Avoid duplication of beam and detector parameters for pinkIndexer

7 files changed, 47 insertions, 35 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 201b9041..aab72341 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -1070,6 +1070,19 @@ static void parse_toplevel(struct detector *det, struct beam_params *beam,
 			}
 		}
 
+	} else if ( strcmp(key, "photon_energy_bandwidth") == 0 ) {
+		if ( beam != NULL ) {
+			double v;
+			char *end;
+			v = strtod(val, &end);
+			if ( (val[0] != '\0') && (end[0] == '\0') ) {
+				beam->bandwidth = v;
+			} else {
+				ERROR("Invalid value for "
+				      "photon_energy_bandwidth\n");
+			}
+		}
+
 	} else if ( strcmp(key, "photon_energy_scale") == 0 ) {
 		if ( beam != NULL ) {
 			beam->photon_energy_scale = atof(val);
@@ -1202,6 +1215,7 @@ struct detector *get_detector_geometry_from_string(const char *string,
 		beam->photon_energy = 0.0;
 		beam->photon_energy_from = NULL;
 		beam->photon_energy_scale = 1.0;
+		beam->bandwidth = 0.0;
 	}
 
 	det->n_panels = 0;
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 706b06b1..04fb18a0 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -110,6 +110,8 @@ struct beam_params
 	char  *photon_energy_from;  /**< HDF5 dataset name */
 	double photon_energy_scale; /**< Scale factor for photon energy, if it
 	                             *   comes from an image header */
+	double bandwidth;           /**< FWHM bandwidth as a fraction of
+	                             *   wavelength */
 };
 
 
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 80a773ab..d48a6634 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -238,6 +238,7 @@ static char *friendly_indexer_name(IndexingMethod m)
 
 
 static void *prepare_method(IndexingMethod *m, UnitCell *cell,
+                            struct detector *det, struct beam_params *beam,
                             struct xgandalf_options *xgandalf_opts,
                             struct pinkIndexer_options* pinkIndexer_opts,
                             struct felix_options *felix_opts)
@@ -285,7 +286,8 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
 		break;
 
 		case INDEXING_PINKINDEXER :
-		priv = pinkIndexer_prepare(m, cell, pinkIndexer_opts);
+		priv = pinkIndexer_prepare(m, cell, pinkIndexer_opts,
+		                           det, beam);
 		break;
 
 		default :
@@ -316,8 +318,8 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
 
 
 IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
-                                struct detector *det, float *tols,
-                                IndexingFlags flags,
+                                struct detector *det, struct beam_params *beam,
+                                float *tols, IndexingFlags flags,
                                 struct taketwo_options *ttopts,
                                 struct xgandalf_options *xgandalf_opts,
                                 struct pinkIndexer_options *pinkIndexer_opts,
@@ -415,7 +417,9 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
 		int j;
 
 		ipriv->engine_private[i] = prepare_method(&methods[i], cell,
-		                                          xgandalf_opts, pinkIndexer_opts,
+		                                          det, beam,
+		                                          xgandalf_opts,
+		                                          pinkIndexer_opts,
 		                                          felix_opts);
 
 		if ( ipriv->engine_private[i] == NULL ) return NULL;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index ab38016f..883df4a3 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -153,7 +153,8 @@ extern IndexingMethod get_indm_from_string_2(const char *method, int *err);
 #include "felix.h"
 
 extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell,
-                                       struct detector *det, float *ltl,
+                                       struct detector *det,
+                                       struct beam_params *beam, float *ltl,
                                        IndexingFlags flags,
                                        struct taketwo_options *ttopts,
                                        struct xgandalf_options *xgandalf_opts,
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c
index fe3b1625..eb8ec05e 100644
--- a/libcrystfel/src/pinkindexer.c
+++ b/libcrystfel/src/pinkindexer.c
@@ -154,26 +154,19 @@ int run_pinkIndexer(struct image *image, void *ipriv)
 }
 
 void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
-        struct pinkIndexer_options *pinkIndexer_opts)
+                          struct pinkIndexer_options *pinkIndexer_opts,
+                          struct detector *det, struct beam_params *beam)
 {
-	if (pinkIndexer_opts->beamEnergy == 0.0) {
+	if ( beam->photon_energy_from != NULL ) {
 		ERROR("For pinkIndexer, the photon_energy must be defined as a "
 		      "constant in the geometry file\n");
 		return NULL;
 	}
-	if (pinkIndexer_opts->beamBandwidth == 0.0) {
-		STATUS("Using default bandwidth of 0.01 for pinkIndexer\n");
-		pinkIndexer_opts->beamBandwidth = 0.01;
-	}
-	if (pinkIndexer_opts->detectorDistance == 0.0 && pinkIndexer_opts->refinement_type ==
+	if ( (det->panels[0].clen_from != NULL) && pinkIndexer_opts->refinement_type ==
 	        REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed) {
 		ERROR("Using center refinement makes it necessary to have the detector distance fixed in the geometry file!");
 	}
 
-	if(pinkIndexer_opts->detectorDistance <= 0.0){
-		pinkIndexer_opts->detectorDistance = 0.25; //fake value
-	}
-
 	struct pinkIndexer_private_data* pinkIndexer_private_data = malloc(sizeof(struct pinkIndexer_private_data));
 	allocReciprocalPeaks(&(pinkIndexer_private_data->reciprocalPeaks_1_per_A));
 	pinkIndexer_private_data->intensities = malloc(MAX_PEAK_COUNT_FOR_INDEXER * sizeof(float));
@@ -199,9 +192,15 @@ void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
 	        .bx = bsz * 1e-10, .by = bsx * 1e-10, .bz = bsy * 1e-10,
 	        .cx = csz * 1e-10, .cy = csx * 1e-10, .cz = csy * 1e-10 };
 
-	float detectorDistance_m = pinkIndexer_opts->detectorDistance;
-	float beamEenergy_eV = pinkIndexer_opts->beamEnergy;
-	float nonMonochromaticity = pinkIndexer_opts->beamBandwidth;
+	float detectorDistance_m;
+	if ( det->panels[0].clen_from != NULL ) {
+		detectorDistance_m =  0.25;  /* fake value */
+	} else {
+		detectorDistance_m = det->panels[0].clen + det->panels[0].coffset;
+	}
+
+	float beamEenergy_eV = beam->photon_energy;
+	float nonMonochromaticity = beam->bandwidth;
 	float reflectionRadius_1_per_A;
 	if (pinkIndexer_opts->reflectionRadius < 0) {
 		reflectionRadius_1_per_A = 0.02
@@ -350,7 +349,8 @@ int run_pinkIndexer(struct image *image, void *ipriv)
 }
 
 extern void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
-		struct pinkIndexer_options *pinkIndexer_opts)
+		struct pinkIndexer_options *pinkIndexer_opts,
+		struct detector *det, struct beam_params *beam)
 {
 	ERROR("This copy of CrystFEL was compiled without PINKINDEXER support.\n");
 	ERROR("To use PINKINDEXER indexing, recompile with PINKINDEXER.\n");
diff --git a/libcrystfel/src/pinkindexer.h b/libcrystfel/src/pinkindexer.h
index 5be2c1e7..1fcb3711 100644
--- a/libcrystfel/src/pinkindexer.h
+++ b/libcrystfel/src/pinkindexer.h
@@ -42,14 +42,8 @@ struct pinkIndexer_options {
 	int multi;
 	int thread_count;
 	int min_peaks;
-
 	int no_check_indexed;
-
-	float beamEnergy; //in eV
-	float beamBandwidth; //(delta lambda)/lambda
-	float detectorDistance; //in m
-
-	float reflectionRadius; //in 1/A
+	float reflectionRadius; /* In m^-1 */
 };
 
 #include <stddef.h>
@@ -58,7 +52,8 @@ struct pinkIndexer_options {
 extern int run_pinkIndexer(struct image *image, void *ipriv);
 
 extern void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
-        struct pinkIndexer_options *pinkIndexer_opts);
+                                 struct pinkIndexer_options *pinkIndexer_opts,
+                                 struct detector *det, struct beam_params *beam);
 
 extern void pinkIndexer_cleanup(void *pp);
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 9aef3f2e..9fe14c65 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -1048,6 +1048,8 @@ int main(int argc, char *argv[])
 				      "--pinkIndexer-reflection-radius\n");
 				return 1;
 			}
+			/* A^-1 to m^-1 */
+			iargs.pinkIndexer_opts.reflectionRadius /= 1e10;
 			break;
 
 			case 0 :
@@ -1149,12 +1151,6 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 	add_geom_beam_stuff_to_field_list(iargs.copyme, iargs.det, iargs.beam);
-	iargs.pinkIndexer_opts.beamEnergy = iargs.beam->photon_energy;
-	iargs.pinkIndexer_opts.beamBandwidth = 0.01;
-	iargs.pinkIndexer_opts.detectorDistance = iargs.det->panels[0].clen;
-	if(iargs.det->panels[0].clen_from != NULL){
-		iargs.pinkIndexer_opts.detectorDistance = 0;
-	}
 
 	/* If no peak path from geometry file, use these (but see later) */
 	if ( iargs.hdf5_peak_path == NULL ) {
@@ -1394,7 +1390,7 @@ int main(int argc, char *argv[])
 		}
 
 		iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det,
-		                             iargs.tols, flags,
+		                             iargs.beam, iargs.tols, flags,
 		                             &iargs.taketwo_opts,
 		                             &iargs.xgandalf_opts,
 		                             &iargs.pinkIndexer_opts,