indexamajig: Add --fix-{profile-radius,bandwidth,divergence}

3 files changed, 86 insertions, 22 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index 44f067e2..4f28aec5 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -3,13 +3,13 @@
  *
  * Index patterns, output hkl+intensity etc.
  *
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Richard Kirian
  * Copyright © 2012 Lorenzo Galli
  *
  * Authors:
- *   2010-2014 Thomas White <taw@physics.org>
+ *   2010-2015 Thomas White <taw@physics.org>
  *   2011      Richard Kirian
  *   2012      Lorenzo Galli
  *   2012      Chunhong Yoon
@@ -127,6 +127,10 @@ static void show_help(const char *s)
 "    --int-radius=<r>    Set the integration radii.  Default: 4,5,7.\n"
 "    --push-res=<n>      Integrate higher than apparent resolution cutoff.\n"
 "    --highres=<n>       Absolute resolution cutoff in Angstroms.\n"
+"    --fix-profile-radius Fix the reciprocal space profile radius for spot\n"
+"                         prediction (default: automatically determine.\n"
+"    --fix-bandwidth     Set the bandwidth for spot prediction.\n"
+"    --fix-divergence    Set the divergence (full angle) for spot prediction.\n"
 "\n"
 "\nFor time-resolved stuff, you might want to use:\n\n"
 "     --copy-hdf5-field <f>  Copy the value of field <f> into the stream. You\n"
@@ -238,6 +242,9 @@ int main(int argc, char *argv[])
 	iargs.int_meth = integration_method("rings-nocen", NULL);
 	iargs.push_res = 0.0;
 	iargs.highres = +INFINITY;
+	iargs.fix_profile_r = -1.0;
+	iargs.fix_bandwidth = -1.0;
+	iargs.fix_divergence = -1.0;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -293,6 +300,9 @@ int main(int argc, char *argv[])
 		{"res-push",           1, NULL,               19}, /* compat */
 		{"peak-radius",        1, NULL,               20},
 		{"highres",            1, NULL,               21},
+		{"fix-profile-radius", 1, NULL,               22},
+		{"fix-bandwidth",      1, NULL,               23},
+		{"fix-divergence",     1, NULL,               24},
 
 		{0, 0, NULL, 0}
 	};
@@ -440,6 +450,28 @@ int main(int argc, char *argv[])
 			iargs.highres = 1.0 / (iargs.highres/1e10);
 			break;
 
+			case 22 :
+			if ( sscanf(optarg, "%f", &iargs.fix_profile_r) != 1 ) {
+				ERROR("Invalid value for "
+				      "--fix-profile-radius\n");
+				return 1;
+			}
+			break;
+
+			case 23 :
+			if ( sscanf(optarg, "%f", &iargs.fix_bandwidth) != 1 ) {
+				ERROR("Invalid value for --fix-bandwidth\n");
+				return 1;
+			}
+			break;
+
+			case 24 :
+			if ( sscanf(optarg, "%f", &iargs.fix_divergence) != 1 ) {
+				ERROR("Invalid value for --fix-divergence\n");
+				return 1;
+			}
+			break;
+
 			case 0 :
 			break;
 
diff --git a/src/process_image.c b/src/process_image.c
index 84c3e996..2f6aa70f 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -279,31 +279,60 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		crystal_set_image(image.crystals[i], &image);
 	}
 
-	/* Default parameters */
-	image.div = 0.0;
-	image.bw = 0.00000001;
-	for ( i=0; i<image.n_crystals; i++ ) {
-		crystal_set_profile_radius(image.crystals[i], 0.01e9);
-		crystal_set_mosaicity(image.crystals[i], 0.0);  /* radians */
+	/* Set beam/crystal parameters */
+	if ( iargs->fix_divergence >= 0.0 ) {
+		image.div = iargs->fix_divergence;
+	} else {
+		image.div = 0.0;
+	}
+	if ( iargs->fix_bandwidth >= 0.0 ) {
+		image.bw = iargs->fix_bandwidth;
+	} else {
+		image.bw = 0.00000001;
+	}
+	if ( iargs->fix_profile_r >= 0.0 ) {
+		for ( i=0; i<image.n_crystals; i++ ) {
+			crystal_set_profile_radius(image.crystals[i],
+			                           iargs->fix_profile_r);
+			crystal_set_mosaicity(image.crystals[i], 0.0);
+		}
+	} else {
+		for ( i=0; i<image.n_crystals; i++ ) {
+			crystal_set_profile_radius(image.crystals[i], 0.01e9);
+			crystal_set_mosaicity(image.crystals[i], 0.0);
+		}
 	}
 
 	/* Integrate all the crystals at once - need all the crystals so that
 	 * overlaps can be detected. */
-	integrate_all_4(&image, iargs->int_meth, PMODEL_SCSPHERE, iargs->push_res,
-	                iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
-	                INTDIAG_NONE, 0, 0, 0, results_pipe);
+	if ( iargs->fix_profile_r < 0.0 ) {
 
-	for ( i=0; i<image.n_crystals; i++ ) {
-		refine_radius(image.crystals[i], image.features);
-		reflist_free(crystal_get_reflections(image.crystals[i]));
-	}
+		integrate_all_4(&image, iargs->int_meth, PMODEL_SCSPHERE,
+		                iargs->push_res,
+		                iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
+		                INTDIAG_NONE, 0, 0, 0, results_pipe);
+
+		for ( i=0; i<image.n_crystals; i++ ) {
+			refine_radius(image.crystals[i], image.features);
+			reflist_free(crystal_get_reflections(image.crystals[i]));
+		}
 
-	integrate_all_4(&image, iargs->int_meth, PMODEL_SCSPHERE,
+		integrate_all_4(&image, iargs->int_meth, PMODEL_SCSPHERE,
 		                iargs->push_res,
-			        iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
-			        iargs->int_diag, iargs->int_diag_h,
-			        iargs->int_diag_k, iargs->int_diag_l,
-			        results_pipe);
+		                iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
+		                iargs->int_diag, iargs->int_diag_h,
+		                iargs->int_diag_k, iargs->int_diag_l,
+		                results_pipe);
+	} else {
+
+		integrate_all_4(&image, iargs->int_meth, PMODEL_SCSPHERE,
+		                iargs->push_res,
+		                iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
+		                iargs->int_diag, iargs->int_diag_h,
+		                iargs->int_diag_k, iargs->int_diag_l,
+		                results_pipe);
+
+	}
 
 	ret = write_chunk(st, &image, hdfile,
 	                  iargs->stream_peaks, iargs->stream_refls,
diff --git a/src/process_image.h b/src/process_image.h
index a0bd6a83..53e2c66a 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -3,11 +3,11 @@
  *
  * The processing pipeline for one image
  *
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2014 Thomas White <taw@physics.org>
+ *   2010-2015 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *
  * This file is part of CrystFEL.
@@ -83,6 +83,9 @@ struct index_args
 	signed int int_diag_l;
 	float push_res;
 	float highres;
+	float fix_profile_r;
+	float fix_bandwidth;
+	float fix_divergence;
 };