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-rw-r--r--src/cell_explorer.c11
-rw-r--r--src/compare_hkl.c30
-rw-r--r--src/geoptimiser.c2
-rw-r--r--src/get_hkl.c4
-rw-r--r--src/im-sandbox.c2
-rw-r--r--src/indexamajig.c67
-rw-r--r--src/merge.c5
-rw-r--r--src/partialator.c6
-rw-r--r--src/process_hkl.c3
-rw-r--r--src/process_image.c3
-rw-r--r--src/process_image.h3
11 files changed, 74 insertions, 62 deletions
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index c8bbb069..f6c2c590 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -658,7 +658,9 @@ static void scan_cells(CellWindow *w)
if ( ignore ) continue;
- cell_get_parameters(cells[i], &a, &b, &c, &al, &be, &ga);
+ if ( cell_get_parameters(cells[i], &a, &b, &c, &al, &be, &ga) ) {
+ continue;
+ }
a *= 1e10; b *= 1e10; c *= 1e10;
al = rad2deg(al); be = rad2deg(be); ga = rad2deg(ga);
@@ -719,7 +721,10 @@ static void scan_minmax(CellWindow *w)
int j;
int found = 0;
- cell_get_parameters(w->cells[i], &a, &b, &c, &al, &be, &ga);
+ if ( cell_get_parameters(w->cells[i], &a, &b, &c, &al, &be, &ga) ) {
+ ERROR("Cell %i is bad\n", i);
+ continue;
+ }
a *= 1e10; b *= 1e10; c *= 1e10;
al = rad2deg(al); be = rad2deg(be); ga = rad2deg(ga);
@@ -1555,6 +1560,8 @@ int main(int argc, char *argv[])
return 1;
}
+ gsl_set_error_handler_off();
+
w.cells = NULL;
w.indms = NULL;
w.n_cells = 0;
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 51e51dc9..81f12c94 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -286,13 +286,13 @@ static void add_to_fom(struct fom_context *fctx, double i1, double i2,
break;
case FOM_D1SIG :
- if ( fabs(i1-i2) < (sig1+sig2)/2.0 ) {
+ if ( fabs(i1-i2) < sqrt(sig1*sig1 + sig2*sig2) ) {
fctx->n_within[bin]++;
}
break;
case FOM_D2SIG :
- if ( fabs(i1-i2) < sig1+sig2 ) { /* = 2 * (sig1+sig2)/2 */
+ if ( fabs(i1-i2) < 2.0*sqrt(sig1*sig1 + sig2*sig2) ) {
fctx->n_within[bin]++;
}
break;
@@ -1125,7 +1125,7 @@ int main(int argc, char *argv[])
char *bfile = NULL;
char *sym_str = NULL;
SymOpList *sym;
- int ncom, nrej, nneg, nres, nbij, ncen;
+ int ncom, nrej, nmul, nneg, nres, nbij, ncen;
RefList *list1_acc;
RefList *list2_acc;
RefList *list1;
@@ -1149,6 +1149,7 @@ int main(int argc, char *argv[])
double min_I = +INFINITY;
double max_I = -INFINITY;
float highres, lowres;
+ int mul_cutoff = 0;
/* Long options */
const struct option longopts[] = {
@@ -1164,6 +1165,7 @@ int main(int argc, char *argv[])
{"shell-file", 1, NULL, 7},
{"highres", 1, NULL, 8},
{"lowres", 1, NULL, 9},
+ {"min-measurements", 1, NULL, 11},
{"ignore-negs", 0, &config_ignorenegs, 1},
{"zero-negs", 0, &config_zeronegs, 1},
{"intensity-shells", 0, &config_intshells, 1},
@@ -1260,6 +1262,13 @@ int main(int argc, char *argv[])
rmin_fix = 1.0 / (lowres/1e10);
break;
+ case 11 :
+ if ( sscanf(optarg, "%i", &mul_cutoff) != 1 ) {
+ ERROR("Invalid value for --min-measurements\n");
+ return 1;
+ }
+ break;
+
case '?' :
break;
@@ -1413,6 +1422,7 @@ int main(int argc, char *argv[])
/* Select reflections to be used */
ncom = 0;
nrej = 0;
+ nmul = 0;
nneg = 0;
nres = 0;
nbij = 0;
@@ -1426,6 +1436,7 @@ int main(int argc, char *argv[])
signed int h, k, l;
double val1, val2;
double esd1, esd2;
+ int mul1, mul2;
Reflection *refl2;
Reflection *refl1_acc;
Reflection *refl2_acc;
@@ -1441,6 +1452,9 @@ int main(int argc, char *argv[])
esd1 = get_esd_intensity(refl1);
esd2 = get_esd_intensity(refl2);
+ mul1 = get_redundancy(refl1);
+ mul2 = get_redundancy(refl2);
+
if ( (val1 < sigma_cutoff * esd1)
|| (val2 < sigma_cutoff * esd2) )
{
@@ -1453,6 +1467,11 @@ int main(int argc, char *argv[])
continue;
}
+ if ( (mul1 < mul_cutoff) || (mul2 < mul_cutoff) ) {
+ nmul++;
+ continue;
+ }
+
if ( config_zeronegs ) {
int d = 0;
if ( val1 < 0.0 ) {
@@ -1544,6 +1563,11 @@ int main(int argc, char *argv[])
" negative intensities which were set to zero.\n", nneg);
}
+ if ( nmul > 0 ) {
+ STATUS("%i reflection pairs rejected because either or both"
+ " versions had too few measurements.\n", nmul);
+ }
+
if ( nres > 0 ) {
STATUS("%i reflection pairs rejected because either or both"
" versions were outside the resolution range.\n", nres);
diff --git a/src/geoptimiser.c b/src/geoptimiser.c
index e0337358..4ba2c5d0 100644
--- a/src/geoptimiser.c
+++ b/src/geoptimiser.c
@@ -2488,8 +2488,10 @@ int main(int argc, char *argv[])
}
#ifdef HAVE_SAVE_TO_PNG
+#if !GLIB_CHECK_VERSION(2,36,0)
g_type_init();
#endif
+#endif
ret_val = optimize_geometry(gparams, det, quadrants, connected);
diff --git a/src/get_hkl.c b/src/get_hkl.c
index d6efe747..77f34da2 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -98,7 +98,9 @@ static void show_help(const char *s)
static void copy_notes(RefList *out, RefList *in)
{
- reflist_add_notes(out, reflist_get_notes(in));
+ if ( reflist_get_notes(in) != NULL ) {
+ reflist_add_notes(out, reflist_get_notes(in));
+ }
}
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index f5493453..2dabf3e9 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -372,7 +372,7 @@ static void run_work(const struct index_args *iargs, Stream *st,
}
time_accounts_set(taccs, TACC_FINALCLEANUP);
- cleanup_indexing(iargs->indm, iargs->ipriv);
+ cleanup_indexing(iargs->ipriv);
free_detector_geometry(iargs->det);
free(iargs->hdf5_peak_path);
free_copy_hdf5_field_list(iargs->copyme);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index ef803931..6300f7ff 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -3,13 +3,13 @@
*
* Index patterns, output hkl+intensity etc.
*
- * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
* Copyright © 2012 Lorenzo Galli
*
* Authors:
- * 2010-2015 Thomas White <taw@physics.org>
+ * 2010-2017 Thomas White <taw@physics.org>
* 2011 Richard Kirian
* 2012 Lorenzo Galli
* 2012 Chunhong Yoon
@@ -202,8 +202,6 @@ int main(int argc, char *argv[])
int config_checkprefix = 1;
int config_basename = 0;
int integrate_saturated = 0;
- IndexingMethod *indm;
- IndexingPrivate **ipriv;
char *indm_str = NULL;
char *cellfile = NULL;
char *prefix = NULL;
@@ -262,7 +260,6 @@ int main(int argc, char *argv[])
ERROR("Couldn't allocate HDF5 field list.\n");
return 1;
}
- iargs.indm = NULL; /* No default */
iargs.ipriv = NULL; /* No default */
iargs.int_meth = integration_method("rings-nocen-nosat-nograd", NULL);
iargs.push_res = 0.0;
@@ -644,35 +641,6 @@ int main(int argc, char *argv[])
iargs.hdf5_peak_path = command_line_peak_path;
}
- /* Parse indexing methods */
- if ( indm_str == NULL ) {
-
- STATUS("You didn't specify an indexing method, so I won't try "
- " to index anything.\n"
- "If that isn't what you wanted, re-run with"
- " --indexing=<methods>.\n");
- indm = NULL;
-
- } else {
-
- int i = 0;
-
- indm = build_indexer_list(indm_str);
- if ( indm == NULL ) {
- ERROR("Invalid indexer list '%s'\n", indm_str);
- return 1;
- }
- free(indm_str);
-
- /* If --no-refine, unset the refinement flag on all methods */
- if ( no_refine ) {
- while ( indm[i] != INDEXING_NONE ) {
- indm[i] &= ~INDEXING_REFINE;
- i++;
- }
- }
- }
-
/* Parse integration method */
if ( int_str != NULL ) {
@@ -808,23 +776,30 @@ int main(int argc, char *argv[])
}
free(outfile);
- /* Prepare the indexer */
- if ( indm != NULL ) {
- ipriv = prepare_indexing(indm, iargs.cell, iargs.det,
- iargs.tols, iargs.felix_options);
- if ( ipriv == NULL ) {
- ERROR("Failed to prepare indexing.\n");
+ /* Prepare the indexing system */
+ if ( indm_str == NULL ) {
+
+ STATUS("You didn't specify an indexing method, so I won't try "
+ " to index anything.\n"
+ "If that isn't what you wanted, re-run with"
+ " --indexing=<methods>.\n");
+ iargs.ipriv = NULL;
+
+ } else {
+
+ iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det,
+ iargs.tols, no_refine,
+ iargs.felix_options);
+ if ( iargs.ipriv == NULL ) {
+ ERROR("Failed to set up indexing system\n");
return 1;
}
- } else {
- ipriv = NULL;
+ free(indm_str);
+
}
gsl_set_error_handler_off();
- iargs.indm = indm;
- iargs.ipriv = ipriv;
-
create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
st, tempdir);
@@ -836,7 +811,7 @@ int main(int argc, char *argv[])
free_detector_geometry(iargs.det);
free(iargs.hdf5_peak_path);
close_stream(st);
- cleanup_indexing(indm, ipriv);
+ cleanup_indexing(iargs.ipriv);
return 0;
}
diff --git a/src/merge.c b/src/merge.c
index 8d1fae0f..9734c469 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -237,10 +237,7 @@ RefList *merge_intensities(Crystal **crystals, int n, int n_threads,
Reflection *refl;
RefListIterator *iter;
- if ( n == 0 ) {
- ERROR("No crystals!\n");
- return NULL;
- }
+ if ( n == 0 ) return NULL;
full = reflist_new();
diff --git a/src/partialator.c b/src/partialator.c
index 09feebb4..569145e8 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -191,6 +191,12 @@ static void write_split(Crystal **crystals, int n_crystals, const char *outfile,
snprintf(tmp, 1024, "%s1", outfile);
split = merge_intensities(crystals1, n_crystals1, nthreads,
pmodel, min_measurements, push_res, 1);
+
+ if ( split == NULL ) {
+ ERROR("Not enough crystals for two way split!\n");
+ return;
+ }
+
STATUS("Writing two-way split to %s ", tmp);
write_reflist_2(tmp, split, sym);
reflist_free(split);
diff --git a/src/process_hkl.c b/src/process_hkl.c
index d2cf640b..301bc6e4 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -287,7 +287,8 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr,
if ( isnan(scale) ) return 1;
if ( scale <= 0.0 ) return 1;
if ( stat != NULL ) {
- fprintf(stat, "%s %f %f\n", image->filename, scale, cc);
+ fprintf(stat, "%s %s %f %f\n", image->filename,
+ get_event_string(image->event), scale, cc);
}
} else {
diff --git a/src/process_image.c b/src/process_image.c
index d54e5a79..e6e6d22a 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -241,8 +241,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Index the pattern */
time_accounts_set(taccs, TACC_INDEXING);
- index_pattern_2(&image, iargs->indm, iargs->ipriv,
- &sb_shared->pings[cookie]);
+ index_pattern_2(&image, iargs->ipriv, &sb_shared->pings[cookie]);
r = chdir(rn);
if ( r ) {
diff --git a/src/process_image.h b/src/process_image.h
index 2ac48b83..bc8b31fd 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -62,8 +62,7 @@ struct index_args
float min_snr;
int check_hdf5_snr;
struct detector *det;
- IndexingMethod *indm;
- IndexingPrivate **ipriv;
+ IndexingPrivate *ipriv;
int peaks; /* Peak detection method */
float tols[4];
struct beam_params *beam;
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 11:41:18 +0000