/filters.c src/diffraction.c src/dirax.c \
-                          src/mosflm.c src/reflist-utils.c src/symmetry.c \
-                          src/geometry.c src/stream.c src/reax.c
-
-@BUILD_HDFSEE_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c src/filters.c
-src_get_hkl_SOURCES = src/get_hkl.c src/reflist-utils.c src/symmetry.c
-src_compare_hkl_SOURCES = src/compare_hkl.c  src/reflist-utils.c \
-                          src/statistics.c src/symmetry.c
-
-src_check_hkl_SOURCES = src/check_hkl.c src/reflist-utils.c src/statistics.c \
-                        src/symmetry.c
-
-src_powder_plot_SOURCES = src/powder_plot.c src/reflist-utils.c src/stream.c \
-                          src/symmetry.c
-
-src_render_hkl_SOURCES = src/render_hkl.c src/reflist-utils.c src/povray.c \
-                         src/symmetry.c src/render.c src/filters.c
-
-src_sum_stack_SOURCES = src/sum_stack.c src/filters.c src/peaks.c
-src_calibrate_detector_SOURCES = src/calibrate_detector.c src/stream.c \
-                                 src/reflist-utils.c src/symmetry.c \
-                                 src/peaks.c
-
-src_partialator_SOURCES = src/partialator.c src/peaks.c src/geometry.c \
-	src/reflist-utils.c src/stream.c src/symmetry.c \
-	src/post-refinement.c src/hrs-scaling.c $(am__append_5)
+src_partial_sim_SOURCES = src/partial_sim.c
+src_pattern_sim_SOURCES = src/pattern_sim.c
+@HAVE_OPENCL_TRUE@tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c
+src_process_hkl_SOURCES = src/process_hkl.c
+src_indexamajig_SOURCES = src/indexamajig.c src/index.c src/dirax.c \
+                          src/mosflm.c src/reax.c
+
+@BUILD_HDFSEE_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c
+src_get_hkl_SOURCES = src/get_hkl.c
+src_compare_hkl_SOURCES = src/compare_hkl.c
+src_check_hkl_SOURCES = src/check_hkl.c
+src_powder_plot_SOURCES = src/powder_plot.c
+src_render_hkl_SOURCES = src/render_hkl.c src/povray.c src/render.c
+src_sum_stack_SOURCES = src/sum_stack.c
+src_calibrate_detector_SOURCES = src/calibrate_detector.c
+src_partialator_SOURCES = src/partialator.c src/post-refinement.c \
+	src/hrs-scaling.c $(am__append_4)
 tests_list_check_SOURCES = tests/list_check.c
-tests_integration_check_SOURCES = tests/integration_check.c src/peaks.c
-tests_symmetry_check_SOURCES = tests/symmetry_check.c src/symmetry.c
-tests_pr_gradient_check_SOURCES = tests/pr_gradient_check.c src/peaks.c \
-                                  src/symmetry.c src/post-refinement.c \
-                                  src/geometry.c
+tests_integration_check_SOURCES = tests/integration_check.c
+tests_symmetry_check_SOURCES = tests/symmetry_check.c
+tests_pr_gradient_check_SOURCES = tests/pr_gradient_check.c \
+                                  src/post-refinement.c
 
 INCLUDES = -I$(top_srcdir)/libcrystfel/src -I$(top_srcdir)/data
 crystfeldir = $(datadir)/crystfel
@@ -808,20 +741,11 @@ src/$(DEPDIR)/$(am__dirstamp):
 	@: > src/$(DEPDIR)/$(am__dirstamp)
 src/calibrate_detector.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/stream.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
-src/reflist-utils.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
-src/symmetry.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
-src/peaks.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/calibrate_detector$(EXEEXT): $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/calibrate_detector$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_LDADD) $(LIBS)
 src/check_hkl.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/statistics.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
 src/check_hkl$(EXEEXT): $(src_check_hkl_OBJECTS) $(src_check_hkl_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/check_hkl$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(src_check_hkl_OBJECTS) $(src_check_hkl_LDADD) $(LIBS)
@@ -841,21 +765,15 @@ src/dw-hdfsee.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/render.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/filters.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
 src/hdfsee$(EXEEXT): $(src_hdfsee_OBJECTS) $(src_hdfsee_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/hdfsee$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(src_hdfsee_OBJECTS) $(src_hdfsee_LDADD) $(LIBS)
 src/indexamajig.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/index.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
-src/diffraction.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
 src/dirax.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/mosflm.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/geometry.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
 src/reax.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/indexamajig$(EXEEXT): $(src_indexamajig_OBJECTS) $(src_indexamajig_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/indexamajig$(EXEEXT)
@@ -878,10 +796,6 @@ src/partialator$(EXEEXT): $(src_partialator_OBJECTS) $(src_partialator_DEPENDENC
 	$(AM_V_CCLD)$(LINK) $(src_partialator_OBJECTS) $(src_partialator_LDADD) $(LIBS)
 src/pattern_sim.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/diffraction-gpu.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
-src/cl-utils.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
 src/pattern_sim$(EXEEXT): $(src_pattern_sim_OBJECTS) $(src_pattern_sim_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/pattern_sim$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(src_pattern_sim_OBJECTS) $(src_pattern_sim_LDADD) $(LIBS)
@@ -943,14 +857,9 @@ mostlyclean-compile:
 	-rm -f *.$(OBJEXT)
 	-rm -f src/calibrate_detector.$(OBJEXT)
 	-rm -f src/check_hkl.$(OBJEXT)
-	-rm -f src/cl-utils.$(OBJEXT)
 	-rm -f src/compare_hkl.$(OBJEXT)
-	-rm -f src/diffraction-gpu.$(OBJEXT)
-	-rm -f src/diffraction.$(OBJEXT)
 	-rm -f src/dirax.$(OBJEXT)
 	-rm -f src/dw-hdfsee.$(OBJEXT)
-	-rm -f src/filters.$(OBJEXT)
-	-rm -f src/geometry.$(OBJEXT)
 	-rm -f src/get_hkl.$(OBJEXT)
 	-rm -f src/hdfsee.$(OBJEXT)
 	-rm -f src/hrs-scaling.$(OBJEXT)
@@ -960,20 +869,15 @@ mostlyclean-compile:
 	-rm -f src/partial_sim.$(OBJEXT)
 	-rm -f src/partialator.$(OBJEXT)
 	-rm -f src/pattern_sim.$(OBJEXT)
-	-rm -f src/peaks.$(OBJEXT)
 	-rm -f src/post-refinement.$(OBJEXT)
 	-rm -f src/povray.$(OBJEXT)
 	-rm -f src/powder_plot.$(OBJEXT)
 	-rm -f src/process_hkl.$(OBJEXT)
 	-rm -f src/reax.$(OBJEXT)
-	-rm -f src/reflist-utils.$(OBJEXT)
 	-rm -f src/render.$(OBJEXT)
 	-rm -f src/render_hkl.$(OBJEXT)
 	-rm -f src/scaling-report.$(OBJEXT)
-	-rm -f src/statistics.$(OBJEXT)
-	-rm -f src/stream.$(OBJEXT)
 	-rm -f src/sum_stack.$(OBJEXT)
-	-rm -f src/symmetry.$(OBJEXT)
 	-rm -f tests/gpu_sim_check.$(OBJEXT)
 	-rm -f tests/integration_check.$(OBJEXT)
 	-rm -f tests/list_check.$(OBJEXT)
@@ -985,14 +889,9 @@ distclean-compile:
 
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/calibrate_detector.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/check_hkl.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cl-utils.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/compare_hkl.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction-gpu.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/dirax.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/dw-hdfsee.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/filters.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/geometry.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/get_hkl.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hdfsee.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hrs-scaling.Po@am__quote@
@@ -1002,20 +901,15 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/partial_sim.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/partialator.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/pattern_sim.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/peaks.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/post-refinement.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/povray.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/powder_plot.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/process_hkl.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reax.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflist-utils.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render_hkl.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/scaling-report.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/statistics.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/stream.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/sum_stack.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/symmetry.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@tests/$(DEPDIR)/gpu_sim_check.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@tests/$(DEPDIR)/integration_check.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@tests/$(DEPDIR)/list_check.Po@am__quote@
diff --git a/configure b/configure
index 860ad20e..7689717f 100755
--- a/configure
+++ b/configure
@@ -14231,7 +14231,7 @@ fi
 if test "${with_html_dir+set}" = set; then :
   withval=$with_html_dir;
 else
-  with_html_dir='${datadir}/gtk-doc/html'
+  with_html_dir='${docdir}/reference'
 fi
 
   HTML_DIR="$with_html_dir"
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index daf2ef33..304eb7bb 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -1,5 +1,11 @@
 lib_LTLIBRARIES        = libcrystfel.la
 libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/thread-pool.c src/image.c src/hdf5-file.c \
-                         src/beam-parameters.c
+                         src/beam-parameters.c src/geometry.c src/statistics.c \
+                         src/symmetry.c src/stream.c src/peaks.c \
+                         src/reflist-utils.c src/filters.c src/diffraction.c \
+                         src/diffraction-gpu.c src/cl-utils.c
+
 INCLUDES = "-I$(top_srcdir)/data"
+AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib
+AM_CPPFLAGS += -I$(top_srcdir)/lib
diff --git a/libcrystfel/Makefile.in b/libcrystfel/Makefile.in
index 3465345d..9464b1e6 100644
--- a/libcrystfel/Makefile.in
+++ b/libcrystfel/Makefile.in
@@ -83,7 +83,10 @@ libcrystfel_la_LIBADD =
 am__dirstamp = $(am__leading_dot)dirstamp
 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/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
 libcrystfel_la_OBJECTS = $(am_libcrystfel_la_OBJECTS)
 AM_V_lt = $(am__v_lt_$(V))
 am__v_lt_ = $(am__v_lt_$(AM_DEFAULT_VERBOSITY))
@@ -341,9 +344,14 @@ top_srcdir = @top_srcdir@
 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/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
 
 INCLUDES = "-I$(top_srcdir)/data"
+AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib \
+	-I$(top_srcdir)/lib
 all: all-am
 
 .SUFFIXES:
@@ -424,6 +432,18 @@ src/image.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/hdf5-file.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/beam-parameters.lo: src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/geometry.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/statistics.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/symmetry.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/stream.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/peaks.lo: src/$(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)
 libcrystfel.la: $(libcrystfel_la_OBJECTS) $(libcrystfel_la_DEPENDENCIES) 
 	$(AM_V_CCLD)$(LINK) -rpath $(libdir) $(libcrystfel_la_OBJECTS) $(libcrystfel_la_LIBADD) $(LIBS)
 
@@ -433,14 +453,34 @@ mostlyclean-compile:
 	-rm -f src/beam-parameters.lo
 	-rm -f src/cell.$(OBJEXT)
 	-rm -f src/cell.lo
+	-rm -f src/cl-utils.$(OBJEXT)
+	-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.$(OBJEXT)
+	-rm -f src/diffraction.lo
+	-rm -f src/filters.$(OBJEXT)
+	-rm -f src/filters.lo
+	-rm -f src/geometry.$(OBJEXT)
+	-rm -f src/geometry.lo
 	-rm -f src/hdf5-file.$(OBJEXT)
 	-rm -f src/hdf5-file.lo
 	-rm -f src/image.$(OBJEXT)
 	-rm -f src/image.lo
+	-rm -f src/peaks.$(OBJEXT)
+	-rm -f src/peaks.lo
+	-rm -f src/reflist-utils.$(OBJEXT)
+	-rm -f src/reflist-utils.lo
 	-rm -f src/reflist.$(OBJEXT)
 	-rm -f src/reflist.lo
+	-rm -f src/statistics.$(OBJEXT)
+	-rm -f src/statistics.lo
+	-rm -f src/stream.$(OBJEXT)
+	-rm -f src/stream.lo
+	-rm -f src/symmetry.$(OBJEXT)
+	-rm -f src/symmetry.lo
 	-rm -f src/thread-pool.$(OBJEXT)
 	-rm -f src/thread-pool.lo
 	-rm -f src/utils.$(OBJEXT)
@@ -451,10 +491,20 @@ distclean-compile:
 
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/beam-parameters.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(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/$(DEPDIR)/filters.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/geometry.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hdf5-file.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/image.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/peaks.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflist-utils.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflist.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/statistics.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/stream.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/symmetry.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/thread-pool.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/utils.Plo@am__quote@
 
diff --git a/src/cl-utils.c b/libcrystfel/src/cl-utils.c
index 65a09363..65a09363 100644
--- a/src/cl-utils.c
+++ b/libcrystfel/src/cl-utils.c
diff --git a/src/cl-utils.h b/libcrystfel/src/cl-utils.h
index 21a7ecd2..21a7ecd2 100644
--- a/src/cl-utils.h
+++ b/libcrystfel/src/cl-utils.h
diff --git a/src/diffraction-gpu.c b/libcrystfel/src/diffraction-gpu.c
index 605b1514..605b1514 100644
--- a/src/diffraction-gpu.c
+++ b/libcrystfel/src/diffraction-gpu.c
diff --git a/src/diffraction-gpu.h b/libcrystfel/src/diffraction-gpu.h
index a3bde4e1..a3bde4e1 100644
--- a/src/diffraction-gpu.h
+++ b/libcrystfel/src/diffraction-gpu.h
diff --git a/src/diffraction.c b/libcrystfel/src/diffraction.c
index 9532a6ce..9532a6ce 100644
--- a/src/diffraction.c
+++ b/libcrystfel/src/diffraction.c
diff --git a/src/diffraction.h b/libcrystfel/src/diffraction.h
index f71d3cce..f71d3cce 100644
--- a/src/diffraction.h
+++ b/libcrystfel/src/diffraction.h
diff --git a/src/filters.c b/libcrystfel/src/filters.c
index c4e409df..c4e409df 100644
--- a/src/filters.c
+++ b/libcrystfel/src/filters.c
diff --git a/src/filters.h b/libcrystfel/src/filters.h
index 6b35d7e8..6b35d7e8 100644
--- a/src/filters.h
+++ b/libcrystfel/src/filters.h
diff --git a/src/geometry.c b/libcrystfel/src/geometry.c
index 485abba3..485abba3 100644
--- a/src/geometry.c
+++ b/libcrystfel/src/geometry.c
diff --git a/src/geometry.h b/libcrystfel/src/geometry.h
index ddf04b80..ddf04b80 100644
--- a/src/geometry.h
+++ b/libcrystfel/src/geometry.h
diff --git a/src/peaks.c b/libcrystfel/src/peaks.c
index f1a58d23..ad524c61 100644
--- a/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -26,7 +26,6 @@
 
 #include "image.h"
 #include "utils.h"
-#include "index.h"
 #include "peaks.h"
 #include "detector.h"
 #include "filters.h"
diff --git a/src/peaks.h b/libcrystfel/src/peaks.h
index 9d475ea9..9d475ea9 100644
--- a/src/peaks.h
+++ b/libcrystfel/src/peaks.h
diff --git a/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index b64e9979..b64e9979 100644
--- a/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
diff --git a/src/reflist-utils.h b/libcrystfel/src/reflist-utils.h
index d14e5f8e..d14e5f8e 100644
--- a/src/reflist-utils.h
+++ b/libcrystfel/src/reflist-utils.h
diff --git a/src/statistics.c b/libcrystfel/src/statistics.c
index 7990672d..7990672d 100644
--- a/src/statistics.c
+++ b/libcrystfel/src/statistics.c
diff --git a/src/statistics.h b/libcrystfel/src/statistics.h
index 8fa78ea6..8fa78ea6 100644
--- a/src/statistics.h
+++ b/libcrystfel/src/statistics.h
diff --git a/src/stream.c b/libcrystfel/src/stream.c
index a7cdc2d9..a7cdc2d9 100644
--- a/src/stream.c
+++ b/libcrystfel/src/stream.c
diff --git a/src/stream.h b/libcrystfel/src/stream.h
index ba218fb9..ba218fb9 100644
--- a/src/stream.h
+++ b/libcrystfel/src/stream.h
diff --git a/src/symmetry.c b/libcrystfel/src/symmetry.c
index f0b24146..f0b24146 100644
--- a/src/symmetry.c
+++ b/libcrystfel/src/symmetry.c
diff --git a/src/symmetry.h b/libcrystfel/src/symmetry.h
index 071ebbde..071ebbde 100644
--- a/src/symmetry.h
+++ b/libcrystfel/src/symmetry.h