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-rw-r--r--src/reflections.c83
1 files changed, 34 insertions, 49 deletions
diff --git a/src/reflections.c b/src/reflections.c
index bd9b446d..0ab7a91e 100644
--- a/src/reflections.c
+++ b/src/reflections.c
@@ -21,12 +21,12 @@
#include "reflections.h"
-void write_reflections(const char *filename, unsigned int *counts,
- double *ref, double *phases, int zone_axis,
- UnitCell *cell, unsigned int min_counts)
+void write_reflections(const char *filename, ReflItemList *items,
+ double *intensities, double *phases,
+ unsigned int *counts, UnitCell *cell)
{
FILE *fh;
- signed int h, k, l;
+ int i;
if ( filename == NULL ) {
fh = stdout;
@@ -40,23 +40,16 @@ void write_reflections(const char *filename, unsigned int *counts,
}
/* 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",
- (0.5/resolution(cell, 1, 0, 0))*1e9);
- fprintf(fh, "b %5.3f nm\n",
- (0.5/resolution(cell, 0, 1, 0))*1e9);
- fprintf(fh, "angle %5.3f deg\n", rad2deg(alpha));
- fprintf(fh, "scale 10\n");
- } else {
- fprintf(fh, " h k l I phase sigma(I) "
- " 1/d(nm^-1) counts\n");
- }
+ fprintf(fh, " h k l I phase sigma(I) "
+ " 1/d(nm^-1) counts\n");
+
+ for ( i=0; i<num_items(items); i++ ) {
+
+ struct refl_item *it;
+ signed int h, k, l;
- for ( h=-INDMAX; h<INDMAX; h++ ) {
- for ( k=-INDMAX; k<INDMAX; k++ ) {
- for ( l=-INDMAX; l<INDMAX; l++ ) {
+ it = get_item(items, i);
+ h = it->h; k = it->k; l = it->l;
int N;
double intensity, s;
@@ -64,14 +57,12 @@ void write_reflections(const char *filename, unsigned int *counts,
if ( counts ) {
N = lookup_count(counts, h, k, l);
- if ( N < min_counts ) continue;
} else {
N = 1;
}
- if ( zone_axis && (l != 0) ) continue;
- /* Divide measured intensity by the number of counts */
- intensity = lookup_intensity(ref, h, k, l) / N;
+ intensity = lookup_intensity(intensities, h, k, l);
+
if ( phases != NULL ) {
double p;
p = lookup_phase(phases, h, k, l);
@@ -91,18 +82,25 @@ void write_reflections(const char *filename, unsigned int *counts,
h, k, l, intensity, ph, 0.0, s/1.0e9, N);
}
- }
- }
fclose(fh);
}
-double *read_reflections(const char *filename, unsigned int *counts,
- double *phases)
+/* Read reflections from file. Returns the list of reflections successfully
+ * read in. "intensities", "phases" and "counts" are lists which will be
+ * populated with the values read from the file. Existing values in either list
+ * will be overwritten if the reflection is read from the file, but other values
+ * will be left intact.
+ *
+ * "intensities", "phases" or "counts" can be NULL, if you don't need them.
+ */
+ReflItemList *read_reflections(const char *filename,
+ double *intensities, double *phases,
+ unsigned int *counts)
{
- double *ref;
FILE *fh;
char *rval;
+ ReflItemList *items;
fh = fopen(filename, "r");
if ( fh == NULL ) {
@@ -110,7 +108,7 @@ double *read_reflections(const char *filename, unsigned int *counts,
return NULL;
}
- ref = new_list_intensity();
+ items = new_items();
do {
@@ -147,24 +145,24 @@ double *read_reflections(const char *filename, unsigned int *counts,
continue;
}
- set_intensity(ref, h, k, l, intensity);
+ add_item(items, h, k, l);
+
+ if ( intensities != NULL ) {
+ set_intensity(intensities, h, k, l, intensity);
+ }
if ( phases != NULL ) {
ph = atof(phs);
set_phase(phases, h, k, l, ph);
}
if ( counts != NULL ) {
set_count(counts, h, k, l, cts);
- /* In this case, the intensity must be multiplied up
- * because other parts of the program will try to
- * divide it down. */
- set_intensity(ref, h, k, l, intensity*(double)cts);
}
} while ( rval != NULL );
fclose(fh);
- return ref;
+ return items;
}
@@ -188,16 +186,3 @@ double *ideal_intensities(double complex *sfac)
return ref;
}
-
-
-void divide_down(double *intensities, unsigned int *counts)
-{
- int i;
-
- for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
- if ( counts[i] > 0 ) {
- intensities[i] /= (double)counts[i];
- counts[i] = 1;
- }
- }
-}