Move indexers out of API

18 files changed, 42 insertions, 44 deletions

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index b62f1926..a50d4d31 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -46,18 +46,18 @@
 #include "image.h"
 #include "utils.h"
 #include "peaks.h"
-#include "dirax.h"
-#include "asdf.h"
-#include "mosflm.h"
-#include "xds.h"
 #include "index.h"
 #include "geometry.h"
 #include "cell-utils.h"
-#include "felix.h"
 #include "predict-refine.h"
-#include "taketwo.h"
-#include "xgandalf.h"
-#include "pinkindexer.h"
+#include "indexers/dirax.h"
+#include "indexers/asdf.h"
+#include "indexers/mosflm.h"
+#include "indexers/xds.h"
+#include "indexers/felix.h"
+#include "indexers/taketwo.h"
+#include "indexers/xgandalf.h"
+#include "indexers/pinkindexer.h"
 
 
 /** \file index.h */
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 58fe64b7..8fc6db09 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -142,12 +142,18 @@ extern IndexingMethod get_indm_from_string_2(const char *method, int *err);
 
 #include "cell.h"
 #include "image.h"
-#include "taketwo.h"
-#include "xgandalf.h"
-#include "pinkindexer.h"
-#include "felix.h"
 #include "datatemplate.h"
 
+typedef struct felix_options FelixOptions;
+typedef struct taketwo_options TakeTwoOptions;
+typedef struct xgandalf_options XGandalfOptions;
+typedef struct pinkIndexer_options PinkIndexerOptions;
+
+extern struct argp felix_argp;
+extern struct argp pinkIndexer_argp;
+extern struct argp taketwo_argp;
+extern struct argp xgandalf_argp;
+
 extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell,
                                        const DataTemplate *dtempl,
                                        float *ltl,
diff --git a/libcrystfel/src/asdf.c b/libcrystfel/src/indexers/asdf.c
index 1536a109..1536a109 100644
--- a/libcrystfel/src/asdf.c
+++ b/libcrystfel/src/indexers/asdf.c
diff --git a/libcrystfel/src/asdf.h b/libcrystfel/src/indexers/asdf.h
index b3ccffcc..b3ccffcc 100644
--- a/libcrystfel/src/asdf.h
+++ b/libcrystfel/src/indexers/asdf.h
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/indexers/dirax.c
index 24be87ba..24be87ba 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/indexers/dirax.c
diff --git a/libcrystfel/src/dirax.h b/libcrystfel/src/indexers/dirax.h
index da4ae3d5..da4ae3d5 100644
--- a/libcrystfel/src/dirax.h
+++ b/libcrystfel/src/indexers/dirax.h
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/indexers/felix.c
index 524e68a7..524e68a7 100644
--- a/libcrystfel/src/felix.c
+++ b/libcrystfel/src/indexers/felix.c
diff --git a/libcrystfel/src/felix.h b/libcrystfel/src/indexers/felix.h
index f7e4d26a..3c9d4a94 100644
--- a/libcrystfel/src/felix.h
+++ b/libcrystfel/src/indexers/felix.h
@@ -39,9 +39,6 @@
  * Felix indexer interface
  */
 
-typedef struct felix_options FelixOptions;
-extern struct argp felix_argp;
-
 extern void *felix_prepare(IndexingMethod *indm, UnitCell *cell,
                            struct felix_options *opts);
 
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/indexers/mosflm.c
index bacd345f..bacd345f 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/indexers/mosflm.c
diff --git a/libcrystfel/src/mosflm.h b/libcrystfel/src/indexers/mosflm.h
index 9e956066..9e956066 100644
--- a/libcrystfel/src/mosflm.h
+++ b/libcrystfel/src/indexers/mosflm.h
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/indexers/pinkindexer.c
index e82f2f02..67bd48f5 100644
--- a/libcrystfel/src/pinkindexer.c
+++ b/libcrystfel/src/indexers/pinkindexer.c
@@ -32,17 +32,36 @@
 
 #include "pinkindexer.h"
 
-#ifdef HAVE_PINKINDEXER
 
 #include <stdlib.h>
+#include <sys/errno.h>
+#include <argp.h>
 
 #include "utils.h"
 #include "cell-utils.h"
 #include "peaks.h"
 
-#include "pinkIndexer/adaptions/crystfel/Lattice.h"
-#include "pinkIndexer/adaptions/crystfel/ExperimentSettings.h"
-#include "pinkIndexer/adaptions/crystfel/PinkIndexer.h"
+struct pinkIndexer_options {
+	unsigned int considered_peaks_count;
+	unsigned int angle_resolution;
+	unsigned int refinement_type;
+	float maxResolutionForIndexing_1_per_A;
+	float tolerance;
+	int multi;
+	int thread_count;
+	int min_peaks;
+	int no_check_indexed;
+	float reflectionRadius; /* In m^-1 */
+	float customPhotonEnergy;
+	float customBandwidth;
+	float maxRefinementDisbalance;
+};
+
+#ifdef HAVE_PINKINDEXER
+
+#include <pinkIndexer/adaptions/crystfel/Lattice.h>
+#include <pinkIndexer/adaptions/crystfel/ExperimentSettings.h>
+#include <pinkIndexer/adaptions/crystfel/PinkIndexer.h>
 
 #define MAX_MULTI_LATTICE_COUNT 8
 
diff --git a/libcrystfel/src/pinkindexer.h b/libcrystfel/src/indexers/pinkindexer.h
index 83e879db..cab88a75 100644
--- a/libcrystfel/src/pinkindexer.h
+++ b/libcrystfel/src/indexers/pinkindexer.h
@@ -29,26 +29,8 @@
 #ifndef LIBCRYSTFEL_SRC_PINKINDEXER_H_
 #define LIBCRYSTFEL_SRC_PINKINDEXER_H_
 
-typedef struct pinkIndexer_options PinkIndexerOptions;
-extern struct argp pinkIndexer_argp;
-
-struct pinkIndexer_options {
-	unsigned int considered_peaks_count;
-	unsigned int angle_resolution;
-	unsigned int refinement_type;
-	float maxResolutionForIndexing_1_per_A;
-	float tolerance;
-	int multi;
-	int thread_count;
-	int min_peaks;
-	int no_check_indexed;
-	float reflectionRadius; /* In m^-1 */
-	float customPhotonEnergy;
-	float customBandwidth;
-	float maxRefinementDisbalance;
-};
-
 #include <stddef.h>
+
 #include "index.h"
 #include "datatemplate.h"
 
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 65265b0e..65265b0e 100644
--- a/libcrystfel/src/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
diff --git a/libcrystfel/src/taketwo.h b/libcrystfel/src/indexers/taketwo.h
index 2239a77a..50fa221d 100644
--- a/libcrystfel/src/taketwo.h
+++ b/libcrystfel/src/indexers/taketwo.h
@@ -38,9 +38,6 @@
 
 /** \file taketwo.h */
 
-typedef struct taketwo_options TakeTwoOptions;
-extern struct argp taketwo_argp;
-
 extern void *taketwo_prepare(IndexingMethod *indm, struct taketwo_options *opts,
                              UnitCell *cell);
 extern const char *taketwo_probe(UnitCell *cell);
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/indexers/xds.c
index 02610d5e..02610d5e 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/indexers/xds.c
diff --git a/libcrystfel/src/xds.h b/libcrystfel/src/indexers/xds.h
index 8c4dc6d0..8c4dc6d0 100644
--- a/libcrystfel/src/xds.h
+++ b/libcrystfel/src/indexers/xds.h
diff --git a/libcrystfel/src/xgandalf.c b/libcrystfel/src/indexers/xgandalf.c
index 2d2dca48..2d2dca48 100644
--- a/libcrystfel/src/xgandalf.c
+++ b/libcrystfel/src/indexers/xgandalf.c
diff --git a/libcrystfel/src/xgandalf.h b/libcrystfel/src/indexers/xgandalf.h
index 86294354..288d141a 100644
--- a/libcrystfel/src/xgandalf.h
+++ b/libcrystfel/src/indexers/xgandalf.h
@@ -37,9 +37,6 @@
  * XGANDALF indexer interface
  */
 
-typedef struct xgandalf_options XGandalfOptions;
-extern struct argp xgandalf_argp;
-
 #include "index.h"
 
 extern int run_xgandalf(struct image *image, void *ipriv);