add option -pinkIndexer-max-refinement-disbalance

3 files changed, 30 insertions, 2 deletions

diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 7bc71471..c9e156e3 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -448,6 +448,7 @@ These set low-level parameters for the XGANDALF indexing algorithm.
 .IP \fB--pinkIndexer-multi=\fIn\fR
 .IP \fB--pinkIndexer-thread-count=\fIn\fR
 .IP \fB--pinkIndexer-no-check-indexed=\fIn\fR
+.IP \fB--pinkIndexer-max-refinement-disbalance=\fIn\fR
 .IP \fB--pinkIndexer-override-bandwidth=\fIn\fR
 .IP \fB--pinkIndexer-override-photon-energy=\fIn\fR
 .IP \fB--pinkIndexer-override-visible-energy-range=\fImin-max\fR
@@ -473,6 +474,8 @@ These set low-level parameters for the PinkIndexer indexing algorithm.
 .IP
 \fB--pinkIndexer-no-check-indexed\fR Leave the check whether a pattern is indexed completely to CrystFEL. Useful for monochromatic (since CrystFEL's prediction model is smarter than the one of pinkIndexer) or in combnation with --no-check-peaks for geometry optimization. This flag is meant to eventually disappear, when the full pink pipeline is implemented.
 .IP
+\fB--pinkIndexer-max-refinement-disbalance Indexing solutions are dismissed if the refinement refined very well to one side of the detector and very badly to the other side. Allowed values range from 0 (no disbalance) to 2 (extreme disbalance), default 0.4. Disbalance after refinement usually appears for bad geometries or bad prior unit cell parameters.
+.IP
 \fB--pinkIndexer-override-bandwidth=\fIn\fR Overrides the bandwidth in (delta energy)/(mean energy) to use for indexing (which usually is defined in the geometry file). Should be used together with \fB--pinkIndexer-override-photon-energy=\fIn\fR. Note: this option sets the borders for the spectrum, whereas the option in the geometry file sets the standard deviation for a Gaussian that fits the spectrum. Internally, the standard deviation is multiplied by 5 to compute the hard borders of the spectrum. I.e., photon_energy_bandwith = 0.005 in the geometry file equals --pinkIndexer-override-bandwidth=0.025. For monochromatic experiments usually --pinkIndexer-override-bandwidth=0.02 is sufficiently large. If in doubt, use --pinkIndexer-override-visible-energy-range.
 .IP
 \fB--pinkIndexer-override-photon-energy=\fIn\fR Overrides the mean energy in eV to use for indexing (which usually is defined in the geometry file). Should be used together with \fB--pinkIndexer-override-bandwidth=\fIn\fR
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c
index e3ecf5a9..22208885 100644
--- a/libcrystfel/src/pinkindexer.c
+++ b/libcrystfel/src/pinkindexer.c
@@ -55,6 +55,8 @@ struct pinkIndexer_private_data {
 
 	int no_check_indexed;
 
+	float maxRefinementDisbalance;
+
 	IntegerMatrix *centeringTransformation;
 	LatticeTransform_t latticeReductionTransform;
 };
@@ -95,15 +97,24 @@ int run_pinkIndexer(struct image *image, void *ipriv)
 	Lattice_t indexedLattice[MAX_MULTI_LATTICE_COUNT];
 	float center_shift[MAX_MULTI_LATTICE_COUNT][2];
 
-	float maxRefinementDisbalance = 0.4;
+
 
 	do {
 		int peakCount = reciprocalPeaks_1_per_A->peakCount;
 		int matchedPeaksCount = PinkIndexer_indexPattern(pinkIndexer_private_data->pinkIndexer,
 		        &(indexedLattice[indexed]), center_shift[indexed], reciprocalPeaks_1_per_A, intensities,
-		        maxRefinementDisbalance,
+		        pinkIndexer_private_data->maxRefinementDisbalance,
 		        pinkIndexer_private_data->threadCount);
 
+		if(matchedPeaksCount == -1){
+			STATUS("WARNING: Indexing solution was rejected due to too large disbalance of the refinement."
+			        "If you see this message often, check the documentation for the parameter "
+			        "--pinkIndexer-max-refinement-disbalance\n");
+
+			matchedPeaksCount = 0;
+		}
+
+		printf("matchedPeaksCount %d from %d\n",matchedPeaksCount,peakCount);
 		if ((matchedPeaksCount >= 25 && matchedPeaksCount >= peakCount * 0.30)
 		        || matchedPeaksCount >= peakCount * 0.4
 		        || matchedPeaksCount >= 70
@@ -181,6 +192,7 @@ void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
 	pinkIndexer_private_data->multi = pinkIndexer_opts->multi;
 	pinkIndexer_private_data->min_peaks = pinkIndexer_opts->min_peaks;
 	pinkIndexer_private_data->no_check_indexed = pinkIndexer_opts->no_check_indexed;
+	pinkIndexer_private_data->maxRefinementDisbalance = pinkIndexer_opts->maxRefinementDisbalance;
 
 	UnitCell* primitiveCell = uncenter_cell(cell, &pinkIndexer_private_data->centeringTransformation, NULL);
 
@@ -412,6 +424,9 @@ static void show_help()
 "     --pinkIndexer-no-check-indexed\n"
 "                           Disable internal check for correct indexing\n"
 "                            solutions\n"
+"     --pinkIndexer-max-refinement-disbalance=n\n"
+"                           Maximum disbalance after refinement:\n"
+"                            0 (no disbalance) to 2 (extreme disbalance), default 0.4\n"
 "     --pinkIndexer-override-photon-energy=ev\n"
 "                           Mean energy in eV to use for indexing.\n"
 "     --pinkIndexer-override-bandwidth=n\n"
@@ -447,6 +462,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		(*opts_ptr)->reflectionRadius = -1;
 		(*opts_ptr)->customPhotonEnergy = -1;
 		(*opts_ptr)->customBandwidth = -1;
+		(*opts_ptr)->maxRefinementDisbalance = 0.4;
 		break;
 
 		case 1 :
@@ -548,6 +564,12 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 			(*opts_ptr)->customBandwidth *= -1;
 		}
 		break;
+		case 14 :
+		if (sscanf(arg, "%f", &(*opts_ptr)->maxRefinementDisbalance) != 1)
+		{
+			ERROR("Invalid value for --pinkIndexer-max-refinement-disbalance\n");
+			return EINVAL;
+		}
 	}
 
 	return 0;
@@ -589,6 +611,8 @@ static struct argp_option options[] = {
 
 	{"pinkIndexer-override-visible-energy-range", 13, "overridenVisibleEnergyRange", OPTION_HIDDEN, NULL},
 
+	{"pinkIndexer-max-refinement-disbalance", 14, "maxDisbalance", OPTION_HIDDEN, NULL},
+
 	{0}
 };
 
diff --git a/libcrystfel/src/pinkindexer.h b/libcrystfel/src/pinkindexer.h
index f1c4f5b0..f79f4331 100644
--- a/libcrystfel/src/pinkindexer.h
+++ b/libcrystfel/src/pinkindexer.h
@@ -49,6 +49,7 @@ struct pinkIndexer_options {
 	float reflectionRadius; /* In m^-1 */
 	float customPhotonEnergy;
 	float customBandwidth;
+	float maxRefinementDisbalance;
 };
 
 #include <stddef.h>