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authorThomas White <taw@physics.org>2019-10-24 15:30:27 +0200
committerThomas White <taw@physics.org>2019-10-24 15:38:43 +0200
commit70cb465c18a8b14796607fa32b2d945af500560b (patch)
tree5c7835431798a441825f1e883308decd69b556e8 /src
parent2dfc662ba054de3f7725bc6b2eafb85606931000 (diff)
get_hkl: Clean up resolution cutoffs and add --lowres
Diffstat (limited to 'src')
-rw-r--r--src/get_hkl.c101
1 files changed, 53 insertions, 48 deletions
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 2a17aab5..057a5ce7 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -84,6 +84,8 @@ static void show_help(const char *s)
"You can restrict which reflections are written out:\n"
" -t, --template=<filename> Only include reflections mentioned in file.\n"
" --cutoff-angstroms=<n> Only include reflections with d < n Angstroms.\n"
+" --highres=<n> Synonym for --cutoff-angstroms.\n"
+" --lowres=<n> Only include reflections with d > n Angstroms.\n"
"\n"
"You might sometimes need to do this:\n"
" --multiplicity Multiply intensities by the number of\n"
@@ -404,6 +406,37 @@ static RefList *trim_centrics(RefList *in, const SymOpList *sym)
}
+static RefList *apply_resolution_cutoff(RefList *input, double lowres,
+ double highres, UnitCell *cell)
+{
+ RefList *n;
+ Reflection *refl;
+ RefListIterator *iter;
+
+ n = reflist_new();
+ copy_notes(n, input);
+
+ for ( refl = first_refl(input, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ signed int h, k, l;
+ double res;
+ get_indices(refl, &h, &k, &l);
+ res = 2.0 * resolution(cell, h, k, l);
+ if ( (res < 1e10/highres) && (res > 1e10/lowres) ) {
+ Reflection *a;
+ a = add_refl(n, h, k, l);
+ copy_data(a, refl);
+ }
+ }
+
+ cell_free(cell);
+ reflist_free(input);
+ return n;
+}
+
+
int main(int argc, char *argv[])
{
int c;
@@ -425,14 +458,15 @@ int main(int argc, char *argv[])
RefList *input;
double adu_per_photon = 0.0;
int have_adu_per_photon = 0;
- int have_cutoff_iso = 0;
int have_cutoff_aniso = 0;
char *cutoff_str = NULL;
- double cutiso = 0.0;
float cutn1, cutn2, cutn3;
char *cellfile = NULL;
char *reindex_str = NULL;
SymOpList *reindex = NULL;
+ float lowres = 0.0;
+ double highres = INFINITY;
+ UnitCell *cell = NULL;
/* Long options */
const struct option longopts[] = {
@@ -452,7 +486,9 @@ int main(int argc, char *argv[])
{"no-need-all-parts", 0, &config_nap, 0},
{"adu-per-photon", 1, NULL, 2},
{"cutoff-angstroms", 1, NULL, 3},
+ {"highres", 1, NULL, 3},
{"reindex", 1, NULL, 4},
+ {"lowres", 1, NULL, 6},
{0, 0, NULL, 0}
};
@@ -512,6 +548,13 @@ int main(int argc, char *argv[])
reindex_str = strdup(optarg);
break;
+ case 6 :
+ if (sscanf(optarg, "%f", &lowres) != 1) {
+ ERROR("Invalid value for --lowres\n");
+ return 1;
+ }
+ break;
+
case 0 :
break;
@@ -538,19 +581,20 @@ int main(int argc, char *argv[])
/* Convert Angstroms -> m */
cutn1 /= 1e10; cutn2 /= 1e10; cutn3 /= 1e10;
+ /* Set isotropic cutoff to the largest */
+ highres = biggest(cutn1, biggest(cutn2, cutn3));
+
} else {
char *rval;
errno = 0;
- cutiso = strtod(cutoff_str, &rval);
+ highres = strtod(cutoff_str, &rval);
if ( *rval != '\0' ) {
ERROR("Invalid value for --cutoff-angstroms.\n");
return 1;
}
- have_cutoff_iso = 1;
-
}
free(cutoff_str);
@@ -729,16 +773,11 @@ int main(int argc, char *argv[])
}
- if ( have_cutoff_iso ) {
-
- RefList *n;
- Reflection *refl;
- RefListIterator *iter;
- UnitCell *cell;
+ if ( (highres < INFINITY) || have_cutoff_aniso || (lowres > 0.0) ) {
if ( cellfile == NULL ) {
ERROR("You must provide a unit cell when using "
- "--cutoff-angstroms.\n");
+ "--cutoff-angstroms, --highres or --lowres.\n");
return 1;
}
@@ -749,54 +788,20 @@ int main(int argc, char *argv[])
}
free(cellfile);
- n = reflist_new();
- copy_notes(n, input);
-
- for ( refl = first_refl(input, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) )
- {
- signed int h, k, l;
- double res;
- get_indices(refl, &h, &k, &l);
- res = 2.0 * resolution(cell, h, k, l);
- if ( res < 1e10 / cutiso ) {
- Reflection *a;
- a = add_refl(n, h, k, l);
- copy_data(a, refl);
- }
- }
-
- cell_free(cell);
- reflist_free(input);
- input = n;
-
}
+ input = apply_resolution_cutoff(input, lowres, highres, cell);
+
if ( have_cutoff_aniso ) {
RefList *n;
Reflection *refl;
RefListIterator *iter;
- UnitCell *cell;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
double as, bs, cs;
- if ( cellfile == NULL ) {
- ERROR("You must provide a unit cell when using "
- "--cutoff-angstroms.\n");
- return 1;
- }
-
- cell = load_cell_from_file(cellfile);
- if ( cell == NULL ) {
- ERROR("Failed to load cell from '%s'\n", cellfile);
- return 1;
- }
- free(cellfile);
-
cell_get_reciprocal(cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);