From 59b99486be3865a53049d0c6317157d9f22bc0e1 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 19 Feb 2013 18:13:13 +0100
Subject: Add -cell and -nocell to indexing methods

---
 libcrystfel/src/dirax.c        |  6 ++++--
 libcrystfel/src/grainspotter.c |  6 ++----
 libcrystfel/src/index.c        | 25 +++++++++++++++++++++++++
 libcrystfel/src/index.h        |  4 ++++
 libcrystfel/src/mosflm.c       |  7 +++++--
 libcrystfel/src/xds.c          |  2 +-
 6 files changed, 41 insertions(+), 9 deletions(-)

(limited to 'libcrystfel/src')

diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index e6ff36b1..fb60656a 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -637,8 +637,10 @@ IndexingPrivate *dirax_prepare(IndexingMethod *indm, UnitCell *cell,
 	if ( *indm & INDEXING_CHECK_CELL_AXES ) need_cell = 1;
 
 	if ( need_cell && (cell == NULL) ) {
-		ERROR("DirAx needs a unit cell for this set of flags.\n");
-		return NULL;
+		ERROR("Altering your DirAx flags because no PDB file was"
+		      " provided.\n");
+		*indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
+		*indm &= ~INDEXING_CHECK_CELL_AXES;
 	}
 
 	/* Flags that DirAx knows about */
diff --git a/libcrystfel/src/grainspotter.c b/libcrystfel/src/grainspotter.c
index 8bdb03aa..8def8091 100644
--- a/libcrystfel/src/grainspotter.c
+++ b/libcrystfel/src/grainspotter.c
@@ -482,10 +482,8 @@ IndexingPrivate *grainspotter_prepare(IndexingMethod *indm, UnitCell *cell,
 	if ( gp == NULL ) return NULL;
 
 	/* Flags that GrainSpotter knows about */
-	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS;
-
-	/* Flags that GrainSpotter requires */
-	*indm |= INDEXING_USE_LATTICE_TYPE;
+	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
+	       | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
 
 	gp->cell = cell;
 	gp->indm = *indm;
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 0ab467a6..311dc2ce 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -316,6 +316,19 @@ static IndexingMethod set_lattice(IndexingMethod a)
 }
 
 
+/* Set the indexer flags for "use no unit cell parameters" */
+static IndexingMethod set_nocellparams(IndexingMethod a)
+{
+	return a & ~INDEXING_USE_CELL_PARAMETERS;
+}
+
+
+/* Set the indexer flags for "use unit cell parameters" */
+static IndexingMethod set_cellparams(IndexingMethod a)
+{
+	return a | INDEXING_USE_CELL_PARAMETERS;
+}
+
 char *indexer_str(IndexingMethod indm)
 {
 	char *str;
@@ -379,6 +392,12 @@ char *indexer_str(IndexingMethod indm)
 		strcat(str, "-nolatt");
 	}
 
+	if ( indm & INDEXING_USE_CELL_PARAMETERS ) {
+		strcat(str, "-cell");
+	} else {
+		strcat(str, "-nocell");
+	}
+
 	return str;
 }
 
@@ -433,6 +452,12 @@ IndexingMethod *build_indexer_list(const char *str)
 		} else if ( strcmp(methods[i], "nolatt") == 0) {
 			list[nmeth] = set_nolattice(list[nmeth]);
 
+		} else if ( strcmp(methods[i], "cell") == 0) {
+			list[nmeth] = set_cellparams(list[nmeth]);
+
+		} else if ( strcmp(methods[i], "nocell") == 0) {
+			list[nmeth] = set_nocellparams(list[nmeth]);
+
 		} else {
 			ERROR("Bad list of indexing methods: '%s'\n", str);
 			return NULL;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 94b0d457..f60bb18f 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -52,13 +52,16 @@
                                      | INDEXING_USE_LATTICE_TYPE)
 
 #define INDEXING_DEFAULTS_REAX (INDEXING_REAX | INDEXING_USE_LATTICE_TYPE      \
+                                     | INDEXING_USE_CELL_PARAMETERS            \
                                      | INDEXING_CHECK_PEAKS)
 
 #define INDEXING_DEFAULTS_GRAINSPOTTER (INDEXING_GRAINSPOTTER                  \
                                      | INDEXING_USE_LATTICE_TYPE               \
+                                     | INDEXING_USE_CELL_PARAMETERS            \
                                      | INDEXING_CHECK_PEAKS)
 
 #define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE        \
+                                     | INDEXING_USE_CELL_PARAMETERS            \
                                      | INDEXING_CHECK_PEAKS)
 
 /**
@@ -87,6 +90,7 @@ typedef enum {
 	INDEXING_CHECK_CELL_AXES         = 512,
 	INDEXING_CHECK_PEAKS             = 1024,
 	INDEXING_USE_LATTICE_TYPE        = 2048,
+	INDEXING_USE_CELL_PARAMETERS     = 4096,
 
 } IndexingMethod;
 
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index a03e621d..187d0c9b 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -817,8 +817,11 @@ IndexingPrivate *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
 	if ( *indm & INDEXING_USE_LATTICE_TYPE ) need_cell = 1;
 
 	if ( need_cell && (cell == NULL) ) {
-		ERROR("MOSFLM needs a unit cell for this set of flags.\n");
-		return NULL;
+		ERROR("Altering your MOSFLM flags because no PDB file was"
+		      " provided.\n");
+		*indm &= ~INDEXING_CHECK_CELL_COMBINATIONS;
+		*indm &= ~INDEXING_CHECK_CELL_AXES;
+		*indm &= ~INDEXING_USE_LATTICE_TYPE;
 	}
 
 	/* Flags that MOSFLM knows about */
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 786e2ae0..9660b5bc 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -577,7 +577,7 @@ IndexingPrivate *xds_prepare(IndexingMethod *indm, UnitCell *cell,
 	/* Flags that XDS knows about */
 	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
 	          | INDEXING_CHECK_CELL_AXES | INDEXING_USE_LATTICE_TYPE
-	          | INDEXING_CHECK_PEAKS;
+	          | INDEXING_CHECK_PEAKS | INDEXING_USE_CELL_PARAMETERS;
 
 	xp->ltl = ltl;
 	xp->cell = cell;
-- 
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