process_hkl: Placeholder for detwinning

5 files changed, 20 insertions, 7 deletions

diff --git a/Makefile.am b/Makefile.am
index 9b0d96f6..96fa0839 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -5,5 +5,5 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \
              data/displaywindow.ui src/dirax.h src/peaks.h src/index.h \
              src/filters.h src/diffraction-gpu.h src/cl-utils.h \
              data/defs.h src/parameters-lcls.tmp src/geometry-lcls.tmp \
-             data/diffraction.cl data/sfac
+             data/diffraction.cl data/sfac src/likelihood.h
 SUBDIRS = src data
diff --git a/Makefile.in b/Makefile.in
index e0b2d1a6..0a98e459 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -202,7 +202,7 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \
              data/displaywindow.ui src/dirax.h src/peaks.h src/index.h \
              src/filters.h src/diffraction-gpu.h src/cl-utils.h \
              data/defs.h src/parameters-lcls.tmp src/geometry-lcls.tmp \
-             data/diffraction.cl data/sfac
+             data/diffraction.cl data/sfac src/likelihood.h
 
 SUBDIRS = src data
 all: config.h
diff --git a/src/Makefile.am b/src/Makefile.am
index d1d2c274..9dbf685a 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -17,7 +17,7 @@ endif
 pattern_sim_LDADD = @LIBS@
 
 process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
-                      reflections.c
+                      reflections.c likelihood.c
 process_hkl_LDADD = @LIBS@
 
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
diff --git a/src/Makefile.in b/src/Makefile.in
index 008e248a..28146741 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -97,7 +97,7 @@ powder_plot_OBJECTS = $(am_powder_plot_OBJECTS)
 powder_plot_DEPENDENCIES =
 am_process_hkl_OBJECTS = process_hkl.$(OBJEXT) sfac.$(OBJEXT) \
 	statistics.$(OBJEXT) cell.$(OBJEXT) utils.$(OBJEXT) \
-	reflections.$(OBJEXT)
+	reflections.$(OBJEXT) likelihood.$(OBJEXT)
 process_hkl_OBJECTS = $(am_process_hkl_OBJECTS)
 process_hkl_DEPENDENCIES =
 am_render_hkl_OBJECTS = render_hkl.$(OBJEXT) cell.$(OBJEXT) \
@@ -232,7 +232,7 @@ pattern_sim_SOURCES = pattern_sim.c diffraction.c utils.c image.c \
 	$(am__append_2)
 pattern_sim_LDADD = @LIBS@
 process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
-                      reflections.c
+                      reflections.c likelihood.c
 
 process_hkl_LDADD = @LIBS@
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
@@ -373,6 +373,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/image.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/index.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/indexamajig.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/likelihood.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pattern_sim.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/peaks.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/powder_plot.Po@am__quote@
diff --git a/src/process_hkl.c b/src/process_hkl.c
index e76835a0..dfb84ee1 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -25,6 +25,7 @@
 #include "statistics.h"
 #include "sfac.h"
 #include "reflections.h"
+#include "likelihood.h"
 
 
 /* Number of divisions for R vs |q| graphs */
@@ -61,7 +62,11 @@ static void show_help(const char *s)
 "  -r, --rvsq                Output lists of R vs |q| (\"Luzzatti plots\")\n"
 "                             when analysing figures of merit.\n"
 "      --zone-axis           Output an [001] zone axis pattern each time the\n"
-"                             figures of merit are analysed.\n");
+"                             figures of merit are analysed.\n"
+"      --detwin              Correlate each new pattern with the current\n"
+"                             model and choose the best fitting out of the\n"
+"                             allowable twins.\n"
+);
 }
 
 
@@ -230,6 +235,7 @@ int main(int argc, char *argv[])
 	int config_stopafter = 0;
 	int config_zoneaxis = 0;
 	int config_sum = 0;
+	int config_detwin = 0;
 	char *intfile = NULL;
 	double *new_pattern = NULL;
 	unsigned int *new_counts = NULL;
@@ -246,7 +252,8 @@ int main(int argc, char *argv[])
 		{"stop-after",         1, NULL,               's'},
 		{"zone-axis",          0, &config_zoneaxis,    1},
 		{"compare-with",       0, NULL,               'c'},
-		{"sum",                0, &config_sum,    1},
+		{"sum",                0, &config_sum,         1},
+		{"detwin",             0, &config_detwin,      1},
 		{0, 0, NULL, 0}
 	};
 
@@ -362,6 +369,11 @@ int main(int argc, char *argv[])
 				continue;
 			}
 
+			if ( config_detwin ) {
+				detwin_intensities(model, new_pattern,
+				                   model_counts, new_counts);
+			}
+
 			/* Start of second or later pattern */
 			merge_pattern(model, new_pattern, model_counts,
 			              new_counts, config_maxonly, config_sum);