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authorThomas White <taw@physics.org>2014-03-11 17:41:07 +0100
committerThomas White <taw@physics.org>2014-03-11 17:41:07 +0100
commit074d07c2491f37e50160399d01b58af64f86946f (patch)
tree342ef7c943a850a6967ea8899d1e4b16a5838998
parent0235e13c0f97f6a70291aeb2dada31cb8a8afdba (diff)
partialator: Add polarisation correction
-rw-r--r--doc/man/partialator.15
-rw-r--r--src/partialator.c30
2 files changed, 24 insertions, 11 deletions
diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index 15992646..b3871ed7 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -94,6 +94,11 @@ Specify the partiality model. See the list below for possible choices.
.PD
Run \fIn\fR analyses in parallel.
+.PD 0
+.IP \fB--no-polarisation\fR
+.PD
+Disable the polarisation correction.
+
.SH PARTIALITY MODELS
The available partiality models are:
diff --git a/src/partialator.c b/src/partialator.c
index 8e80d076..910ed539 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -66,23 +66,16 @@ static void show_help(const char *s)
" -h, --help Display this help message.\n"
"\n"
" -i, --input=<filename> Specify the name of the input 'stream'.\n"
-" (must be a file, not e.g. stdin)\n"
" -o, --output=<filename> Output filename. Default: partialator.hkl.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
-" -b, --beam=<file> Get beam parameters from file, which provides\n"
-" initial values for parameters, and nominal\n"
-" wavelengths if no per-shot value is found in \n"
-" an HDF5 file.\n"
+" -b, --beam=<file> Get beam parameters from file.\n"
" -y, --symmetry=<sym> Merge according to symmetry <sym>.\n"
" -n, --iterations=<n> Run <n> cycles of scaling and post-refinement.\n"
" --no-scale Fix all the scaling factors at unity.\n"
" -r, --reference=<file> Refine images against reflections in <file>,\n"
-" instead of taking the mean of the intensity\n"
-" estimates.\n"
" -m, --model=<model> Specify partiality model.\n"
-" --min-measurements=<n> Require at least <n> measurements before a\n"
-" reflection appears in the output. Default: 2\n"
-"\n"
+" --min-measurements=<n> Minimum number of measurements to require.\n"
+" --no-polarisation Disable polarisation correction.\n"
" -j <n> Run <n> analyses in parallel.\n");
}
@@ -361,9 +354,11 @@ int main(int argc, char *argv[])
int min_measurements = 2;
char *rval;
struct srdata srdata;
+ int polarisation = 1;
/* Long options */
const struct option longopts[] = {
+
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
@@ -371,11 +366,17 @@ int main(int argc, char *argv[])
{"beam", 1, NULL, 'b'},
{"symmetry", 1, NULL, 'y'},
{"iterations", 1, NULL, 'n'},
- {"no-scale", 0, &noscale, 1},
{"reference", 1, NULL, 'r'},
{"model", 1, NULL, 'm'},
+
{"min-measurements", 1, NULL, 2},
+ {"no-scale", 0, &noscale, 1},
+ {"no-polarisation", 0, &polarisation, 0},
+ {"no-polarization", 0, &polarisation, 0},
+ {"polarisation", 0, &polarisation, 1}, /* compat */
+ {"polarization", 0, &polarisation, 1}, /* compat */
+
{0, 0, NULL, 0}
};
@@ -593,6 +594,13 @@ int main(int argc, char *argv[])
/* This is the raw list of reflections */
cr_refl = crystal_get_reflections(cr);
+
+ if ( polarisation ) {
+ polarisation_correction(cr_refl,
+ crystal_get_cell(cr),
+ cur);
+ }
+
as = asymmetric_indices(cr_refl, sym);
crystal_set_reflections(cr, as);
reflist_free(cr_refl);