Add new program: get_hkl, for generating ideal intensity lists

7 files changed, 205 insertions, 73 deletions

diff --git a/.gitignore b/.gitignore
index 2e09d144..0ca4d405 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,4 +11,5 @@ src/*.o
 src/.deps
 src/pattern_sim
 src/process_hkl
+src/get_hkl
 *~
diff --git a/Makefile.am b/Makefile.am
index 604c2a15..b5e1b3fe 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,4 +1,4 @@
 EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h src/relrod.h \
              src/utils.h src/diffraction.h src/detector.h src/ewald.h \
-             src/sfac.h src/intensities.h
+             src/sfac.h src/intensities.h src/reflections.h
 SUBDIRS = src
diff --git a/src/Makefile.am b/src/Makefile.am
index efaf09a8..81b52045 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,10 +1,15 @@
-bin_PROGRAMS = pattern_sim process_hkl
+bin_PROGRAMS = pattern_sim process_hkl get_hkl
 
 AM_CFLAGS = -Wall
 
 pattern_sim_SOURCES = pattern_sim.c diffraction.c utils.c image.c cell.c \
-                      hdf5-file.c ewald.c detector.c sfac.c intensities.c
+                      hdf5-file.c ewald.c detector.c sfac.c intensities.c \
+                      reflections.c
 pattern_sim_LDADD = @LIBS@
 
-process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c
+process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
+                      reflections.c
 process_hkl_LDADD = @LIBS@
+
+get_hkl_SOURCES = get_hkl.c sfac.c cell.c utils.c reflections.c
+get_hkl_LDADD = @LIBS@
diff --git a/src/get_hkl.c b/src/get_hkl.c
new file mode 100644
index 00000000..907a47d4
--- /dev/null
+++ b/src/get_hkl.c
@@ -0,0 +1,78 @@
+/*
+ * get_hkl.c
+ *
+ * Small program to write out a list of h,k,l,I values given a structure
+ *
+ * (c) 2006-2009 Thomas White <thomas.white@desy.de>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <getopt.h>
+
+#include "utils.h"
+#include "sfac.h"
+#include "reflections.h"
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s [options]\n\n", s);
+	printf(
+"Write idealised intensity lists.\n"
+"\n"
+"  -h, --help              Display this help message.\n");
+}
+
+
+int main(int argc, char *argv[])
+{
+	int c;
+	double *ref;
+	struct molecule *mol;
+
+	/* Long options */
+	const struct option longopts[] = {
+		{"help",               0, NULL,               'h'},
+		{0, 0, NULL, 0}
+	};
+
+	/* Short options */
+	while ((c = getopt_long(argc, argv, "hi:e:r", longopts, NULL)) != -1) {
+
+		switch (c) {
+		case 'h' : {
+			show_help(argv[0]);
+			return 0;
+		}
+
+		case 0 : {
+			break;
+		}
+
+		default : {
+			return 1;
+		}
+		}
+
+	}
+
+	mol = load_molecule();
+	get_reflections_cached(mol, eV_to_J(2.0e3));
+	ref = ideal_intensities(mol->reflections);
+	write_reflections("results/ideal-reflections.hkl", NULL, ref, 1,
+	                  mol->cell);
+
+	return 0;
+}
diff --git a/src/process_hkl.c b/src/process_hkl.c
index aed9856e..9142d5c7 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -24,6 +24,7 @@
 #include "utils.h"
 #include "statistics.h"
 #include "sfac.h"
+#include "reflections.h"
 
 
 /* Number of divisions for R vs |q| graphs */
@@ -124,72 +125,6 @@ static void write_RvsQ(const char *name, double *ref, double *trueref,
 }
 
 
-static void write_reflections(const char *filename, unsigned int *counts,
-                              double *ref, int zone_axis, UnitCell *cell)
-{
-	FILE *fh;
-	signed int h, k, l;
-
-	fh = fopen(filename, "w");
-
-	/* Write spacings and angle if zone axis pattern */
-	if ( zone_axis ) {
-		double a, b, c, alpha, beta, gamma;
-		cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
-		fprintf(fh, "a %5.3f nm\n", a*1e9);
-		fprintf(fh, "b %5.3f nm\n", b*1e9);
-		fprintf(fh, "angle %5.3f deg\n", rad2deg(gamma));
-		fprintf(fh, "scale 10\n");
-	}
-
-	for ( h=-INDMAX; h<INDMAX; h++ ) {
-	for ( k=-INDMAX; k<INDMAX; k++ ) {
-	for ( l=-INDMAX; l<INDMAX; l++ ) {
-
-		int N;
-		double F;
-
-		if ( counts ) {
-			N = lookup_count(counts, h, k, l);
-			if ( N == 0 ) continue;
-		} else {
-			N = 1;
-		}
-
-		F = lookup_intensity(ref, h, k, l) / N;
-		if ( zone_axis && (l != 0) ) continue;
-
-		fprintf(fh, "%3i %3i %3i %f\n", h, k, l, F);
-
-	}
-	}
-	}
-	fclose(fh);
-}
-
-
-static double *ideal_intensities(double complex *sfac)
-{
-	double *ref;
-	signed int h, k, l;
-
-	ref = new_list_intensity();
-
-	/* Generate ideal reflections from complex structure factors */
-	for ( h=-INDMAX; h<=INDMAX; h++ ) {
-	for ( k=-INDMAX; k<=INDMAX; k++ ) {
-	for ( l=-INDMAX; l<=INDMAX; l++ ) {
-		double complex F = lookup_sfac(sfac, h, k, l);
-		double intensity = pow(cabs(F), 2.0);
-		set_intensity(ref, h, k, l, intensity);
-	}
-	}
-	}
-
-	return ref;
-}
-
-
 static void process_reflections(double *ref, double *trueref,
                                 unsigned int *counts, unsigned int n_patterns,
                                 UnitCell *cell, int do_rvsq, int do_zoneaxis)
@@ -315,9 +250,6 @@ int main(int argc, char *argv[])
 	counts = new_list_count();
 	trueref = ideal_intensities(mol->reflections);
 
-	write_reflections("results/ideal-reflections.hkl", NULL, trueref, 1,
-	                  mol->cell);
-
 	if ( strcmp(filename, "-") == 0 ) {
 		fh = stdin;
 	} else {
diff --git a/src/reflections.c b/src/reflections.c
new file mode 100644
index 00000000..5790b543
--- /dev/null
+++ b/src/reflections.c
@@ -0,0 +1,87 @@
+/*
+ * reflections.c
+ *
+ * Utilities for handling reflections
+ *
+ * (c) 2007-2009 Thomas White <thomas.white@desy.de>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#include <stdlib.h>
+#include <math.h>
+#include <stdio.h>
+#include <complex.h>
+#include <string.h>
+
+#include "utils.h"
+#include "cell.h"
+#include "reflections.h"
+
+
+void write_reflections(const char *filename, unsigned int *counts,
+                       double *ref, int zone_axis, UnitCell *cell)
+{
+	FILE *fh;
+	signed int h, k, l;
+
+	fh = fopen(filename, "w");
+
+	/* Write spacings and angle if zone axis pattern */
+	if ( zone_axis ) {
+		double a, b, c, alpha, beta, gamma;
+		cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
+		fprintf(fh, "a %5.3f nm\n", a*1e9);
+		fprintf(fh, "b %5.3f nm\n", b*1e9);
+		fprintf(fh, "angle %5.3f deg\n", rad2deg(gamma));
+		fprintf(fh, "scale 10\n");
+	}
+
+	for ( h=-INDMAX; h<INDMAX; h++ ) {
+	for ( k=-INDMAX; k<INDMAX; k++ ) {
+	for ( l=-INDMAX; l<INDMAX; l++ ) {
+
+		int N;
+		double F;
+
+		if ( counts ) {
+			N = lookup_count(counts, h, k, l);
+			if ( N == 0 ) continue;
+		} else {
+			N = 1;
+		}
+
+		F = lookup_intensity(ref, h, k, l) / N;
+		if ( zone_axis && (l != 0) ) continue;
+
+		fprintf(fh, "%3i %3i %3i %f\n", h, k, l, F);
+
+	}
+	}
+	}
+	fclose(fh);
+}
+
+
+double *ideal_intensities(double complex *sfac)
+{
+	double *ref;
+	signed int h, k, l;
+
+	ref = new_list_intensity();
+
+	/* Generate ideal reflections from complex structure factors */
+	for ( h=-INDMAX; h<=INDMAX; h++ ) {
+	for ( k=-INDMAX; k<=INDMAX; k++ ) {
+	for ( l=-INDMAX; l<=INDMAX; l++ ) {
+		double complex F = lookup_sfac(sfac, h, k, l);
+		double intensity = pow(cabs(F), 2.0);
+		set_intensity(ref, h, k, l, intensity);
+	}
+	}
+	}
+
+	return ref;
+}
diff --git a/src/reflections.h b/src/reflections.h
new file mode 100644
index 00000000..ac35ae1e
--- /dev/null
+++ b/src/reflections.h
@@ -0,0 +1,29 @@
+/*
+ * reflections.h
+ *
+ * Utilities for handling reflections
+ *
+ * (c) 2007-2009 Thomas White <thomas.white@desy.de>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifndef REFLECTIONS_H
+#define REFLECTIONS_H
+
+
+#include "cell.h"
+
+
+extern void write_reflections(const char *filename, unsigned int *counts,
+                              double *ref, int zone_axis, UnitCell *cell);
+
+extern double *ideal_intensities(double complex *sfac);
+
+
+#endif	/* REFLECTIONS_H */