Introduce "libcrystfel"

1 files changed, 53 insertions, 114 deletions

diff --git a/Makefile.am b/Makefile.am
index 8104eb02..28eb179e 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,12 +1,11 @@
 EXTRA_DIST = configure m4/gnulib-cache.m4
-SUBDIRS = lib doc/reference
+SUBDIRS = lib doc/reference libcrystfel
 ACLOCAL_AMFLAGS = -I m4
 
 bin_PROGRAMS = src/pattern_sim src/process_hkl src/get_hkl src/indexamajig \
                src/compare_hkl src/powder_plot src/render_hkl \
                src/calibrate_detector src/partialator \
-               src/check_hkl src/sum_stack src/partial_sim \
-               contrib/alter_stream
+               src/check_hkl src/sum_stack src/partial_sim
 
 noinst_PROGRAMS = tests/list_check tests/integration_check \
                   tests/pr_gradient_check tests/symmetry_check
@@ -25,149 +24,89 @@ if BUILD_HDFSEE
 bin_PROGRAMS += src/hdfsee
 endif
 
-if BUILD_CUBEIT
-bin_PROGRAMS += contrib/cubeit
-endif
-
 AM_CFLAGS = -Wall
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib
 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/cell.c src/detector.c \
-                          src/beam-parameters.c src/thread-pool.c src/utils.c \
-                          src/reflist-utils.c src/reflist.c src/symmetry.c \
-                          src/hdf5-file.c src/image.c src/geometry.c \
-                          src/peaks.c src/stream.c
-
-src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c src/utils.c \
-                          src/image.c src/cell.c src/hdf5-file.c \
-                          src/detector.c src/peaks.c \
-                          src/reflist-utils.c src/beam-parameters.c \
-                          src/symmetry.c src/thread-pool.c src/reflist.c
+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
 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/utils.c \
-                              src/diffraction.c src/diffraction-gpu.c \
-                              src/thread-pool.c src/cell.c src/cl-utils.c \
-                              src/symmetry.c src/detector.c src/hdf5-file.c \
-                              src/image.c
+tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c  src/diffraction.c \
+                              src/diffraction-gpu.c src/cl-utils.c \
+                              src/symmetry.c
 endif
 
-src_process_hkl_SOURCES = src/process_hkl.c src/statistics.c \
-                          src/cell.c src/utils.c \
-                          src/symmetry.c src/stream.c src/beam-parameters.c \
-                          src/thread-pool.c src/image.c src/detector.c \
-                          src/hdf5-file.c src/reflist.c src/reflist-utils.c
-
-src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c src/utils.c \
-                          src/cell.c src/image.c src/peaks.c src/index.c \
-                          src/filters.c src/diffraction.c src/detector.c \
-                          src/dirax.c src/mosflm.c \
-                          src/reflist-utils.c src/symmetry.c \
-                          src/geometry.c src/thread-pool.c \
-                          src/beam-parameters.c src/reflist.c src/stream.c \
-                          src/reax.c
-
-if HAVE_OPENCL
-src_indexamajig_SOURCES += src/diffraction-gpu.c src/cl-utils.c
-endif
+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
 
 if BUILD_HDFSEE
-src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c \
-                     src/hdf5-file.c src/utils.c src/image.c src/filters.c \
-                     src/thread-pool.c src/detector.c
+src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c src/filters.c
 endif
 
-src_get_hkl_SOURCES = src/get_hkl.c src/cell.c src/utils.c \
-                      src/reflist-utils.c src/symmetry.c src/beam-parameters.c \
-                      src/thread-pool.c src/reflist.c
-
-src_compare_hkl_SOURCES = src/compare_hkl.c src/cell.c src/utils.c \
-                          src/reflist-utils.c src/statistics.c src/symmetry.c \
-                          src/thread-pool.c src/reflist.c
-
-src_check_hkl_SOURCES = src/check_hkl.c src/cell.c src/utils.c \
-                        src/reflist-utils.c src/statistics.c src/symmetry.c \
-                        src/thread-pool.c src/reflist.c
-
-src_powder_plot_SOURCES = src/powder_plot.c src/cell.c src/utils.c src/image.c \
-                          src/hdf5-file.c src/detector.c src/thread-pool.c \
-                          src/reflist-utils.c src/beam-parameters.c src/stream.c \
-                          src/reflist.c src/symmetry.c
-
-src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflist-utils.c \
-                         src/utils.c src/povray.c src/symmetry.c src/render.c \
-                         src/hdf5-file.c src/image.c src/filters.c \
-                         src/thread-pool.c src/reflist.c src/detector.c
-
-src_sum_stack_SOURCES = src/sum_stack.c src/utils.c src/hdf5-file.c \
-                        src/image.c src/filters.c src/peaks.c src/detector.c \
-                        src/cell.c src/thread-pool.c src/reflist.c
-
-src_calibrate_detector_SOURCES = src/calibrate_detector.c src/utils.c \
-                                 src/hdf5-file.c src/image.c src/thread-pool.c \
-                                 src/detector.c src/stream.c src/cell.c \
-                                 src/reflist-utils.c src/reflist.c \
-                                 src/symmetry.c src/peaks.c
-
-src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
-                          src/utils.c src/detector.c src/peaks.c src/image.c \
-                          src/geometry.c src/reflist-utils.c src/stream.c \
-                          src/thread-pool.c src/beam-parameters.c \
-                          src/symmetry.c src/post-refinement.c \
-                          src/hrs-scaling.c src/reflist.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
 
 if HAVE_CAIRO
 src_partialator_SOURCES += src/scaling-report.c
 endif
 
-if BUILD_CUBEIT
-contrib_cubeit_SOURCES = contrib/cubeit.c src/cell.c src/hdf5-file.c \
-                     src/utils.c src/detector.c src/render.c src/filters.c \
-                     src/image.c src/symmetry.c src/stream.c src/thread-pool.c \
-                     src/reflist.c src/reflist-utils.c
-endif
-
-contrib_alter_stream_SOURCES = contrib/alter_stream.c src/stream.c src/image.c \
-                               src/thread-pool.c src/detector.c src/utils.c \
-                               src/cell.c src/reflist-utils.c src/reflist.c \
-                               src/symmetry.c src/hdf5-file.c \
-                               src/beam-parameters.c src/geometry.c src/peaks.c
-
-tests_list_check_SOURCES = tests/list_check.c src/reflist.c src/thread-pool.c \
-                           src/utils.c
+tests_list_check_SOURCES = tests/list_check.c
 
-tests_integration_check_SOURCES = tests/integration_check.c src/peaks.c \
-                                  src/reflist.c src/cell.c src/detector.c \
-                                  src/thread-pool.c src/utils.c src/image.c \
-                                  src/hdf5-file.c
+tests_integration_check_SOURCES = tests/integration_check.c src/peaks.c
 
-tests_symmetry_check_SOURCES = tests/symmetry_check.c src/symmetry.c \
-                               src/utils.c src/thread-pool.c
+tests_symmetry_check_SOURCES = tests/symmetry_check.c src/symmetry.c
 
 
-tests_pr_gradient_check_SOURCES = tests/pr_gradient_check.c src/detector.c \
-                                  src/cell.c src/geometry.c src/reflist.c \
-                                  src/thread-pool.c src/utils.c src/peaks.c \
-                                  src/symmetry.c src/image.c src/hdf5-file.c \
-                                  src/post-refinement.c
+tests_pr_gradient_check_SOURCES = tests/pr_gradient_check.c src/peaks.c \
+                                  src/symmetry.c src/post-refinement.c \
+                                  src/geometry.c
 
-INCLUDES = "-I$(top_srcdir)/data"
+INCLUDES = -I$(top_srcdir)/libcrystfel/src -I$(top_srcdir)/data
 
-EXTRA_DIST += src/cell.h src/hdf5-file.h src/image.h src/utils.h \
-              src/diffraction.h src/detector.h src/reflist-utils.h \
-              src/list_tmp.h src/statistics.h src/dw-hdfsee.h \
+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/thread-pool.h \
-              src/beam-parameters.h src/post-refinement.h src/hrs-scaling.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
 
 crystfeldir = $(datadir)/crystfel