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-rw-r--r--libcrystfel/src/index.c12
-rw-r--r--libcrystfel/src/index.h7
-rw-r--r--libcrystfel/src/indexers/fromfile.c96
-rw-r--r--libcrystfel/src/indexers/fromfile.h18
-rw-r--r--src/gui_index.c4
-rw-r--r--src/indexamajig.c7
6 files changed, 104 insertions, 40 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index f9001968..0ce9e2a2 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -208,7 +208,7 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
struct pinkIndexer_options* pinkIndexer_opts,
struct felix_options *felix_opts,
struct taketwo_options *taketwo_opts,
- char *filename)
+ struct fromfile_options *fromfile_opts)
{
char *str;
IndexingMethod in = *m;
@@ -237,7 +237,7 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
break;
case INDEXING_FILE :
- priv = fromfile_prepare(filename, cell);
+ priv = fromfile_prepare(m, fromfile_opts);
break;
case INDEXING_FELIX :
@@ -336,7 +336,7 @@ IndexingPrivate *setup_indexing(const char *method_list,
struct xgandalf_options *xgandalf_opts,
struct pinkIndexer_options *pinkIndexer_opts,
struct felix_options *felix_opts,
- char *filename)
+ struct fromfile_options *fromfile_opts)
{
IndexingPrivate *ipriv;
IndexingMethod *methods;
@@ -406,7 +406,7 @@ IndexingPrivate *setup_indexing(const char *method_list,
pinkIndexer_opts,
felix_opts,
ttopts,
- filename);
+ fromfile_opts);
if ( ipriv->engine_private[i] == NULL ) return NULL;
@@ -1213,10 +1213,12 @@ char *detect_indexing_methods(UnitCell *cell)
void default_method_options(TakeTwoOptions **ttopts,
XGandalfOptions **xgandalf_opts,
PinkIndexerOptions **pinkIndexer_opts,
- FelixOptions **felix_opts)
+ FelixOptions **felix_opts,
+ FromFileOptions **fromfile_opts)
{
taketwo_default_options(ttopts);
xgandalf_default_options(xgandalf_opts);
pinkIndexer_default_options(pinkIndexer_opts);
felix_default_options(felix_opts);
+ fromfile_default_options(fromfile_opts);
}
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 5cee29b2..88b9b67e 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -152,16 +152,19 @@ 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);
+ FelixOptions **felix_opts,
+ FromFileOptions **fromfile_opts);
extern IndexingPrivate *setup_indexing(const char *methods,
UnitCell *cell,
@@ -173,7 +176,7 @@ extern IndexingPrivate *setup_indexing(const char *methods,
struct xgandalf_options *xgandalf_opts,
struct pinkIndexer_options *pinkIndexer_opts,
struct felix_options *felix_opts,
- char *filename);
+ struct fromfile_options *fromfile_opts);
extern const IndexingMethod *indexing_methods(IndexingPrivate *p, int *n);
diff --git a/libcrystfel/src/indexers/fromfile.c b/libcrystfel/src/indexers/fromfile.c
index 73cee547..400683ae 100644
--- a/libcrystfel/src/indexers/fromfile.c
+++ b/libcrystfel/src/indexers/fromfile.c
@@ -5,6 +5,7 @@
*
* Authors:
* 2020 Pascal Hogan-Lamarre <pascal.hogan.lamarre@mail.utoronto.ca>
+ * 2021 Thomas White <thomas.white@desy.de>
*
* This file is part of CrystFEL.
*
@@ -30,6 +31,7 @@
#include <assert.h>
#include <fenv.h>
#include <unistd.h>
+#include <argp.h>
#include "image.h"
#include "uthash.h"
@@ -45,6 +47,12 @@
#define NKEYS_PER_LINE 2
+struct fromfile_options
+{
+ char *filename;
+};
+
+
struct fromfile_keys
{
char filename[100];
@@ -162,7 +170,7 @@ char *read_unknown_string(FILE *fh)
}
-void *fromfile_prepare(char *solution_filename, UnitCell *cell)
+void *fromfile_prepare(IndexingMethod *indm, struct fromfile_options *opts)
{
FILE *fh;
int nlines;
@@ -177,27 +185,15 @@ void *fromfile_prepare(char *solution_filename, UnitCell *cell)
struct fromfile_entries *item = NULL;
float params[NPARAMS_PER_LINE];
- /* Assembling solution file name from input file name*/
- char *path_to_sol;
- size_t path_len;
- char *core_name = strtok(solution_filename, ".");
- char *extension = ".sol";
- path_len = sizeof(core_name) + sizeof(extension) + sizeof("../");
- path_to_sol = realloc(NULL, sizeof(char)*path_len);
- strcpy(path_to_sol, "../");
- strcat(path_to_sol, core_name);
- strcat(path_to_sol, extension);
-
- fh = fopen(path_to_sol, "r");
-
+ fh = fopen(opts->filename, "r");
if ( fh == NULL ) {
- ERROR("%s not found by fromfile_prepare\n", path_to_sol);
- return 0;
+ ERROR("%s not found by fromfile_prepare\n", opts->filename);
+ return NULL;
} else {
- STATUS("Found solution file %s\n", path_to_sol);
+ STATUS("Found solution file %s\n", opts->filename);
}
- nlines = ncrystals_in_sol(path_to_sol);
+ nlines = ncrystals_in_sol(opts->filename);
/* Total crystal parameters in solution file */
nparams_in_solution = nlines*NPARAMS_PER_LINE;
/* Total entries in solution file */
@@ -375,3 +371,67 @@ void fromfile_cleanup(void *mpriv)
free(dp);
}
+
+
+static void fromfile_show_help()
+{
+ printf("Parameters for 'fromfile' indexing:\n"
+" --fromfile-input-file\n"
+" Filename of indexing solution file\n"
+);
+}
+
+
+int fromfile_default_options(FromFileOptions **opts_ptr)
+{
+ FromFileOptions *opts;
+ opts = malloc(sizeof(struct fromfile_options));
+ if ( opts == NULL ) return ENOMEM;
+ opts->filename = NULL;
+ *opts_ptr = opts;
+ return 0;
+}
+
+
+static error_t fromfile_parse_arg(int key, char *arg,
+ struct argp_state *state)
+{
+ struct fromfile_options **opts_ptr = state->input;
+ int r;
+
+ switch ( key ) {
+
+ case ARGP_KEY_INIT :
+ r = fromfile_default_options(opts_ptr);
+ if ( r ) return r;
+ break;
+
+ case 1 :
+ fromfile_show_help();
+ return EINVAL;
+
+ case 2 :
+ (*opts_ptr)->filename = strdup(arg);
+ break;
+
+ default :
+ return ARGP_ERR_UNKNOWN;
+
+ }
+
+ return 0;
+}
+
+
+static struct argp_option fromfile_options[] = {
+
+ {"help-fromfile", 1, NULL, OPTION_NO_USAGE,
+ "Show options for 'from file' indexing", 99},
+
+ {"fromfile-input-file", 2, "filename", OPTION_HIDDEN, NULL},
+ {0}
+};
+
+
+struct argp fromfile_argp = { fromfile_options, fromfile_parse_arg,
+ NULL, NULL, NULL, NULL, NULL };
diff --git a/libcrystfel/src/indexers/fromfile.h b/libcrystfel/src/indexers/fromfile.h
index deb7b105..ba7e1ee4 100644
--- a/libcrystfel/src/indexers/fromfile.h
+++ b/libcrystfel/src/indexers/fromfile.h
@@ -5,6 +5,7 @@
*
* Authors:
* 2020 Pascal Hogan-Lamarre <pascal.hogan.lamarre@mail.utoronto.ca>
+ * 2021 Thomas White <thomas.white@desy.de>
*
* This file is part of CrystFEL.
*
@@ -26,23 +27,14 @@
#ifndef FROMFILE_H
#define FROMFILE_H
-struct fromfile_keys;
-struct fromfile_entries;
-struct fromfile_private;
+#include <argp.h>
#include "image.h"
-#include "cell.h"
-#include "uthash.h"
-
-extern void print_struct(struct fromfile_entries *sol_hash);
-
-extern void full_print_struct(struct fromfile_entries *sol_hash);
-
-extern void *fromfile_prepare(char *solution_filename, UnitCell *cell);
+extern int fromfile_default_options(FromFileOptions **opts_ptr);
+extern void *fromfile_prepare(IndexingMethod *indm,
+ struct fromfile_options *opts);
extern int fromfile_index(struct image *image, void *mpriv, int crystal_number);
-
extern void fromfile_cleanup(void *mpriv);
-
#endif /* FROMFILE_H */
diff --git a/src/gui_index.c b/src/gui_index.c
index 85a9f9c3..145d0f1e 100644
--- a/src/gui_index.c
+++ b/src/gui_index.c
@@ -486,6 +486,7 @@ static void run_indexing_once(struct crystfelproject *proj)
XGandalfOptions *xgandalf_opts;
PinkIndexerOptions *pinkIndexer_opts;
FelixOptions *felix_opts;
+ FromFileOptions *fromfile_opts;
char *old_cwd;
char *tmpdir;
int r;
@@ -514,7 +515,8 @@ static void run_indexing_once(struct crystfelproject *proj)
default_method_options(&taketwoopts,
&xgandalf_opts,
&pinkIndexer_opts,
- &felix_opts);
+ &felix_opts,
+ &fromfile_opts);
ipriv = setup_indexing(methods, cell,
proj->indexing_params.tols,
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 7f73cef6..d5d3d31a 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -97,6 +97,7 @@ struct indexamajig_arguments
FelixOptions **felix_opts_ptr;
XGandalfOptions **xgandalf_opts_ptr;
PinkIndexerOptions **pinkindexer_opts_ptr;
+ FromFileOptions **fromfile_opts_ptr;
};
@@ -135,6 +136,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
state->child_inputs[1] = args->felix_opts_ptr;
state->child_inputs[2] = args->xgandalf_opts_ptr;
state->child_inputs[3] = args->pinkindexer_opts_ptr;
+ state->child_inputs[4] = args->fromfile_opts_ptr;
break;
case 'h' :
@@ -601,6 +603,7 @@ int main(int argc, char *argv[])
FelixOptions *felix_opts = NULL;
XGandalfOptions *xgandalf_opts = NULL;
PinkIndexerOptions *pinkindexer_opts = NULL;
+ FromFileOptions *fromfile_opts = NULL;
double wl_from_dt;
/* Defaults for "top level" arguments */
@@ -628,6 +631,7 @@ int main(int argc, char *argv[])
args.felix_opts_ptr = &felix_opts;
args.xgandalf_opts_ptr = &xgandalf_opts;
args.pinkindexer_opts_ptr = &pinkindexer_opts;
+ args.fromfile_opts_ptr = &fromfile_opts;
/* Defaults for process_image arguments */
args.iargs.cell = NULL;
@@ -818,6 +822,7 @@ int main(int argc, char *argv[])
{&felix_argp, 0, NULL, -2},
{&xgandalf_argp, 0, NULL, -2},
{&pinkIndexer_argp, 0, NULL, -2},
+ {&fromfile_argp, 0, NULL, -2},
{0}
};
@@ -996,7 +1001,7 @@ int main(int argc, char *argv[])
xgandalf_opts,
pinkindexer_opts,
felix_opts,
- args.filename);
+ fromfile_opts);
free(args.filename);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 08:23:52 +0000