indexamajig: Add --camera-length-estimate

Unfortunately, PinkIndexer needs the real camera length for its centre
refinement.  Giving a fake value and scaling the resulting shift does
not work - the indexing rate drops with even a small error.

Ideally, this would work in the same way as --wavelength-estimate, by
using a static value from the geometry file if it's given.  However,
this is rather complicated to implement because of the way all the units
stuff is implemented.  Therefore, this is left as an improvement for the
future.

4 files changed, 22 insertions, 49 deletions

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 1c78cc58..37ced03d 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -204,6 +204,7 @@ static char *friendly_indexer_name(IndexingMethod m)
 
 static void *prepare_method(IndexingMethod *m, UnitCell *cell,
                             double wavelength_estimate,
+                            double clen_estimate,
                             struct xgandalf_options *xgandalf_opts,
                             struct pinkIndexer_options* pinkIndexer_opts,
                             struct felix_options *felix_opts,
@@ -254,7 +255,8 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
 
 		case INDEXING_PINKINDEXER :
 		priv = pinkIndexer_prepare(m, cell, pinkIndexer_opts,
-		                           wavelength_estimate);
+		                           wavelength_estimate,
+		                           clen_estimate);
 		break;
 
 		default :
@@ -331,6 +333,7 @@ IndexingPrivate *setup_indexing(const char *method_list,
                                 float *tols,
                                 IndexingFlags flags,
                                 double wavelength_estimate,
+                                double clen_estimate,
                                 int n_threads,
                                 struct taketwo_options *ttopts,
                                 struct xgandalf_options *xgandalf_opts,
@@ -402,6 +405,7 @@ IndexingPrivate *setup_indexing(const char *method_list,
 
 		ipriv->engine_private[i] = prepare_method(&methods[i], cell,
 		                                          wavelength_estimate,
+		                                          clen_estimate,
 		                                          xgandalf_opts,
 		                                          pinkIndexer_opts,
 		                                          felix_opts,
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 88b9b67e..a4aef671 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -171,6 +171,7 @@ extern IndexingPrivate *setup_indexing(const char *methods,
                                        float *ltl,
                                        IndexingFlags flags,
                                        double wavelength_estimate,
+                                       double clen_estimate,
                                        int n_threads,
                                        struct taketwo_options *ttopts,
                                        struct xgandalf_options *xgandalf_opts,
diff --git a/libcrystfel/src/indexers/pinkindexer.c b/libcrystfel/src/indexers/pinkindexer.c
index 149bb5bd..5cb979a9 100644
--- a/libcrystfel/src/indexers/pinkindexer.c
+++ b/libcrystfel/src/indexers/pinkindexer.c
@@ -43,8 +43,6 @@
 #include "peaks.h"
 
 
-#define FAKE_CLEN (0.25)
-
 struct pinkIndexer_options {
 	unsigned int considered_peaks_count;
 	unsigned int angle_resolution;
@@ -81,39 +79,6 @@ static void restoreReciprocalCell(UnitCell *cell, LatticeTransform_t* appliedRed
 static void makeRightHanded(UnitCell* cell);
 
 
-/* Return mean clen in m */
-static double mean_clen(struct detgeom *dg)
-{
-	int i;
-	double total = 0.0;
-	for ( i=0; i<dg->n_panels; i++ ) {
-		total += dg->panels[i].cnz * dg->panels[i].pixel_pitch;
-	}
-	return total / dg->n_panels;
-}
-
-
-static void scale_detector_shift(double fake_clen,
-                                 struct detgeom *dg,
-                                 double inx, double iny,
-                                 double *pdx, double *pdy)
-{
-	int i;
-	double mean = mean_clen(dg);
-	for ( i=0; i<dg->n_panels; i++ ) {
-		if ( !within_tolerance(dg->panels[i].cnz*dg->panels[i].pixel_pitch, mean, 2.0) ) {
-			ERROR("WARNING: Detector is not flat enough to apply "
-			      "detector position offset\n");
-			*pdx = 0.0;
-			*pdy = 0.0;
-			return;
-		}
-	}
-	*pdx = (mean/fake_clen)*inx;
-	*pdy = (mean/fake_clen)*iny;
-}
-
-
 int run_pinkIndexer(struct image *image, void *ipriv, int n_threads)
 {
 	struct pinkIndexer_private_data *pinkIndexer_private_data = ipriv;
@@ -206,19 +171,14 @@ int run_pinkIndexer(struct image *image, void *ipriv, int n_threads)
 			ERROR("pinkIndexer: problem with returned cell!\n");
 		} else {
 
-			double dx, dy;
 			Crystal *cr = crystal_new();
 			if ( cr == NULL ) {
 				ERROR("Failed to allocate crystal.\n");
 				return 0;
 			}
 			crystal_set_cell(cr, new_cell_trans);
-			scale_detector_shift(FAKE_CLEN,
-			                     image->detgeom,
-			                     center_shift[0],
-			                     center_shift[1],
-			                     &dx, &dy);
-			crystal_set_det_shift(cr, dx, dy);
+			crystal_set_det_shift(cr, center_shift[0],
+			                          center_shift[1]);
 			image_add_crystal(image, cr);
 			indexed++;
 
@@ -233,7 +193,8 @@ int run_pinkIndexer(struct image *image, void *ipriv, int n_threads)
 void *pinkIndexer_prepare(IndexingMethod *indm,
                           UnitCell *cell,
                           struct pinkIndexer_options *pinkIndexer_opts,
-                          double wavelength_estimate)
+                          double wavelength_estimate,
+                          double clen_estimate)
 {
 	float beamEenergy_eV;
 
@@ -245,9 +206,14 @@ void *pinkIndexer_prepare(IndexingMethod *indm,
 		beamEenergy_eV = J_to_eV(ph_lambda_to_en(wavelength_estimate));
 	}
 
+	if ( isnan(clen_estimate) ) {
+		ERROR("PinkIndexer requires a camera length estimate.  "
+		      "Try again with --camera-length-estimate=xx\n");
+		return NULL;
+	}
+
 	if ( cell == NULL ) {
-		ERROR("Unit cell information is required for "
-		      "PinkIndexer.\n");
+		ERROR("Unit cell information is required for PinkIndexer.\n");
 		return NULL;
 	}
 
@@ -294,7 +260,7 @@ void *pinkIndexer_prepare(IndexingMethod *indm,
 	Lattice_t sampleReciprocalLattice_1_per_A = lattice;
 	float detectorRadius_m = 0.03; //fake, only for prediction
 	ExperimentSettings *experimentSettings = ExperimentSettings_new(beamEenergy_eV,
-	                                                                FAKE_CLEN,
+	                                                                clen_estimate,
 	                                                                detectorRadius_m,
 	                                                                divergenceAngle_deg,
 	                                                                nonMonochromaticity,
@@ -420,7 +386,8 @@ int run_pinkIndexer(struct image *image, void *ipriv, int n_threads)
 extern void *pinkIndexer_prepare(IndexingMethod *indm,
                                  UnitCell *cell,
                                  struct pinkIndexer_options *pinkIndexer_opts,
-                                 double wavelength_estimate)
+                                 double wavelength_estimate,
+                                 double clen_estimate)
 {
 	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/indexers/pinkindexer.h b/libcrystfel/src/indexers/pinkindexer.h
index 358a8221..122bac87 100644
--- a/libcrystfel/src/indexers/pinkindexer.h
+++ b/libcrystfel/src/indexers/pinkindexer.h
@@ -42,7 +42,8 @@ extern int run_pinkIndexer(struct image *image, void *ipriv, int n_threads);
 extern void *pinkIndexer_prepare(IndexingMethod *indm,
                                  UnitCell *cell,
                                  struct pinkIndexer_options *pinkIndexer_opts,
-                                 double wavelength_estimate);
+                                 double wavelength_estimate,
+                                 double clen_estimate);
 
 extern void pinkIndexer_cleanup(void *pp);