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-rw-r--r--libcrystfel/CMakeLists.txt24
-rw-r--r--libcrystfel/meson.build24
-rw-r--r--libcrystfel/src/index.c16
-rw-r--r--libcrystfel/src/index.h14
-rw-r--r--libcrystfel/src/indexers/asdf.c (renamed from libcrystfel/src/asdf.c)0
-rw-r--r--libcrystfel/src/indexers/asdf.h (renamed from libcrystfel/src/asdf.h)0
-rw-r--r--libcrystfel/src/indexers/dirax.c (renamed from libcrystfel/src/dirax.c)0
-rw-r--r--libcrystfel/src/indexers/dirax.h (renamed from libcrystfel/src/dirax.h)0
-rw-r--r--libcrystfel/src/indexers/felix.c (renamed from libcrystfel/src/felix.c)0
-rw-r--r--libcrystfel/src/indexers/felix.h (renamed from libcrystfel/src/felix.h)3
-rw-r--r--libcrystfel/src/indexers/mosflm.c (renamed from libcrystfel/src/mosflm.c)0
-rw-r--r--libcrystfel/src/indexers/mosflm.h (renamed from libcrystfel/src/mosflm.h)0
-rw-r--r--libcrystfel/src/indexers/pinkindexer.c (renamed from libcrystfel/src/pinkindexer.c)27
-rw-r--r--libcrystfel/src/indexers/pinkindexer.h (renamed from libcrystfel/src/pinkindexer.h)20
-rw-r--r--libcrystfel/src/indexers/taketwo.c (renamed from libcrystfel/src/taketwo.c)0
-rw-r--r--libcrystfel/src/indexers/taketwo.h (renamed from libcrystfel/src/taketwo.h)3
-rw-r--r--libcrystfel/src/indexers/xds.c (renamed from libcrystfel/src/xds.c)0
-rw-r--r--libcrystfel/src/indexers/xds.h (renamed from libcrystfel/src/xds.h)0
-rw-r--r--libcrystfel/src/indexers/xgandalf.c (renamed from libcrystfel/src/xgandalf.c)0
-rw-r--r--libcrystfel/src/indexers/xgandalf.h (renamed from libcrystfel/src/xgandalf.h)3
-rw-r--r--src/indexamajig.c6
21 files changed, 62 insertions, 78 deletions
diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt
index 394156ed..6bac46f0 100644
--- a/libcrystfel/CMakeLists.txt
+++ b/libcrystfel/CMakeLists.txt
@@ -45,19 +45,12 @@ set(LIBCRYSTFEL_SOURCES
src/reflist-utils.c
src/filters.c
src/index.c
- src/dirax.c
- src/mosflm.c
src/cell-utils.c
src/integer_matrix.c
src/crystal.c
- src/xds.c
src/integration.c
src/predict-refine.c
- src/felix.c
src/peakfinder8.c
- src/taketwo.c
- src/xgandalf.c
- src/pinkindexer.c
src/rational.c
src/spectrum.c
src/datatemplate.c
@@ -66,9 +59,16 @@ set(LIBCRYSTFEL_SOURCES
src/image-cbf.c
src/image-hdf5.c
src/image-msgpack.c
- src/asdf.c
${BISON_symopp_OUTPUTS}
${FLEX_symopl_OUTPUTS}
+ src/indexers/dirax.c
+ src/indexers/mosflm.c
+ src/indexers/xds.c
+ src/indexers/felix.c
+ src/indexers/taketwo.c
+ src/indexers/asdf.c
+ src/indexers/xgandalf.c
+ src/indexers/pinkindexer.c
)
set(LIBCRYSTFEL_HEADERS
@@ -85,20 +85,12 @@ set(LIBCRYSTFEL_HEADERS
src/index.h
src/image.h
src/filters.h
- src/dirax.h
- src/mosflm.h
src/cell-utils.h
src/integer_matrix.h
src/crystal.h
- src/xds.h
src/predict-refine.h
src/integration.h
- src/asdf.h
- src/felix.h
src/peakfinder8.h
- src/taketwo.h
- src/xgandalf.h
- src/pinkindexer.h
src/rational.h
src/spectrum.h
src/datatemplate.h
diff --git a/libcrystfel/meson.build b/libcrystfel/meson.build
index 412fe90a..d8543eb8 100644
--- a/libcrystfel/meson.build
+++ b/libcrystfel/meson.build
@@ -80,21 +80,13 @@ libcrystfel_sources = ['src/image.c',
'src/crystal.c',
'src/integration.c',
'src/symmetry.c',
- 'src/mosflm.c',
- 'src/taketwo.c',
- 'src/dirax.c',
'src/peakfinder8.c',
'src/thread-pool.c',
'src/peaks.c',
'src/utils.c',
- 'src/felix.c',
'src/predict-refine.c',
- 'src/xds.c',
- 'src/asdf.c',
'src/filters.c',
'src/rational.c',
- 'src/xgandalf.c',
- 'src/pinkindexer.c',
'src/geometry.c',
'src/reflist.c',
'src/reflist-utils.c',
@@ -104,6 +96,14 @@ libcrystfel_sources = ['src/image.c',
'src/image-cbf.c',
'src/image-hdf5.c',
'src/image-msgpack.c',
+ 'src/indexers/dirax.c',
+ 'src/indexers/felix.c',
+ 'src/indexers/mosflm.c',
+ 'src/indexers/taketwo.c',
+ 'src/indexers/xds.c',
+ 'src/indexers/asdf.c',
+ 'src/indexers/xgandalf.c',
+ 'src/indexers/pinkindexer.c',
symop_lex_ch,
symop_parse_ch,
]
@@ -138,20 +138,12 @@ install_headers(['src/reflist.h',
'src/index.h',
'src/image.h',
'src/filters.h',
- 'src/dirax.h',
- 'src/mosflm.h',
'src/cell-utils.h',
'src/integer_matrix.h',
'src/crystal.h',
- 'src/xds.h',
'src/predict-refine.h',
'src/integration.h',
- 'src/asdf.h',
- 'src/felix.h',
'src/peakfinder8.h',
- 'src/taketwo.h',
- 'src/xgandalf.h',
- 'src/pinkindexer.h',
'src/rational.h',
'src/spectrum.h',
'src/datatemplate.h',
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);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 7ef4f35c..2d0e53c8 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -59,7 +59,6 @@
#include <reflist-utils.h>
#include <cell-utils.h>
#include <integration.h>
-#include <taketwo.h>
#include <image.h>
#include <datatemplate.h>
@@ -244,7 +243,10 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
ERROR("Invalid value for --min-peaks\n");
return EINVAL;
}
- (*(args->pinkindexer_opts_ptr))->min_peaks = args->iargs.min_peaks;
+ /* FIXME: Horrible layering violation, needed for
+ * pinkIndexer multi-lattice indexing but no longer
+ * possible. */
+ //(*(args->pinkindexer_opts_ptr))->min_peaks = args->iargs.min_peaks;
break;
case 304 :
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-23 02:40:17 +0000