Polarisation correction for extracted intensities

1 files changed, 7 insertions, 1 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index bd3b53e2..0f7154e8 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -57,6 +57,7 @@ struct process_args
 	int config_gpu;
 	int config_simulate;
 	int config_nomatch;
+	int config_unpolar;
 	IndexingMethod indm;
 	const double *intensities;
 	const unsigned int *counts;
@@ -118,6 +119,7 @@ static void show_help(const char *s)
 "      --no-match          Don't attempt to match the indexed cell to the\n"
 "                           model, just proceed with the one generated by the\n"
 "                           auto-indexing procedure.\n"
+"      --unpolarized       Don't correct for the polarisation of the X-rays.\n"
 "\n\nOptions for greater performance or verbosity:\n\n"
 "      --verbose           Be verbose about indexing.\n"
 "      --gpu               Use the GPU to speed up the simulation.\n"
@@ -237,6 +239,7 @@ static void *process_image(void *pargsv)
 	int config_gpu = pargs->config_gpu;
 	int config_simulate = pargs->config_simulate;
 	int config_nomatch = pargs->config_nomatch;
+	int config_unpolar = pargs->config_unpolar;
 	IndexingMethod indm = pargs->indm;
 	const double *intensities = pargs->intensities;
 	const unsigned int *counts = pargs->counts;
@@ -321,7 +324,7 @@ static void *process_image(void *pargsv)
 		/* Use original data (temporarily) */
 		simage->data = data_for_measurement;
 		output_intensities(simage, image.indexed_cell,
-		                   pargs->output_mutex);
+		                   pargs->output_mutex, config_unpolar);
 		simage->data = NULL;
 	}
 
@@ -382,6 +385,7 @@ int main(int argc, char *argv[])
 	int config_gpu = 0;
 	int config_verbose = 0;
 	int config_alternate = 0;
+	int config_unpolar = 0;
 	IndexingMethod indm;
 	char *indm_str = NULL;
 	UnitCell *cell;
@@ -417,6 +421,7 @@ int main(int argc, char *argv[])
 		{"intensities",        1, NULL,               'q'},
 		{"pdb",                1, NULL,               'p'},
 		{"prefix",             1, NULL,               'x'},
+		{"unpolarized",        0, &config_unpolar,     1},
 		{0, 0, NULL, 0}
 	};
 
@@ -570,6 +575,7 @@ int main(int argc, char *argv[])
 		pargs->config_gpu = config_gpu;
 		pargs->config_simulate = config_simulate;
 		pargs->config_nomatch = config_nomatch;
+		pargs->config_unpolar = config_unpolar;
 		pargs->cell = cell;
 		pargs->indm = indm;
 		pargs->intensities = intensities;