Make all the indexer-specific option structures non-opaque

Making them opaque seemed like a nice idea, because all the indexers
could take care of their own command-line arguments.  However, it
doesn't work at all when indexing is run via the API.

12 files changed, 94 insertions, 88 deletions

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index c6876468..ce341197 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -204,7 +204,7 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
                             double wavelength_estimate,
                             double clen_estimate,
                             struct xgandalf_options *xgandalf_opts,
-                            struct pinkIndexer_options* pinkIndexer_opts,
+                            struct pinkindexer_options* pinkIndexer_opts,
                             struct felix_options *felix_opts,
                             struct taketwo_options *taketwo_opts,
                             struct fromfile_options *fromfile_opts)
@@ -335,7 +335,7 @@ IndexingPrivate *setup_indexing(const char *method_list,
                                 int n_threads,
                                 struct taketwo_options *ttopts,
                                 struct xgandalf_options *xgandalf_opts,
-                                struct pinkIndexer_options *pinkIndexer_opts,
+                                struct pinkindexer_options *pinkIndexer_opts,
                                 struct felix_options *felix_opts,
                                 struct fromfile_options *fromfile_opts)
 {
@@ -1189,11 +1189,11 @@ char *detect_indexing_methods(UnitCell *cell)
 }
 
 
-void default_method_options(TakeTwoOptions **ttopts,
-                            XGandalfOptions **xgandalf_opts,
-                            PinkIndexerOptions **pinkIndexer_opts,
-                            FelixOptions **felix_opts,
-                            FromFileOptions **fromfile_opts)
+void default_method_options(struct taketwo_options **ttopts,
+                            struct xgandalf_options **xgandalf_opts,
+                            struct pinkindexer_options **pinkIndexer_opts,
+                            struct felix_options **felix_opts,
+                            struct fromfile_options **fromfile_opts)
 {
 	taketwo_default_options(ttopts);
 	xgandalf_default_options(xgandalf_opts);
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index a4aef671..30bfa7c7 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -125,6 +125,63 @@ typedef enum {
 
 } IndexingFlags;
 
+
+/**
+ * Indexer-specific "private" options
+ */
+struct pinkindexer_options {
+	unsigned int considered_peaks_count;
+	unsigned int angle_resolution;
+	unsigned int refinement_type;
+	float maxResolutionForIndexing_1_per_A;
+	float tolerance;
+	float reflectionRadius; /* In m^-1 */
+	float customBandwidth;
+	float maxRefinementDisbalance;
+};
+
+
+struct xgandalf_options {
+	unsigned int sampling_pitch;
+	unsigned int grad_desc_iterations;
+	float tolerance;
+	unsigned int no_deviation_from_provided_cell;
+	float minLatticeVectorLength_A;
+	float maxLatticeVectorLength_A;
+	int maxPeaksForIndexing;
+};
+
+
+struct taketwo_options
+{
+	int member_thresh;
+	double len_tol;
+	double angle_tol;
+	double trace_tol;
+};
+
+
+struct fromfile_options
+{
+	char *filename;
+};
+
+
+struct felix_options
+{
+	double ttmin;  /* radians */
+	double ttmax;  /* radians */
+	int min_visits;
+	double min_completeness;
+	double max_uniqueness;
+	int n_voxels;
+	double fraction_max_visits;
+	double sigma;
+	double domega;
+	double max_internal_angle;
+};
+
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -148,23 +205,17 @@ extern char *base_indexer_str(IndexingMethod indm);
 #include "image.h"
 #include "datatemplate.h"
 
-typedef struct felix_options FelixOptions;
-typedef struct taketwo_options TakeTwoOptions;
-typedef struct xgandalf_options XGandalfOptions;
-typedef struct pinkIndexer_options PinkIndexerOptions;
-typedef struct fromfile_options FromFileOptions;
-
 extern struct argp felix_argp;
 extern struct argp pinkIndexer_argp;
 extern struct argp taketwo_argp;
 extern struct argp xgandalf_argp;
 extern struct argp fromfile_argp;
 
-extern void default_method_options(TakeTwoOptions **ttopts,
-                                   XGandalfOptions **xgandalf_opts,
-                                   PinkIndexerOptions **pinkIndexer_opts,
-                                   FelixOptions **felix_opts,
-                                   FromFileOptions **fromfile_opts);
+extern void default_method_options(struct taketwo_options **ttopts,
+                                   struct xgandalf_options **xgandalf_opts,
+                                   struct pinkindexer_options **pinkIndexer_opts,
+                                   struct felix_options **felix_opts,
+                                   struct fromfile_options **fromfile_opts);
 
 extern IndexingPrivate *setup_indexing(const char *methods,
                                        UnitCell *cell,
@@ -175,7 +226,7 @@ extern IndexingPrivate *setup_indexing(const char *methods,
                                        int n_threads,
                                        struct taketwo_options *ttopts,
                                        struct xgandalf_options *xgandalf_opts,
-                                       struct pinkIndexer_options *pinkIndexer_opts,
+                                       struct pinkindexer_options *pinkIndexer_opts,
                                        struct felix_options *felix_opts,
                                        struct fromfile_options *fromfile_opts);
 
diff --git a/libcrystfel/src/indexers/felix.c b/libcrystfel/src/indexers/felix.c
index dcd50613..db9cccf8 100644
--- a/libcrystfel/src/indexers/felix.c
+++ b/libcrystfel/src/indexers/felix.c
@@ -62,26 +62,12 @@
 #include "cell.h"
 #include "cell-utils.h"
 #include "felix.h"
+#include "index.h"
 
 
 #define FELIX_VERBOSE 0
 
 
-struct felix_options
-{
-	double ttmin;  /* radians */
-	double ttmax;  /* radians */
-	int min_visits;
-	double min_completeness;
-	double max_uniqueness;
-	int n_voxels;
-	double fraction_max_visits;
-	double sigma;
-	double domega;
-	double max_internal_angle;
-};
-
-
 /* Global private data, prepared once */
 struct felix_private
 {
@@ -820,9 +806,9 @@ static void felix_show_help()
 }
 
 
-int felix_default_options(FelixOptions **opts_ptr)
+int felix_default_options(struct felix_options **opts_ptr)
 {
-	FelixOptions *opts;
+	struct felix_options *opts;
 
 	opts = malloc(sizeof(struct felix_options));
 	if ( opts == NULL ) return ENOMEM;
diff --git a/libcrystfel/src/indexers/felix.h b/libcrystfel/src/indexers/felix.h
index 83179d6f..6379c4ee 100644
--- a/libcrystfel/src/indexers/felix.h
+++ b/libcrystfel/src/indexers/felix.h
@@ -39,7 +39,7 @@
  * Felix indexer interface
  */
 
-extern int felix_default_options(FelixOptions **opts_ptr);
+extern int felix_default_options(struct felix_options **opts_ptr);
 
 extern void *felix_prepare(IndexingMethod *indm, UnitCell *cell,
                            struct felix_options *opts);
diff --git a/libcrystfel/src/indexers/fromfile.c b/libcrystfel/src/indexers/fromfile.c
index 9a99b242..f0372489 100644
--- a/libcrystfel/src/indexers/fromfile.c
+++ b/libcrystfel/src/indexers/fromfile.c
@@ -42,14 +42,10 @@
 
 #include "image.h"
 #include "uthash.h"
+#include "index.h"
 
 /** \file fromfile.h */
 
-struct fromfile_options
-{
-	char *filename;
-};
-
 #define MAX_KEY_LEN (256)
 #define MAX_CRYSTALS (16)
 
@@ -373,9 +369,9 @@ static void fromfile_show_help()
 }
 
 
-int fromfile_default_options(FromFileOptions **opts_ptr)
+int fromfile_default_options(struct fromfile_options **opts_ptr)
 {
-	FromFileOptions *opts;
+	struct fromfile_options *opts;
 	opts = malloc(sizeof(struct fromfile_options));
 	if ( opts == NULL ) return ENOMEM;
 	opts->filename = NULL;
diff --git a/libcrystfel/src/indexers/fromfile.h b/libcrystfel/src/indexers/fromfile.h
index 375a54e5..caff07c5 100644
--- a/libcrystfel/src/indexers/fromfile.h
+++ b/libcrystfel/src/indexers/fromfile.h
@@ -36,7 +36,7 @@
 
 #include "image.h"
 
-extern int fromfile_default_options(FromFileOptions **opts_ptr);
+extern int fromfile_default_options(struct fromfile_options **opts_ptr);
 extern void *fromfile_prepare(IndexingMethod *indm,
                               struct fromfile_options *opts);
 extern int fromfile_index(struct image *image, void *mpriv);
diff --git a/libcrystfel/src/indexers/pinkindexer.c b/libcrystfel/src/indexers/pinkindexer.c
index 7da44f73..7522aad1 100644
--- a/libcrystfel/src/indexers/pinkindexer.c
+++ b/libcrystfel/src/indexers/pinkindexer.c
@@ -39,19 +39,9 @@
 #include "utils.h"
 #include "cell-utils.h"
 #include "peaks.h"
+#include "index.h"
 
 
-struct pinkIndexer_options {
-	unsigned int considered_peaks_count;
-	unsigned int angle_resolution;
-	unsigned int refinement_type;
-	float maxResolutionForIndexing_1_per_A;
-	float tolerance;
-	float reflectionRadius; /* In m^-1 */
-	float customBandwidth;
-	float maxRefinementDisbalance;
-};
-
 #ifdef HAVE_PINKINDEXER
 
 #include <pinkIndexer/adaptions/crystfel/Lattice.h>
@@ -190,7 +180,7 @@ int run_pinkIndexer(struct image *image, void *ipriv, int n_threads)
 
 void *pinkIndexer_prepare(IndexingMethod *indm,
                           UnitCell *cell,
-                          struct pinkIndexer_options *pinkIndexer_opts,
+                          struct pinkindexer_options *pinkIndexer_opts,
                           double wavelength_estimate,
                           double clen_estimate)
 {
@@ -383,7 +373,7 @@ int run_pinkIndexer(struct image *image, void *ipriv, int n_threads)
 
 extern void *pinkIndexer_prepare(IndexingMethod *indm,
                                  UnitCell *cell,
-                                 struct pinkIndexer_options *pinkIndexer_opts,
+                                 struct pinkindexer_options *pinkIndexer_opts,
                                  double wavelength_estimate,
                                  double clen_estimate)
 {
@@ -431,11 +421,11 @@ static void pinkIndexer_show_help()
 }
 
 
-int pinkIndexer_default_options(PinkIndexerOptions **opts_ptr)
+int pinkIndexer_default_options(struct pinkindexer_options **opts_ptr)
 {
-	PinkIndexerOptions *opts;
+	struct pinkindexer_options *opts;
 
-	opts = malloc(sizeof(struct pinkIndexer_options));
+	opts = malloc(sizeof(struct pinkindexer_options));
 	if ( opts == NULL ) return ENOMEM;
 
 	opts->considered_peaks_count = 4;
@@ -456,7 +446,7 @@ static error_t pinkindexer_parse_arg(int key, char *arg,
 {
 	float tmp;
 	int r;
-	struct pinkIndexer_options **opts_ptr = state->input;
+	struct pinkindexer_options **opts_ptr = state->input;
 
 	switch ( key ) {
 
diff --git a/libcrystfel/src/indexers/pinkindexer.h b/libcrystfel/src/indexers/pinkindexer.h
index 122bac87..c75b5551 100644
--- a/libcrystfel/src/indexers/pinkindexer.h
+++ b/libcrystfel/src/indexers/pinkindexer.h
@@ -35,13 +35,13 @@
 #include "index.h"
 #include "datatemplate.h"
 
-extern int pinkIndexer_default_options(PinkIndexerOptions **opts_ptr);
+extern int pinkIndexer_default_options(struct pinkindexer_options **opts_ptr);
 
 extern int run_pinkIndexer(struct image *image, void *ipriv, int n_threads);
 
 extern void *pinkIndexer_prepare(IndexingMethod *indm,
                                  UnitCell *cell,
-                                 struct pinkIndexer_options *pinkIndexer_opts,
+                                 struct pinkindexer_options *pinkIndexer_opts,
                                  double wavelength_estimate,
                                  double clen_estimate);
 
diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 8ce33083..60bb6fed 100644
--- a/libcrystfel/src/indexers/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
@@ -102,14 +102,6 @@
 #include "peaks.h"
 #include "symmetry.h"
 
-struct taketwo_options
-{
-	int member_thresh;
-	double len_tol;
-	double angle_tol;
-	double trace_tol;
-};
-
 /**
  * \param obsvec an observed vector between two spots
  * \param matches array of matching theoretical vectors from unit cell
@@ -2284,9 +2276,9 @@ static void taketwo_show_help()
 }
 
 
-int taketwo_default_options(TakeTwoOptions **opts_ptr)
+int taketwo_default_options(struct taketwo_options **opts_ptr)
 {
-	TakeTwoOptions *opts;
+	struct taketwo_options *opts;
 
 	opts = malloc(sizeof(struct taketwo_options));
 	if ( opts == NULL ) return ENOMEM;
diff --git a/libcrystfel/src/indexers/taketwo.h b/libcrystfel/src/indexers/taketwo.h
index f3157d72..471b08b2 100644
--- a/libcrystfel/src/indexers/taketwo.h
+++ b/libcrystfel/src/indexers/taketwo.h
@@ -38,7 +38,7 @@
 
 /** \file taketwo.h */
 
-extern int taketwo_default_options(TakeTwoOptions **opts_ptr);
+extern int taketwo_default_options(struct taketwo_options **opts_ptr);
 extern void *taketwo_prepare(IndexingMethod *indm, struct taketwo_options *opts,
                              UnitCell *cell);
 extern const char *taketwo_probe(UnitCell *cell);
diff --git a/libcrystfel/src/indexers/xgandalf.c b/libcrystfel/src/indexers/xgandalf.c
index ada0507a..d83af6cb 100644
--- a/libcrystfel/src/indexers/xgandalf.c
+++ b/libcrystfel/src/indexers/xgandalf.c
@@ -35,6 +35,7 @@
 #include "utils.h"
 #include "cell-utils.h"
 #include "peaks.h"
+#include "index.h"
 
 #ifdef HAVE_XGANDALF
 #include "xgandalf/adaptions/crystfel/Lattice.h"
@@ -44,16 +45,6 @@
 
 /** \file xgandalf.h */
 
-struct xgandalf_options {
-	unsigned int sampling_pitch;
-	unsigned int grad_desc_iterations;
-	float tolerance;
-	unsigned int no_deviation_from_provided_cell;
-	float minLatticeVectorLength_A;
-	float maxLatticeVectorLength_A;
-	int maxPeaksForIndexing;
-};
-
 #ifdef HAVE_XGANDALF
 
 struct xgandalf_private_data {
@@ -387,9 +378,9 @@ static void xgandalf_show_help()
 }
 
 
-int xgandalf_default_options(XGandalfOptions **opts_ptr)
+int xgandalf_default_options(struct xgandalf_options **opts_ptr)
 {
-	XGandalfOptions *opts;
+	struct xgandalf_options *opts;
 
 	opts = malloc(sizeof(struct xgandalf_options));
 	if ( opts == NULL ) return ENOMEM;
diff --git a/libcrystfel/src/indexers/xgandalf.h b/libcrystfel/src/indexers/xgandalf.h
index 79078410..b43f09ea 100644
--- a/libcrystfel/src/indexers/xgandalf.h
+++ b/libcrystfel/src/indexers/xgandalf.h
@@ -39,7 +39,7 @@
 
 #include "index.h"
 
-extern int xgandalf_default_options(XGandalfOptions **opts_ptr);
+extern int xgandalf_default_options(struct xgandalf_options **opts_ptr);
 
 extern int run_xgandalf(struct image *image, void *ipriv);