Move indexing and rendering to libcrystfel

16 files changed, 45 insertions, 46 deletions

diff --git a/Makefile.am b/Makefile.am
index b119e288..53321656 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -42,11 +42,10 @@ endif
 
 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
+src_indexamajig_SOURCES = src/indexamajig.c
 
 if BUILD_HDFSEE
-src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c
+src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c
 endif
 
 src_get_hkl_SOURCES = src/get_hkl.c
@@ -57,7 +56,7 @@ 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_render_hkl_SOURCES = src/render_hkl.c src/povray.c
 
 src_sum_stack_SOURCES = src/sum_stack.c
 
@@ -82,10 +81,9 @@ tests_pr_gradient_check_SOURCES = tests/pr_gradient_check.c \
 
 INCLUDES = -I$(top_srcdir)/libcrystfel/src -I$(top_srcdir)/data
 
-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 \
+EXTRA_DIST += src/dw-hdfsee.h src/hdfsee.h src/povray.h \
               src/render_hkl.h src/post-refinement.h src/hrs-scaling.h \
-              src/scaling-report.h src/reax.h
+              src/scaling-report.h
 
 crystfeldir = $(datadir)/crystfel
 crystfel_DATA = data/diffraction.cl data/defs.h data/hdfsee.ui
diff --git a/Makefile.in b/Makefile.in
index e054cd4b..bffe2b0d 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -114,18 +114,14 @@ src_get_hkl_OBJECTS = $(am_src_get_hkl_OBJECTS)
 src_get_hkl_LDADD = $(LDADD)
 src_get_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
 	$(top_builddir)/libcrystfel/libcrystfel.la
-am__src_hdfsee_SOURCES_DIST = src/hdfsee.c src/dw-hdfsee.c \
-	src/render.c
+am__src_hdfsee_SOURCES_DIST = src/hdfsee.c src/dw-hdfsee.c
 @BUILD_HDFSEE_TRUE@am_src_hdfsee_OBJECTS = src/hdfsee.$(OBJEXT) \
-@BUILD_HDFSEE_TRUE@	src/dw-hdfsee.$(OBJEXT) \
-@BUILD_HDFSEE_TRUE@	src/render.$(OBJEXT)
+@BUILD_HDFSEE_TRUE@	src/dw-hdfsee.$(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/index.$(OBJEXT) src/dirax.$(OBJEXT) src/mosflm.$(OBJEXT) \
-	src/reax.$(OBJEXT)
+am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT)
 src_indexamajig_OBJECTS = $(am_src_indexamajig_OBJECTS)
 src_indexamajig_LDADD = $(LDADD)
 src_indexamajig_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
@@ -161,7 +157,7 @@ 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/povray.$(OBJEXT) src/render.$(OBJEXT)
+	src/povray.$(OBJEXT)
 src_render_hkl_OBJECTS = $(am_src_render_hkl_OBJECTS)
 src_render_hkl_LDADD = $(LDADD)
 src_render_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a \
@@ -551,11 +547,10 @@ 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/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 $(crystfel_DATA) \
-	doc/twin-calculator.pdf doc/examples/lcls-dec.geom \
+	src/dw-hdfsee.h src/hdfsee.h src/povray.h src/render_hkl.h \
+	src/post-refinement.h src/hrs-scaling.h src/scaling-report.h \
+	$(crystfel_DATA) doc/twin-calculator.pdf \
+	doc/examples/lcls-dec.geom \
 	doc/examples/lcls-june-r0013-r0128.geom \
 	doc/examples/lcls-xpp-estimate.geom doc/examples/simple.geom \
 	doc/examples/lcls-dec.beam doc/examples/lcls-june.beam \
@@ -579,15 +574,13 @@ src_partial_sim_SOURCES = src/partial_sim.c
 src_pattern_sim_SOURCES = src/pattern_sim.c
 @HAVE_OPENCL_TRUE@tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c
 src_process_hkl_SOURCES = src/process_hkl.c
-src_indexamajig_SOURCES = src/indexamajig.c src/index.c src/dirax.c \
-                          src/mosflm.c src/reax.c
-
-@BUILD_HDFSEE_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c
+src_indexamajig_SOURCES = src/indexamajig.c
+@BUILD_HDFSEE_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c
 src_get_hkl_SOURCES = src/get_hkl.c
 src_compare_hkl_SOURCES = src/compare_hkl.c
 src_check_hkl_SOURCES = src/check_hkl.c
 src_powder_plot_SOURCES = src/powder_plot.c
-src_render_hkl_SOURCES = src/render_hkl.c src/povray.c src/render.c
+src_render_hkl_SOURCES = src/render_hkl.c src/povray.c
 src_sum_stack_SOURCES = src/sum_stack.c
 src_calibrate_detector_SOURCES = src/calibrate_detector.c
 src_partialator_SOURCES = src/partialator.c src/post-refinement.c \
@@ -763,18 +756,11 @@ src/hdfsee.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/dw-hdfsee.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/render.$(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)/$(am__dirstamp)
-src/dirax.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
-src/mosflm.$(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)
 	$(AM_V_CCLD)$(LINK) $(src_indexamajig_OBJECTS) $(src_indexamajig_LDADD) $(LIBS)
@@ -858,14 +844,11 @@ mostlyclean-compile:
 	-rm -f src/calibrate_detector.$(OBJEXT)
 	-rm -f src/check_hkl.$(OBJEXT)
 	-rm -f src/compare_hkl.$(OBJEXT)
-	-rm -f src/dirax.$(OBJEXT)
 	-rm -f src/dw-hdfsee.$(OBJEXT)
 	-rm -f src/get_hkl.$(OBJEXT)
 	-rm -f src/hdfsee.$(OBJEXT)
 	-rm -f src/hrs-scaling.$(OBJEXT)
-	-rm -f src/index.$(OBJEXT)
 	-rm -f src/indexamajig.$(OBJEXT)
-	-rm -f src/mosflm.$(OBJEXT)
 	-rm -f src/partial_sim.$(OBJEXT)
 	-rm -f src/partialator.$(OBJEXT)
 	-rm -f src/pattern_sim.$(OBJEXT)
@@ -873,8 +856,6 @@ mostlyclean-compile:
 	-rm -f src/povray.$(OBJEXT)
 	-rm -f src/powder_plot.$(OBJEXT)
 	-rm -f src/process_hkl.$(OBJEXT)
-	-rm -f src/reax.$(OBJEXT)
-	-rm -f src/render.$(OBJEXT)
 	-rm -f src/render_hkl.$(OBJEXT)
 	-rm -f src/scaling-report.$(OBJEXT)
 	-rm -f src/sum_stack.$(OBJEXT)
@@ -890,14 +871,11 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(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)/compare_hkl.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/$(DEPDIR)/get_hkl.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hdfsee.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hrs-scaling.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/index.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/indexamajig.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/mosflm.Po@am__quote@
 @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/$(DEPDIR)/pattern_sim.Po@am__quote@
@@ -905,8 +883,6 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(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)/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/$(DEPDIR)/sum_stack.Po@am__quote@
diff --git a/configure b/configure
index 7689717f..860ad20e 100755
--- a/configure
+++ b/configure
@@ -14231,7 +14231,7 @@ fi
 if test "${with_html_dir+set}" = set; then :
   withval=$with_html_dir;
 else
-  with_html_dir='${docdir}/reference'
+  with_html_dir='${datadir}/gtk-doc/html'
 fi
 
   HTML_DIR="$with_html_dir"
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 00428a1f..576044a6 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -4,7 +4,8 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.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/diffraction-gpu.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 \
@@ -14,6 +15,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/diffraction-gpu.h \
                                  src/cl-utils.h src/filters.h src/list_tmp.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
 
 INCLUDES = "-I$(top_srcdir)/data"
diff --git a/libcrystfel/Makefile.in b/libcrystfel/Makefile.in
index 7d27bd59..a0b527e4 100644
--- a/libcrystfel/Makefile.in
+++ b/libcrystfel/Makefile.in
@@ -89,7 +89,8 @@ am_libcrystfel_la_OBJECTS = src/reflist.lo src/utils.lo src/cell.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/diffraction-gpu.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))
@@ -351,7 +352,8 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.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/diffraction-gpu.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 \
@@ -361,6 +363,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/diffraction-gpu.h \
                                  src/cl-utils.h src/filters.h src/list_tmp.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
 
 INCLUDES = "-I$(top_srcdir)/data"
@@ -458,6 +461,11 @@ src/diffraction.lo: src/$(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)
+src/dirax.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/mosflm.lo: src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/reax.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)
 
@@ -475,6 +483,8 @@ mostlyclean-compile:
 	-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.$(OBJEXT)
 	-rm -f src/filters.lo
 	-rm -f src/geometry.$(OBJEXT)
@@ -483,12 +493,20 @@ mostlyclean-compile:
 	-rm -f src/hdf5-file.lo
 	-rm -f src/image.$(OBJEXT)
 	-rm -f src/image.lo
+	-rm -f src/index.$(OBJEXT)
+	-rm -f src/index.lo
+	-rm -f src/mosflm.$(OBJEXT)
+	-rm -f src/mosflm.lo
 	-rm -f src/peaks.$(OBJEXT)
 	-rm -f src/peaks.lo
+	-rm -f src/reax.$(OBJEXT)
+	-rm -f src/reax.lo
 	-rm -f src/reflist-utils.$(OBJEXT)
 	-rm -f src/reflist-utils.lo
 	-rm -f src/reflist.$(OBJEXT)
 	-rm -f src/reflist.lo
+	-rm -f src/render.$(OBJEXT)
+	-rm -f src/render.lo
 	-rm -f src/statistics.$(OBJEXT)
 	-rm -f src/statistics.lo
 	-rm -f src/stream.$(OBJEXT)
@@ -509,13 +527,18 @@ distclean-compile:
 @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@
 @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/$(DEPDIR)/index.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/mosflm.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/peaks.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reax.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/$(DEPDIR)/render.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(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@
diff --git a/src/dirax.c b/libcrystfel/src/dirax.c
index bb1cb808..bb1cb808 100644
--- a/src/dirax.c
+++ b/libcrystfel/src/dirax.c
diff --git a/src/dirax.h b/libcrystfel/src/dirax.h
index 8c429710..8c429710 100644
--- a/src/dirax.h
+++ b/libcrystfel/src/dirax.h
diff --git a/src/index-priv.h b/libcrystfel/src/index-priv.h
index 3d8c8a22..3d8c8a22 100644
--- a/src/index-priv.h
+++ b/libcrystfel/src/index-priv.h
diff --git a/src/index.c b/libcrystfel/src/index.c
index d5e76c50..d5e76c50 100644
--- a/src/index.c
+++ b/libcrystfel/src/index.c
diff --git a/src/index.h b/libcrystfel/src/index.h
index 9d4b69bd..9d4b69bd 100644
--- a/src/index.h
+++ b/libcrystfel/src/index.h
diff --git a/src/mosflm.c b/libcrystfel/src/mosflm.c
index 5df5af21..5df5af21 100644
--- a/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
diff --git a/src/mosflm.h b/libcrystfel/src/mosflm.h
index 82b80a44..82b80a44 100644
--- a/src/mosflm.h
+++ b/libcrystfel/src/mosflm.h
diff --git a/src/reax.c b/libcrystfel/src/reax.c
index ff1ea582..ff1ea582 100644
--- a/src/reax.c
+++ b/libcrystfel/src/reax.c
diff --git a/src/reax.h b/libcrystfel/src/reax.h
index 543cd0d5..543cd0d5 100644
--- a/src/reax.h
+++ b/libcrystfel/src/reax.h
diff --git a/src/render.c b/libcrystfel/src/render.c
index dbaca2fd..dbaca2fd 100644
--- a/src/render.c
+++ b/libcrystfel/src/render.c
diff --git a/src/render.h b/libcrystfel/src/render.h
index fbfbbdb2..fbfbbdb2 100644
--- a/src/render.h
+++ b/libcrystfel/src/render.h