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, 3 insertions, 60 deletions

diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index edf8524e..110243cb 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -128,7 +128,6 @@ struct mosflm_data {
 static int check_cell(struct mosflm_private *mp, struct image *image,
                       UnitCell *cell)
 {
-	UnitCell *out;
 	Crystal *cr;
 
 	/* If we sent lattice information, make sure that we got back what we
@@ -163,35 +162,13 @@ static int check_cell(struct mosflm_private *mp, struct image *image,
 
 	}
 
-	if ( mp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
-
-		out = match_cell(cell, mp->template, 0, mp->ltl, 1);
-		if ( out == NULL ) return 0;
-
-	} else if ( mp->indm & INDEXING_CHECK_CELL_AXES ) {
-
-		out = match_cell(cell, mp->template, 0, mp->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 ( mp->indm & INDEXING_CHECK_PEAKS ) {
-		if ( !peak_sanity_check(image, &cr, 1) ) {
-			cell_free(out);
-			crystal_free(cr);
-			return 0;
-		}
-	}
+	crystal_set_cell(cr, cell);
 
 	image_add_crystal(image, cr);
 
@@ -340,8 +317,6 @@ static int read_newmat(struct mosflm_data *mosflm, const char *filename,
 		mosflm->done = 1;
 	}
 
-	cell_free(cell);
-
         return 0;
 }
 
@@ -850,14 +825,10 @@ void *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
 	int need_cell = 0;
 
 	/* Check if cell parameters are needed/provided */
-	if ( *indm & INDEXING_CHECK_CELL_COMBINATIONS ) need_cell = 1;
-	if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
 	if ( *indm & INDEXING_USE_CELL_PARAMETERS ) need_cell = 1;
 	if ( need_cell && !cell_has_parameters(cell) ) {
 		ERROR("Altering your MOSFLM flags because cell parameters were"
 		      " not provided.\n");
-		*indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
-		*indm &= ~INDEXING_CHECK_CELL_AXES;
 		*indm &= ~INDEXING_USE_CELL_PARAMETERS;
 	}
 
@@ -869,36 +840,8 @@ void *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
 	}
 
 	/* Flags that MOSFLM knows about */
-	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
-	       | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
-	       | INDEXING_USE_LATTICE_TYPE| INDEXING_USE_CELL_PARAMETERS
-	       | INDEXING_CONTROL_FLAGS;
-
-	if ( (*indm & INDEXING_USE_LATTICE_TYPE)
-	   && !((*indm & INDEXING_CHECK_CELL_COMBINATIONS)
-	       || (*indm & INDEXING_CHECK_CELL_AXES))
-	   && (cell_has_parameters(cell)
-	       || (cell_get_unique_axis(cell) == 'a')
-	       || (cell_get_unique_axis(cell) == 'b')
-	       || (cell_get_unique_axis(cell) == 'c')) )
-	{
-		ERROR("WARNING: The unit cell from %s might have had "
-		      "its axes permuted from the unit cell you gave.\n"
-		      "If this is a problem, consider using "
-		      "mosflm-axes-latt or mosflm-comb-latt instead of "
-		      "mosflm-raw-latt.\n", indexer_str(*indm));
-		/* It'll be OK if INDEXING_CHECK_CELL_PARAMETERS and
-		 * MOSFLM 7.2.0 or later, but that's getting a bit too
-		 * complicated to explain to the user. */
-	}
-
-	if ( (*indm & INDEXING_USE_CELL_PARAMETERS)
-	  && !((*indm & INDEXING_CHECK_CELL_COMBINATIONS)
-	    || (*indm & INDEXING_CHECK_CELL_AXES)) )
-	{
-		ERROR("WARNING: Using 'mosflm-raw' but providing cell "
-		      "parameters as prior information to mosflm.\n");
-	}
+	*indm &= INDEXING_METHOD_MASK
+	       | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
 
 	mp = malloc(sizeof(struct mosflm_private));
 	if ( mp == NULL ) return NULL;