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-rw-r--r--doc/man/partialator.118
-rw-r--r--src/partialator.c61
-rw-r--r--src/post-refinement.c105
-rw-r--r--src/post-refinement.h4
4 files changed, 128 insertions, 60 deletions
diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index 980af00f..1a598e89 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -1,7 +1,7 @@
.\"
.\" partialator man page
.\"
-.\" Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
.\" a research centre of the Helmholtz Association.
.\"
.\" Part of CrystFEL - crystallography with a FEL
@@ -137,6 +137,20 @@ Write out the per-crystal parameters and reflection lists after every cycle of r
.PD
Do not write the extensive log files needed for plotting contour maps and spectrum graphs. This makes the process a lot faster, but you probably do want these logs to check that post-refinement is working reasonably.
+.PD 0
+.IP "\fB-w\fR \fIpg\fR"
+.PD
+Set the apparent symmetry of the crystals. The ambiguity operator will be determined by comparing this to the actual symmetry.
+.IP
+If you prefer (or the scenario demands it), you can specify the ambiguity operator directly using \fB--operator\fR.
+
+.PD 0
+.IP \fB--operator=\fR\fIop\fR
+.PD
+Specify the indexing ambiguity operator. Example: \fB--operator=k,h,-l\fR.
+.IP
+If you prefer, you can specify the ambiguity operator by specifying the apparent symmetry using \fB-w\fR.
+
.SH PARTIALITY MODELS
The available partiality models are:
@@ -221,7 +235,7 @@ This page was written by Thomas White.
Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
.SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
.P
partialator, and this manual, are part of CrystFEL.
.P
diff --git a/src/partialator.c b/src/partialator.c
index 5c751732..baab84c4 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -327,7 +327,9 @@ static void show_help(const char *s)
" --no-free Disable cross-validation (testing only).\n"
" --custom-split List of files for custom dataset splitting.\n"
" --max-rel-B Maximum allowable relative |B| factor.\n"
-" --no-logs Do not write extensive log files.\n");
+" --no-logs Do not write extensive log files.\n"
+" -w <pg> Apparent point group for resolving ambiguities.\n"
+" --operator=<op> Indexing ambiguity operator for resolving.\n");
}
@@ -820,6 +822,8 @@ int main(int argc, char *argv[])
char *outfile = NULL;
char *sym_str = NULL;
SymOpList *sym;
+ SymOpList *amb;
+ SymOpList *w_sym;
int nthreads = 1;
int i;
int n_iter = 10;
@@ -852,6 +856,8 @@ int main(int argc, char *argv[])
char *rfile = NULL;
RefList *reference = NULL;
int no_logs = 0;
+ char *w_sym_str = NULL;
+ char *operator = NULL;
/* Long options */
const struct option longopts[] = {
@@ -875,6 +881,7 @@ int main(int argc, char *argv[])
{"max-rel-B", 1, NULL, 7},
{"max-rel-b", 1, NULL, 7}, /* compat */
{"reference", 1, NULL, 8}, /* ssshhh! */
+ {"operator", 1, NULL, 9},
{"no-scale", 0, &no_scale, 1},
{"no-pr", 0, &no_pr, 1},
@@ -896,7 +903,7 @@ int main(int argc, char *argv[])
}
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:o:g:b:y:n:j:m:",
+ while ((c = getopt_long(argc, argv, "hi:o:g:b:y:n:j:m:w:",
longopts, NULL)) != -1)
{
@@ -955,6 +962,10 @@ int main(int argc, char *argv[])
pmodel_str = strdup(optarg);
break;
+ case 'w' :
+ w_sym_str = strdup(optarg);
+ break;
+
case 2 :
errno = 0;
min_measurements = strtod(optarg, &rval);
@@ -1005,6 +1016,10 @@ int main(int argc, char *argv[])
rfile = strdup(optarg);
break;
+ case 9 :
+ operator = strdup(optarg);
+ break;
+
case 0 :
break;
@@ -1044,6 +1059,44 @@ int main(int argc, char *argv[])
free(sym_str);
if ( sym == NULL ) return 1;
+ if ( (w_sym_str != NULL) && (operator != NULL) ) {
+ ERROR("Specify the apparent symmetry (-w) or the operator, "
+ "not both.\n");
+ return 1;
+ }
+
+ if ( w_sym_str == NULL ) {
+ w_sym = NULL;
+ amb = NULL;
+ } else {
+ pointgroup_warning(w_sym_str);
+ w_sym = get_pointgroup(w_sym_str);
+ free(w_sym_str);
+ if ( w_sym == NULL ) return 1;
+ amb = get_ambiguities(w_sym, sym);
+ if ( amb == NULL ) {
+ ERROR("Couldn't find ambiguity operator.\n");
+ ERROR("Check that your values for -y and -w are "
+ "correct.\n");
+ return 1;
+ }
+
+ }
+
+ if ( operator ) {
+ amb = parse_symmetry_operations(operator);
+ if ( amb == NULL ) return 1;
+ set_symmetry_name(amb, "Ambiguity");
+ }
+
+ if ( amb != NULL ) {
+ STATUS("Indexing ambiguity resolution enabled. "
+ "The ambiguity operation(s) are:\n");
+ describe_symmetry(amb);
+ /* In contrast to ambigator, partialator can deal with multiple
+ * ambiguities at once */
+ }
+
if ( pmodel_str != NULL ) {
if ( strcmp(pmodel_str, "unity") == 0 ) {
pmodel = PMODEL_UNITY;
@@ -1264,7 +1317,7 @@ int main(int argc, char *argv[])
if ( !no_pr ) {
refine_all(crystals, n_crystals, full, nthreads, pmodel,
- 0, i+1, no_logs);
+ 0, i+1, no_logs, sym, amb);
} else if ( !no_scale ) {
scale_all_to_reference(crystals, n_crystals, full, nthreads);
}
@@ -1357,7 +1410,7 @@ int main(int argc, char *argv[])
crystal_free(crystals[i]);
}
reflist_free(full);
- free(sym);
+ free_symoplist(sym);
free(outfile);
free(crystals);
free(infile);
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 1c33e211..7e5420d3 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -389,7 +389,7 @@ static int check_angle_shifts(gsl_vector *cur, const gsl_vector *initial,
static RefList *reindex_reflections(RefList *input, SymOpList *amb,
- SymOpList *sym)
+ SymOpList *sym, int idx)
{
RefList *n;
Reflection *refl;
@@ -405,13 +405,13 @@ static RefList *reindex_reflections(RefList *input, SymOpList *amb,
Reflection *rn;
get_indices(refl, &h, &k, &l);
- get_equiv(amb, NULL, 0, h, k, l, &h, &k, &l);
+ get_equiv(amb, NULL, idx, h, k, l, &h, &k, &l);
get_asymm(sym, h, k, l, &h, &k, &l);
rn = add_refl(n, h, k, l);
copy_data(rn, refl);
get_symmetric_indices(rn, &h, &k, &l);
- get_equiv(amb, NULL, 0, h, k, l, &h, &k, &l);
+ get_equiv(amb, NULL, idx, h, k, l, &h, &k, &l);
set_symmetric_indices(rn, h, k, l);
}
@@ -419,7 +419,7 @@ static RefList *reindex_reflections(RefList *input, SymOpList *amb,
}
-static void reindex_cell(UnitCell *cell, SymOpList *amb)
+static void reindex_cell(UnitCell *cell, SymOpList *amb, int idx)
{
signed int h, k, l;
struct rvec na, nb, nc;
@@ -429,17 +429,17 @@ static void reindex_cell(UnitCell *cell, SymOpList *amb)
&bs.u, &bs.v, &bs.w,
&cs.u, &cs.v, &cs.w);
- get_equiv(amb, NULL, 0, 1, 0, 0, &h, &k, &l);
+ get_equiv(amb, NULL, idx, 1, 0, 0, &h, &k, &l);
na.u = as.u*h + bs.u*k + cs.u*l;
na.v = as.v*h + bs.v*k + cs.v*l;
na.w = as.w*h + bs.w*k + cs.w*l;
- get_equiv(amb, NULL, 0, 0, 1, 0, &h, &k, &l);
+ get_equiv(amb, NULL, idx, 0, 1, 0, &h, &k, &l);
nb.u = as.u*h + bs.u*k + cs.u*l;
nb.v = as.v*h + bs.v*k + cs.v*l;
nb.w = as.w*h + bs.w*k + cs.w*l;
- get_equiv(amb, NULL, 0, 0, 0, 1, &h, &k, &l);
+ get_equiv(amb, NULL, idx, 0, 0, 1, &h, &k, &l);
nc.u = as.u*h + bs.u*k + cs.u*l;
nc.v = as.v*h + bs.v*k + cs.v*l;
nc.w = as.w*h + bs.w*k + cs.w*l;
@@ -450,45 +450,50 @@ static void reindex_cell(UnitCell *cell, SymOpList *amb)
}
-void try_reindex(Crystal *crin, const RefList *full)
+void try_reindex(Crystal *crin, const RefList *full,
+ SymOpList *sym, SymOpList *amb)
{
RefList *list;
Crystal *cr;
UnitCell *cell;
- SymOpList *amb;
- SymOpList *sym;
double residual_original, residual_flipped;
+ int idx, n;
- amb = parse_symmetry_operations("k,h,-l");
- sym = get_pointgroup("m-3");
+ if ( sym == NULL || amb == NULL ) return;
residual_original = residual(crin, full, 0, NULL, NULL, 0);
cr = crystal_copy(crin);
- cell = cell_new_from_cell(crystal_get_cell(crin));
- if ( cell == NULL ) return;
- reindex_cell(cell, amb);
- crystal_set_cell(cr, cell);
+ n = num_equivs(amb, NULL);
- list = reindex_reflections(crystal_get_reflections(crin), amb, sym);
- crystal_set_reflections(cr, list);
+ for ( idx=0; idx<n; idx++ ) {
- update_predictions(cr);
- calculate_partialities(cr, PMODEL_XSPHERE);
+ cell = cell_new_from_cell(crystal_get_cell(crin));
+ if ( cell == NULL ) return;
+ reindex_cell(cell, amb, idx);
+ crystal_set_cell(cr, cell);
- residual_flipped = residual(cr, full, 0, NULL, NULL, 1);
+ list = reindex_reflections(crystal_get_reflections(crin),
+ amb, sym, idx);
+ crystal_set_reflections(cr, list);
- if ( residual_flipped < residual_original ) {
- crystal_set_cell(crin, cell);
- crystal_set_reflections(crin, list);
- } else {
- cell_free(crystal_get_cell(cr));
- reflist_free(crystal_get_reflections(cr));
- crystal_free(cr);
+ update_predictions(cr);
+ calculate_partialities(cr, PMODEL_XSPHERE);
+
+ residual_flipped = residual(cr, full, 0, NULL, NULL, 1);
+
+ if ( residual_flipped < residual_original ) {
+ crystal_set_cell(crin, cell);
+ crystal_set_reflections(crin, list);
+ residual_original = residual_flipped;
+ } else {
+ cell_free(crystal_get_cell(cr));
+ reflist_free(crystal_get_reflections(cr));
+ }
}
- free_symoplist(amb);
+ crystal_free(cr);
}
@@ -686,7 +691,8 @@ void write_gridscan(Crystal *cr, const RefList *full,
static void do_pr_refine(Crystal *cr, const RefList *full,
PartialityModel pmodel, int verbose, int serial,
- int cycle, int write_logs)
+ int cycle, int write_logs,
+ SymOpList *sym, SymOpList *amb)
{
gsl_multimin_fminimizer *min;
struct rf_priv priv;
@@ -697,7 +703,7 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
double residual_start, residual_free_start;
FILE *fh = NULL;
- try_reindex(cr, full);
+ try_reindex(cr, full, sym, amb);
residual_start = residual(cr, full, 0, NULL, NULL, 0);
residual_free_start = residual(cr, full, 1, NULL, NULL, 0);
@@ -858,24 +864,6 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
}
-static struct prdata pr_refine(Crystal *cr, const RefList *full,
- PartialityModel pmodel, int verbose, int serial,
- int cycle, int write_logs)
-{
- struct prdata prdata;
-
- prdata.refined = 0;
-
- do_pr_refine(cr, full, pmodel, verbose, serial, cycle, write_logs);
-
- if ( crystal_get_user_flag(cr) == 0 ) {
- prdata.refined = 1;
- }
-
- return prdata;
-}
-
-
struct refine_args
{
RefList *full;
@@ -886,6 +874,8 @@ struct refine_args
int verbose;
int cycle;
int no_logs;
+ SymOpList *sym;
+ SymOpList *amb;
};
@@ -906,9 +896,15 @@ static void refine_image(void *task, int id)
int write_logs = 0;
write_logs = !pargs->no_logs && (pargs->serial % 20 == 0);
- pargs->prdata = pr_refine(cr, pargs->full, pargs->pmodel,
- pargs->verbose, pargs->serial, pargs->cycle,
- write_logs);
+ pargs->prdata.refined = 0;
+
+ do_pr_refine(cr, pargs->full, pargs->pmodel, pargs->verbose,
+ pargs->serial, pargs->cycle, write_logs,
+ pargs->sym, pargs->amb);
+
+ if ( crystal_get_user_flag(cr) == 0 ) {
+ pargs->prdata.refined = 1;
+ }
}
@@ -942,7 +938,8 @@ static void done_image(void *vqargs, void *task)
void refine_all(Crystal **crystals, int n_crystals,
RefList *full, int nthreads, PartialityModel pmodel,
- int verbose, int cycle, int no_logs)
+ int verbose, int cycle, int no_logs,
+ SymOpList *sym, SymOpList *amb)
{
struct refine_args task_defaults;
struct queue_args qargs;
@@ -954,6 +951,8 @@ void refine_all(Crystal **crystals, int n_crystals,
task_defaults.verbose = verbose;
task_defaults.cycle = cycle;
task_defaults.no_logs = no_logs;
+ task_defaults.sym = sym;
+ task_defaults.amb = amb;
qargs.task_defaults = task_defaults;
qargs.n_started = 0;
diff --git a/src/post-refinement.h b/src/post-refinement.h
index 3c4ac7ef..a27127ff 100644
--- a/src/post-refinement.h
+++ b/src/post-refinement.h
@@ -41,6 +41,7 @@
#include "utils.h"
#include "crystal.h"
#include "geometry.h"
+#include "symmetry.h"
enum prflag
@@ -59,7 +60,8 @@ extern const char *str_prflag(enum prflag flag);
extern void refine_all(Crystal **crystals, int n_crystals,
RefList *full, int nthreads, PartialityModel pmodel,
- int verbose, int cycle, int no_logs);
+ int verbose, int cycle, int no_logs,
+ SymOpList *sym, SymOpList *amb);
extern void write_gridscan(Crystal *cr, const RefList *full,
int cycle, int serial);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-13 22:15:19 +0000