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authorKenneth R. Beyerlein <ken.beyerlein@gmail.com>2018-01-31 23:29:01 +0100
committerThomas White <taw@physics.org>2018-02-08 16:32:08 +0100
commitb6cdcc6cc47ee81ae63cdb33bc48ce320a90b36f (patch)
tree19bae9f093f6568d0aac70f349adf66d80fbe181 /src/indexamajig.c
parent5384762850fafbe07900baf81c39928e7a8f253a (diff)
Changed the naming of felix options and variables to make them more obvious.
Diffstat (limited to 'src/indexamajig.c')
-rw-r--r--src/indexamajig.c53
1 files changed, 30 insertions, 23 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 0af10f0e..36c52d7d 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -139,24 +139,31 @@ static void show_help(const char *s)
" --taketwo-trace-tolerance\n"
" Rotation matrix equivalence tolerance (in degrees)\n"
"\n"
-" --felix-tthrange-min Minimum 2theta to consider for indexing (degrees)\n"
-" Default: 0\n"
-" --felix-tthrange-max Maximum 2theta to consider for indexing (degrees)\n"
-" Default: 30\n"
-" --felix-min-measurements\n"
-" How many Rodrigue lines cross in the first search\n"
-" Default: 15\n"
+" --felix-domega Degree range of omega (moscaicity) to consider.\n"
+" Default: 2\n"
+" --felix-fraction-max-visits\n"
+" Cutoff for minimum fraction of the max visits.\n"
+" Default: 0.75\n"
+" --felix-max-internal-angle\n"
+" Cutoff for maximum internal angle between observed\n"
+" spots and predicted spots. Default: 0.25"
+" --felix-max-uniqueness\n"
+" Cutoff for maximum fraction of found spots which\n"
+" can belong to other crystallites. Default: 0.5\n"
" --felix-min-completeness\n"
-" Fraction of projected spots found in the pattern\n"
-" Default: 0.001\n"
-" --felix-min-uniqueness\n"
-" Fraction of found spots which can belong to other\n"
-" crystallites. Default: 0.5\n"
+" Cutoff for minimum fraction of projected spots\n"
+" found in the pattern. Default: 0.001\n"
+" --felix-min-visits\n"
+" Cutoff for minimum number of voxel visits.\n"
+" Default: 15\n"
" --felix-num-voxels Number of voxels for Rodrigues space search\n"
" Default: 100\n"
-" --felix-test-fraction Fraction of space to test. Default: 0.75\n"
" --felix-sigma The sigma of the 2theta, eta and omega angles.\n"
" Default: 0.2\n"
+" --felix-tthrange-max Maximum 2theta to consider for indexing (degrees)\n"
+" Default: 30\n"
+" --felix-tthrange-min Minimum 2theta to consider for indexing (degrees)\n"
+" Default: 0\n"
"\nIntegration options:\n\n"
" --integration=<meth> Integration method (rings,prof2d)-(cen,nocen)\n"
" Default: rings-nocen\n"
@@ -292,11 +299,11 @@ int main(int argc, char *argv[])
iargs.taketwo_opts.trace_tol = -1.0;
iargs.felix_opts.ttmin = -1.0;
iargs.felix_opts.ttmax = -1.0;
- iargs.felix_opts.min_measurements = 0;
+ iargs.felix_opts.min_visits = 0;
iargs.felix_opts.min_completeness = -1.0;
iargs.felix_opts.max_uniqueness = -1.0;
iargs.felix_opts.n_voxels = 0;
- iargs.felix_opts.test_fraction = -1.0;
+ iargs.felix_opts.fraction_max_visits = -1.0;
iargs.felix_opts.sigma = -1.0;
iargs.felix_opts.domega = -1.0;
iargs.felix_opts.max_internal_angle = -1.0;
@@ -384,15 +391,15 @@ int main(int argc, char *argv[])
{"taketwo-trace-tol", 1, NULL, 35}, /* compat */
{"felix-tthrange-min", 1, NULL, 36},
{"felix-tthrange-max", 1, NULL, 37},
- {"felix-min-measurements", 1, NULL, 38},
+ {"felix-min-visits", 1, NULL, 38},
{"felix-min-completeness", 1, NULL, 39},
{"felix-max-uniqueness", 1, NULL, 40},
{"felix-num-voxels", 1, NULL, 41},
- {"felix-test-fraction", 1, NULL, 42},
+ {"felix-fraction-max-visits", 1, NULL, 42},
{"felix-sigma", 1, NULL, 43},
{"serial-start", 1, NULL, 44},
{"felix-domega", 1, NULL, 45},
- {"felix-max-inter-angle", 1, NULL, 46},
+ {"felix-max-internal-angle", 1, NULL, 46},
{0, 0, NULL, 0}
};
@@ -648,9 +655,9 @@ int main(int argc, char *argv[])
break;
case 38:
- if ( sscanf(optarg, "%i", &iargs.felix_opts.min_measurements) != 1 )
+ if ( sscanf(optarg, "%i", &iargs.felix_opts.min_visits) != 1 )
{
- ERROR("Invalid value for --felix-min-measurements\n");
+ ERROR("Invalid value for --felix-min-visits\n");
return 1;
}
break;
@@ -680,9 +687,9 @@ int main(int argc, char *argv[])
break;
case 42:
- if ( sscanf(optarg, "%lf", &iargs.felix_opts.test_fraction) != 1 )
+ if ( sscanf(optarg, "%lf", &iargs.felix_opts.fraction_max_visits) != 1 )
{
- ERROR("Invalid value for --felix-test-fraction\n");
+ ERROR("Invalid value for --felix-fraction-max-visits\n");
return 1;
}
break;
@@ -714,7 +721,7 @@ int main(int argc, char *argv[])
case 46:
if ( sscanf(optarg, "%lf", &iargs.felix_opts.max_internal_angle) != 1 )
{
- ERROR("Invalid value for --felix-max-inter-angle\n");
+ ERROR("Invalid value for --felix-max-internal-angle\n");
return 1;
}
break;