Simplify indexing options

mosflm-cell-nolatt-multi-refine-bad-retry.... it's all getting a bit
too much.  This commit removes all the options from the indexing methods
except for the prior information flags (cell/nocell and latt/nolatt).
All the other options are now given at the top level with new
indexamajig options, e.g. --no-multi and --no-retry.  They are applied
to all the methods, with no option to (say) use retry for one method and
not for another.

This also makes the "peak alignment test" default to OFF, and
multi-lattice indexing ON.  I think that the prediction refinement does
a good enough job of checking the validity of indexing solutions,
allowing us to turn off the alignment check which filters out most
multi-lattice solutions.

1 files changed, 2 insertions, 40 deletions

diff --git a/libcrystfel/src/asdf.c b/libcrystfel/src/asdf.c
index 0c43fe7a..bbfd1a56 100644
--- a/libcrystfel/src/asdf.c
+++ b/libcrystfel/src/asdf.c
@@ -272,39 +272,14 @@ static int calc_reciprocal(gsl_vector **direct, gsl_vector **reciprocal)
 static int check_cell(struct asdf_private *dp, struct image *image,
                       UnitCell *cell)
 {
-	UnitCell *out;
 	Crystal *cr;
 
-	if ( dp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
-
-		out = match_cell(cell, dp->template, 0, dp->ltl, 1);
-		if ( out == NULL ) return 0;
-
-	} else if ( dp->indm & INDEXING_CHECK_CELL_AXES ) {
-
-		out = match_cell(cell, dp->template, 0, dp->ltl, 0);
-		if ( out == NULL ) return 0;
-
-	} else {
-		out = cell_new_from_cell(cell);
-	}
-
 	cr = crystal_new();
 	if ( cr == NULL ) {
 		ERROR("Failed to allocate crystal.\n");
 		return 0;
 	}
-
-	crystal_set_cell(cr, out);
-
-	if ( dp->indm & INDEXING_CHECK_PEAKS ) {
-		if ( !peak_sanity_check(image, &cr, 1) ) {
-			crystal_free(cr);  /* Frees the cell as well */
-			cell_free(out);
-			return 0;
-		}
-	}
-
+	crystal_set_cell(cr, cell);
 	image_add_crystal(image, cr);
 
 	return 1;
@@ -1206,22 +1181,9 @@ void *asdf_prepare(IndexingMethod *indm, UnitCell *cell,
                    struct detector *det, float *ltl)
 {
 	struct asdf_private *dp;
-	int need_cell = 0;
-
-	if ( *indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
-	if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
-
-	if ( need_cell && !cell_has_parameters(cell) ) {
-		ERROR("Altering your asdf flags because cell parameters were"
-		      " not provided.\n");
-		*indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
-		*indm &= ~INDEXING_CHECK_CELL_AXES;
-	}
 
 	/* Flags that asdf knows about */
-	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
-	       | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
-	       | INDEXING_CONTROL_FLAGS;
+	*indm &= INDEXING_METHOD_MASK;
 
 	dp = malloc(sizeof(struct asdf_private));
 	if ( dp == NULL ) return NULL;