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-rw-r--r--src/ambigator.c7
-rw-r--r--src/cell_explorer.c11
-rw-r--r--src/check_hkl.c25
-rw-r--r--src/compare_hkl.c81
-rw-r--r--src/get_hkl.c43
-rw-r--r--src/indexamajig.c24
-rw-r--r--src/partial_sim.c46
-rw-r--r--src/partialator.c5
-rw-r--r--src/pattern_sim.c36
-rw-r--r--src/render_hkl.c31
10 files changed, 210 insertions, 99 deletions
diff --git a/src/ambigator.c b/src/ambigator.c
index f7837721..3df66f3b 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -1254,8 +1254,11 @@ int main(int argc, char *argv[])
return 1;
}
- fread(&seed, sizeof(seed), 1, fh);
- gsl_rng_set(rng, seed);
+ if ( fread(&seed, sizeof(seed), 1, fh) == 1 ) {
+ gsl_rng_set(rng, seed);
+ } else {
+ ERROR("Failed to seed RNG\n");
+ }
fclose(fh);
}
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index a8a8a7dc..f3ec7cb7 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -1638,6 +1638,17 @@ int main(int argc, char *argv[])
fprintf(stderr, "\n");
+ if ( stream_has_old_indexers(st) ) {
+ ERROR("----- Notice -----\n");
+ ERROR("This stream contains indexing methods specified in an old way.\n");
+ ERROR("The full indexing method names will not be shown by cell_explorer, \n");
+ ERROR("only the methods themselves and prior information modifiers ");
+ ERROR("('cell' or 'latt').\n");
+ ERROR("Similar indexing methods will be combined. For example\n");
+ ERROR("'mosflm-raw' and 'mosflm-axes' will both show up as 'mosflm'\n");
+ ERROR("To simplify matters, it's best to re-run indexamajig.\n");
+ ERROR("------------------\n");
+ }
close_stream(st);
w.cols_on[0] = 1;
diff --git a/src/check_hkl.c b/src/check_hkl.c
index c7afb6cc..3c71d4cc 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -3,11 +3,11 @@
*
* Characterise reflection lists
*
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2016 Thomas White <taw@physics.org>
+ * 2010-2017 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -690,6 +690,7 @@ int main(int argc, char *argv[])
UnitCell *cell;
char *file = NULL;
char *sym_str = NULL;
+ char *sym_str_fromfile = NULL;
SymOpList *sym;
RefList *raw_list;
RefList *list;
@@ -838,12 +839,6 @@ int main(int argc, char *argv[])
"set!\n");
}
- if ( sym_str == NULL ) {
- sym_str = strdup("1");
- }
- sym = get_pointgroup(sym_str);
- free(sym_str);
-
file = strdup(argv[optind++]);
if ( cellfile == NULL ) {
@@ -857,13 +852,25 @@ int main(int argc, char *argv[])
}
free(cellfile);
- raw_list = read_reflections(file);
+ raw_list = read_reflections_2(file, &sym_str_fromfile);
if ( raw_list == NULL ) {
ERROR("Couldn't read file '%s'\n", file);
return 1;
}
free(file);
+ if ( sym_str == NULL ) {
+ if ( sym_str_fromfile != NULL ) {
+ STATUS("Using symmetry from reflection file: %s\n",
+ sym_str_fromfile);
+ sym_str = sym_str_fromfile;
+ } else {
+ sym_str = strdup("1");
+ }
+ }
+ sym = get_pointgroup(sym_str);
+ free(sym_str);
+
if ( shell_file == NULL ) shell_file = strdup("shells.dat");
/* Check that the intensities have the correct symmetry */
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 81f12c94..fd988b89 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -3,11 +3,11 @@
*
* Compare reflection lists
*
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2016 Thomas White <taw@physics.org>
+ * 2010-2017 Thomas White <taw@physics.org>
* 2013 Lorenzo Galli <lorenzo.galli@desy.de>
*
* This file is part of CrystFEL.
@@ -1124,6 +1124,9 @@ int main(int argc, char *argv[])
char *afile = NULL;
char *bfile = NULL;
char *sym_str = NULL;
+ char *sym_str_fromfile = NULL;
+ char *sym_str_fromfile1 = NULL;
+ char *sym_str_fromfile2 = NULL;
SymOpList *sym;
int ncom, nrej, nmul, nneg, nres, nbij, ncen;
RefList *list1_acc;
@@ -1320,8 +1323,53 @@ int main(int argc, char *argv[])
"set!\n");
}
+ afile = strdup(argv[optind++]);
+ bfile = strdup(argv[optind]);
+
+ if ( shell_file == NULL ) shell_file = strdup("shells.dat");
+
+ cell = load_cell_from_file(cellfile);
+ if ( cellfile == NULL ) {
+ ERROR("You must provide a unit cell.\n");
+ exit(1);
+ }
+ if ( cell == NULL ) {
+ ERROR("Failed to load cell.\n");
+ return 1;
+ }
+ free(cellfile);
+
+ list1_raw = read_reflections_2(afile, &sym_str_fromfile1);
+ if ( list1_raw == NULL ) {
+ ERROR("Couldn't read file '%s'\n", afile);
+ return 1;
+ }
+
+ list2_raw = read_reflections_2(bfile, &sym_str_fromfile2);
+ if ( list2_raw == NULL ) {
+ ERROR("Couldn't read file '%s'\n", bfile);
+ return 1;
+ }
+
+ if ( (sym_str_fromfile1 != NULL) && (sym_str_fromfile2 != NULL) ) {
+ if ( strcmp(sym_str_fromfile1, sym_str_fromfile2) != 0 ) {
+ ERROR("The symmetries of the two list do not match:\n");
+ ERROR(" %s: %s\n", afile, sym_str_fromfile1);
+ ERROR(" %s: %s\n", bfile, sym_str_fromfile2);
+ return 1;
+ }
+ sym_str_fromfile = sym_str_fromfile1;
+ free(sym_str_fromfile2);
+ }
+
if ( sym_str == NULL ) {
- sym_str = strdup("1");
+ if ( sym_str_fromfile != NULL ) {
+ STATUS("Using symmetry from reflection files: %s\n",
+ sym_str_fromfile);
+ sym_str = sym_str_fromfile;
+ } else {
+ sym_str = strdup("1");
+ }
}
sym = get_pointgroup(sym_str);
free(sym_str);
@@ -1354,33 +1402,6 @@ int main(int argc, char *argv[])
}
}
- afile = strdup(argv[optind++]);
- bfile = strdup(argv[optind]);
-
- if ( shell_file == NULL ) shell_file = strdup("shells.dat");
-
- cell = load_cell_from_file(cellfile);
- if ( cellfile == NULL ) {
- ERROR("You must provide a unit cell.\n");
- exit(1);
- }
- if ( cell == NULL ) {
- ERROR("Failed to load cell.\n");
- return 1;
- }
- free(cellfile);
-
- list1_raw = read_reflections(afile);
- if ( list1_raw == NULL ) {
- ERROR("Couldn't read file '%s'\n", afile);
- return 1;
- }
-
- list2_raw = read_reflections(bfile);
- if ( list2_raw == NULL ) {
- ERROR("Couldn't read file '%s'\n", bfile);
- return 1;
- }
/* Check that the intensities have the correct symmetry */
if ( check_list_symmetry(list1_raw, sym) ) {
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 77f34da2..5dddc5be 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -3,11 +3,11 @@
*
* Small program to manipulate reflection lists
*
- * Copyright © 2013-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2013-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2009-2016 Thomas White <taw@physics.org>
+ * 2009-2017 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -415,6 +415,7 @@ int main(int argc, char *argv[])
int config_nap = 1;
char *holo_str = NULL;
char *mero_str = NULL;
+ char *sym_str_fromfile = NULL;
char *expand_str = NULL;
SymOpList *holo = NULL;
SymOpList *mero = NULL;
@@ -569,13 +570,6 @@ int main(int argc, char *argv[])
} else {
holo = NULL;
}
- if ( mero_str != NULL ) {
- pointgroup_warning(mero_str);
- mero = get_pointgroup(mero_str);
- free(mero_str);
- } else {
- mero = NULL;
- }
if ( expand_str != NULL ) {
pointgroup_warning(expand_str);
expand = get_pointgroup(expand_str);
@@ -590,6 +584,30 @@ int main(int argc, char *argv[])
set_symmetry_name(reindex, "Reindex");
}
+ input = read_reflections_2(input_file, &sym_str_fromfile);
+ if ( input == NULL ) {
+ ERROR("Problem reading input file %s\n", input_file);
+ return 1;
+ }
+ free(input_file);
+
+ if ( mero_str == NULL ) {
+ if ( sym_str_fromfile != NULL ) {
+ STATUS("Using symmetry from reflection file: %s\n",
+ sym_str_fromfile);
+ mero_str = sym_str_fromfile;
+ } else {
+ mero_str = strdup("1");
+ }
+ }
+ if ( mero_str != NULL ) {
+ pointgroup_warning(mero_str);
+ mero = get_pointgroup(mero_str);
+ free(mero_str);
+ } else {
+ mero = NULL;
+ }
+
if ( (expand != NULL) || (holo != NULL) || config_trimc
|| config_multi ) {
if ( mero == NULL ) {
@@ -597,13 +615,6 @@ int main(int argc, char *argv[])
}
}
- input = read_reflections(input_file);
- if ( input == NULL ) {
- ERROR("Problem reading input file %s\n", input_file);
- return 1;
- }
- free(input_file);
-
STATUS("%i reflections in input.\n", num_reflections(input));
if ( (mero != NULL) && !config_trimc
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 88b61563..04022441 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -924,17 +924,25 @@ int main(int argc, char *argv[])
}
free(outfile);
+ if ( indm_str == NULL ) {
+
+ STATUS("No indexing methods specified. I will try to ");
+ STATUS("automatically detect the available methods.\n");
+ STATUS("To disable auto-detection of indexing methods, specify ");
+ STATUS("which methods to use with --indexing=<methods>.\n");
+ STATUS("Use --indexing=none to disable indexing and integration.\n");
+ indm_str = detect_indexing_methods(iargs.cell);
+
+ }
+
/* 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");
- if ( iargs.cell != NULL ) {
- STATUS("Ignoring your unit cell.\n");
- }
- iargs.ipriv = NULL;
+ ERROR("No indexing method specified, and no usable indexing ");
+ ERROR("methods auto-detected.\n");
+ ERROR("Install some indexing programs (mosflm,dirax etc), or ");
+ ERROR("try again with --indexing=none.\n");
+ return 1;
} else if ( strcmp(indm_str, "none") == 0 ) {
diff --git a/src/partial_sim.c b/src/partial_sim.c
index c5084955..2f0a0277 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -3,11 +3,11 @@
*
* Generate partials for testing scaling
*
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2011-2016 Thomas White <taw@physics.org>
+ * 2011-2017 Thomas White <taw@physics.org>
* 2014 Valerio Mariani
*
* This file is part of CrystFEL.
@@ -763,23 +763,35 @@ int main(int argc, char *argv[])
}
fixup_geom(det);
- if ( sym_str == NULL ) sym_str = strdup("1");
- sym = get_pointgroup(sym_str);
- free(sym_str);
-
if ( save_file == NULL ) save_file = strdup("partial_sim.hkl");
/* Load (full) reflections */
if ( input_file != NULL ) {
RefList *as;
+ char *sym_str_fromfile = NULL;
- full = read_reflections(input_file);
+ full = read_reflections_2(input_file, &sym_str_fromfile);
if ( full == NULL ) {
ERROR("Failed to read reflections from '%s'\n",
input_file);
return 1;
}
+
+ /* If we don't have a point group yet, and if the file provides
+ * one, use the one from the file */
+ if ( (sym_str == NULL) && (sym_str_fromfile != NULL) ) {
+ sym_str = sym_str_fromfile;
+ STATUS("Using symmetry from reflection file: %s\n",
+ sym_str);
+ }
+
+ /* If we still don't have a point group, use "1" */
+ if ( sym_str == NULL ) sym_str = strdup("1");
+
+ pointgroup_warning(sym_str);
+ sym = get_pointgroup(sym_str);
+
if ( check_list_symmetry(full, sym) ) {
ERROR("The input reflection list does not appear to"
" have symmetry %s\n", symmetry_name(sym));
@@ -798,6 +810,8 @@ int main(int argc, char *argv[])
} else {
random_intensities = 1;
+ if ( sym_str == NULL ) sym_str = strdup("1");
+ sym = get_pointgroup(sym_str);
}
if ( n < 1 ) {
@@ -852,10 +866,11 @@ int main(int argc, char *argv[])
noise_stddev);
if ( random_intensities ) {
STATUS(" Full intensities: randomly generated: "
- "abs(Gaussian(sigma=%.2f))\n", full_stddev);
+ "abs(Gaussian(sigma=%.2f)), symmetry %s\n",
+ full_stddev, sym_str);
} else {
- STATUS(" Full intensities: from %s\n",
- input_file);
+ STATUS(" Full intensities: from %s (symmetry %s)\n",
+ input_file, sym_str);
}
STATUS(" Max error in cell components: %.2f %%\n", cnoise);
@@ -902,10 +917,13 @@ int main(int argc, char *argv[])
for ( i=0; i<n_threads; i++ ) {
unsigned long int seed;
-
- fread(&seed, sizeof(seed), 1, fh);
qargs.rngs[i] = gsl_rng_alloc(gsl_rng_mt19937);
- gsl_rng_set(qargs.rngs[i], seed);
+
+ if ( fread(&seed, sizeof(seed), 1, fh) == 1 ) {
+ gsl_rng_set(qargs.rngs[i], seed);
+ } else {
+ ERROR("Failed to seed RNG %i\n", i);
+ }
}
@@ -931,7 +949,7 @@ int main(int argc, char *argv[])
if ( random_intensities ) {
STATUS("Writing full intensities to %s\n", save_file);
- write_reflist(save_file, full);
+ write_reflist_2(save_file, full, sym);
}
if ( phist_file != NULL ) {
diff --git a/src/partialator.c b/src/partialator.c
index 569145e8..142ca892 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -1018,7 +1018,10 @@ int main(int argc, char *argv[])
ERROR("Failed to open '%s'\n", sparams_fn);
return 1;
}
- fgets(line, 1024, sparams_fh);
+ if ( fgets(line, 1024, sparams_fh) == NULL ) {
+ ERROR("Failed to read header from %s\n", sparams_fn);
+ return 1;
+ }
STATUS("Reading initial scaling factors (G,B) from '%s'\n",
sparams_fn);
free(sparams_fn);
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 347dd618..a3fea8e3 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -633,11 +633,6 @@ int main(int argc, char *argv[])
free(template_file);
}
- if ( sym_str == NULL ) sym_str = strdup("1");
- pointgroup_warning(sym_str);
- sym = get_pointgroup(sym_str);
- /* sym_str is used below */
-
if ( grad_str == NULL ) {
STATUS("You didn't specify a gradient calculation method, so"
" I'm using the 'mosaic' method, which is fastest.\n");
@@ -720,16 +715,35 @@ int main(int argc, char *argv[])
phases = NULL;
flags = NULL;
+ if ( sym_str == NULL ) sym_str = strdup("1");
+ pointgroup_warning(sym_str);
+ sym = get_pointgroup(sym_str);
+
} else {
RefList *reflections;
+ char *sym_str_fromfile = NULL;
- reflections = read_reflections(intfile);
+ reflections = read_reflections_2(intfile, &sym_str_fromfile);
if ( reflections == NULL ) {
ERROR("Problem reading input file %s\n", intfile);
return 1;
}
+ /* If we don't have a point group yet, and if the file provides
+ * one, use the one from the file */
+ if ( (sym_str == NULL) && (sym_str_fromfile != NULL) ) {
+ sym_str = sym_str_fromfile;
+ STATUS("Using symmetry from reflection file: %s\n",
+ sym_str);
+ }
+
+ /* If we still don't have a point group, use "1" */
+ if ( sym_str == NULL ) sym_str = strdup("1");
+
+ pointgroup_warning(sym_str);
+ sym = get_pointgroup(sym_str);
+
if ( grad == GRADIENT_PHASED ) {
phases = phases_from_list(reflections);
} else {
@@ -785,9 +799,12 @@ int main(int argc, char *argv[])
FILE *fh;
unsigned long int seed;
fh = fopen("/dev/urandom", "r");
- fread(&seed, sizeof(seed), 1, fh);
+ if ( fread(&seed, sizeof(seed), 1, fh) == 1 ) {
+ gsl_rng_set(rng, seed);
+ } else {
+ ERROR("Failed to seed random number generator\n");
+ }
fclose(fh);
- gsl_rng_set(rng, seed);
}
powder.det = image.det;
@@ -848,7 +865,8 @@ int main(int argc, char *argv[])
if ( intfile == NULL ) {
STATUS(" Full intensities: all equal\n");
} else {
- STATUS(" Full intensities: from %s\n", intfile);
+ STATUS(" Full intensities: from %s (symmetry %s)\n",
+ intfile, sym_str);
}
do {
diff --git a/src/render_hkl.c b/src/render_hkl.c
index 3996814a..3952940e 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -3,11 +3,11 @@
*
* Draw pretty renderings of reflection lists
*
- * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2015 Thomas White <taw@physics.org>
+ * 2010-2017 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -757,6 +757,7 @@ int main(int argc, char *argv[])
int r = 0;
double boost = 1.0;
char *sym_str = NULL;
+ char *sym_str_fromfile = NULL;
SymOpList *sym;
char *weighting = NULL;
int wght;
@@ -916,13 +917,6 @@ int main(int argc, char *argv[])
return 1;
}
- if ( sym_str == NULL ) {
- sym_str = strdup("1");
- }
- pointgroup_warning(sym_str);
- sym = get_pointgroup(sym_str);
- free(sym_str);
-
if ( weighting == NULL ) {
weighting = strdup("I");
}
@@ -1003,11 +997,28 @@ int main(int argc, char *argv[])
ERROR("Couldn't load unit cell from %s\n", cellfile);
return 1;
}
- list = read_reflections(infile);
+
+ list = read_reflections_2(infile, &sym_str_fromfile);
if ( list == NULL ) {
ERROR("Couldn't read file '%s'\n", infile);
return 1;
}
+
+ if ( sym_str == NULL ) {
+ if ( sym_str_fromfile != NULL ) {
+ STATUS("Using symmetry from reflection file: %s\n",
+ sym_str_fromfile);
+ sym_str = sym_str_fromfile;
+ } else {
+ sym_str = strdup("1");
+ }
+ }
+
+ pointgroup_warning(sym_str);
+ sym = get_pointgroup(sym_str);
+ if ( sym == NULL ) return 1;
+ free(sym_str);
+
if ( check_list_symmetry(list, sym) ) {
ERROR("The input reflection list does not appear to"
" have symmetry %s\n", symmetry_name(sym));
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 07:55:39 +0000