check_hkl: Move "single-list" FoMs into API

Reasons for differences:

1. Resolution shells slightly different
The binning calculation needs to take into account small rounding errors
in the resolution calculation, when not using an explicit resolution
range (--highres).  The old version did this by taking a min/max
resolution range slightly larger than the resolution of the data.  The
new version handles the rounding errors explicitly, so does not need
this.

2. Number of reflections with infinite/invalid I/sigI values halved
The number reported for this count was twice what it should have been,
due to a bug in the old check_hkl.

3. Overall SNR is different
When the above warning message applies, the old version still allowed
the reflections with invalid I/sigI values to contribute to the
denominator of the mean SNR calculation.  The new version does not
include them in the SNR calculation at all.  Note that the reflections
contribute to the other figures of merit unless otherwise stated.

4. Standard deviation of intensity is not calculated
It would've been a lot of work to include this in the new version, and
it's a totally useless number.  If you disagree, please get in touch!

1 files changed, 55 insertions, 34 deletions

diff --git a/libcrystfel/src/fom.h b/libcrystfel/src/fom.h
index d3373044..c9c8dbfe 100644
--- a/libcrystfel/src/fom.h
+++ b/libcrystfel/src/fom.h
@@ -38,6 +38,19 @@
 #include <reflist.h>
 #include <symmetry.h>
 
+struct fom_rejections
+{
+	int common;
+	int low_snr;
+	int negative_deleted;
+	int negative_zeroed;
+	int few_measurements;
+	int outside_resolution_range;
+	int no_bijvoet;
+	int centric;
+	int nan_inf_value;
+};
+
 enum fom_type
 {
 	FOM_R1I,
@@ -51,7 +64,13 @@ enum fom_type
 	FOM_RANO,
 	FOM_RANORSPLIT,
 	FOM_D1SIG,
-	FOM_D2SIG
+	FOM_D2SIG,
+	FOM_NUM_MEASUREMENTS,
+	FOM_REDUNDANCY,
+	FOM_SNR,
+	FOM_MEAN_INTENSITY,
+	FOM_STDDEV_INTENSITY,
+	FOM_COMPLETENESS,
 };
 
 struct fom_shells
@@ -61,51 +80,53 @@ struct fom_shells
 	double *rmaxs;
 };
 
-struct fom_context
-{
-	enum fom_type fom;
-	int nshells;
-	int *cts;
-
-	/* For R-factors */
-	double *num;
-	double *den;
+struct fom_context;
+
+extern struct fom_rejections fom_select_reflection_pairs(RefList *list1,
+                                                         RefList *list2,
+                                                         RefList **plist1_acc,
+                                                         RefList **plist2_acc,
+                                                         UnitCell *cell,
+                                                         SymOpList *sym,
+                                                         int anom,
+                                                         double rmin_fix,
+                                                         double rmax_fix,
+                                                         double sigma_cutoff,
+                                                         int ignore_negs,
+                                                         int zero_negs,
+                                                         int mul_cutoff);
+
+extern struct fom_rejections fom_select_reflections(RefList *list,
+                                                    RefList **plist_acc,
+                                                    UnitCell *cell,
+                                                    SymOpList *sym,
+                                                    double rmin_fix,
+                                                    double rmax_fix,
+                                                    double sigma_cutoff,
+                                                    int ignore_negs,
+                                                    int zero_negs,
+                                                    int mul_cutoff);
 
-	/* For "double" R-factors */
-	double *num2;
-	double *den2;
-
-	/* For CCs */
-	double **vec1;
-	double **vec2;
-	int *n;
-	int nmax;
-
-	/* For "counting" things e.g. d1sig or d2sig */
-	int *n_within;
-};
-
-extern int fom_select_reflections(RefList *list1, RefList *list2,
-                                  RefList *list1_acc, RefList *list2_acc,
-                                  UnitCell *cell, SymOpList *sym,
-                                  int anom, double rmin_fix, double rmax_fix,
-                                  double sigma_cutoff, int ignore_negs,
-                                  int zero_negs, int mul_cutoff);
 
 extern struct fom_context *fom_calculate(RefList *list1, RefList *list2,
                                          UnitCell *cell,
                                          struct fom_shells *shells,
                                          enum fom_type fom, int noscale,
-                                         SymOpList *sym);
+                                         const SymOpList *sym);
 
 extern struct fom_shells *fom_make_resolution_shells(double rmin, double rmax,
                                                      int nshells);
 
-extern double fom_shell_label(struct fom_shells *s, int i);
+extern double fom_shell_centre(struct fom_shells *s, int i);
+
+extern double fom_overall_value(struct fom_context *fctx);
+extern double fom_shell_value(struct fom_context *fctx, int i);
 
-extern double fom_shell(struct fom_context *fctx, int i);
+extern int fom_overall_num_reflections(struct fom_context *fctx);
+extern int fom_shell_num_reflections(struct fom_context *fctx, int i);
 
-extern double fom_overall(struct fom_context *fctx);
+extern int fom_overall_num_possible(struct fom_context *fctx);
+extern int fom_shell_num_possible(struct fom_context *fctx, int i);
 
 extern enum fom_type fom_type_from_string(const char *s);