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-rw-r--r--src/indexamajig.c128
1 files changed, 36 insertions, 92 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 01377de3..3076ea86 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -174,37 +174,13 @@ static void show_help(const char *s)
}
-static int parse_cell_reduction(const char *scellr, int *err,
- int *reduction_needs_cell)
-{
- *err = 0;
- if ( strcmp(scellr, "none") == 0 ) {
- *reduction_needs_cell = 0;
- return CELLR_NONE;
- } else if ( strcmp(scellr, "reduce") == 0) {
- *reduction_needs_cell = 1;
- return CELLR_REDUCE;
- } else if ( strcmp(scellr, "compare") == 0) {
- *reduction_needs_cell = 1;
- return CELLR_COMPARE;
- } else if ( strcmp(scellr, "compare_ab") == 0) {
- *reduction_needs_cell = 1;
- return CELLR_COMPARE_AB;
- } else {
- *err = 1;
- *reduction_needs_cell = 0;
- return CELLR_NONE;
- }
-}
-
-
int main(int argc, char *argv[])
{
int c;
char *filename = NULL;
char *outfile = NULL;
FILE *fh;
- FILE *ofh;
+ Stream *st;
char *rval = NULL;
int config_noindex = 0;
int config_cmfilter = 0;
@@ -213,7 +189,6 @@ int main(int argc, char *argv[])
int config_satcorr = 1;
int config_checkprefix = 1;
int config_closer = 0;
- int config_insane = 0;
int config_bgsub = 1;
int config_basename = 0;
float threshold = 800.0;
@@ -224,17 +199,13 @@ int main(int argc, char *argv[])
char *geometry = NULL;
IndexingMethod *indm;
IndexingPrivate **ipriv;
- int indexer_needs_cell;
- int reduction_needs_cell;
char *indm_str = NULL;
UnitCell *cell;
char *pdb = NULL;
char *prefix = NULL;
char *speaks = NULL;
- char *scellr = NULL;
char *toler = NULL;
float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */
- int cellr;
int peaks;
int n_proc = 1;
char *prepare_line;
@@ -243,7 +214,6 @@ int main(int argc, char *argv[])
struct index_args iargs;
struct beam_params *beam = NULL;
char *element = NULL;
- int stream_flags = STREAM_INTEGRATED;
char *hdf5_peak_path = NULL;
struct copy_hdf5_field *copyme;
char *intrad = NULL;
@@ -255,6 +225,10 @@ int main(int argc, char *argv[])
int no_revalidate = 0;
int integrate_found = 0;
+ /* For ease of upgrading from old method */
+ char *scellr = NULL;
+ int config_insane = 0;
+
copyme = new_copy_hdf5_field_list();
if ( copyme == NULL ) {
ERROR("Couldn't allocate HDF5 field list.\n");
@@ -290,7 +264,6 @@ int main(int argc, char *argv[])
{"peaks", 1, NULL, 2},
{"cell-reduction", 1, NULL, 3},
{"min-gradient", 1, NULL, 4},
- {"record", 1, NULL, 5},
{"cpus", 1, NULL, 6},
{"cpugroup", 1, NULL, 7},
{"cpuoffset", 1, NULL, 8},
@@ -301,6 +274,8 @@ int main(int argc, char *argv[])
{"tolerance", 1, NULL, 13},
{"int-radius", 1, NULL, 14},
+ /* FIXME: Add '--no-peaks' and '--no-reflections' */
+
{"integrate-saturated",0, &integrate_saturated,1},
{"use-saturated", 0, &use_saturated, 1},
{"no-revalidate", 0, &no_revalidate, 1},
@@ -376,8 +351,7 @@ int main(int argc, char *argv[])
break;
case 5 :
- stream_flags = parse_stream_flags(optarg);
- if ( stream_flags < 0 ) return 1;
+ ERROR("The option '--record' is no longer used.\n");
break;
case 6 :
@@ -425,6 +399,12 @@ int main(int argc, char *argv[])
}
+ if ( scellr != NULL ) {
+ ERROR("Old-style indexing method specification.\n");
+ /* FIXME: Translate to new style */
+ return 1;
+ }
+
if ( filename == NULL ) {
filename = strdup("-");
}
@@ -439,17 +419,6 @@ int main(int argc, char *argv[])
}
free(filename);
- if ( outfile == NULL ) {
- ofh = stdout;
- } else {
- ofh = fopen(outfile, "w");
- if ( ofh == NULL ) {
- ERROR("Failed to open output file '%s'\n", outfile);
- return 1;
- }
- free(outfile);
- }
-
if ( hdf5_peak_path == NULL ) {
hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
}
@@ -482,53 +451,24 @@ int main(int argc, char *argv[])
return 1;
}
- if ( (indm_str == NULL) ||
- ((indm_str != NULL) && (strcmp(indm_str, "none") == 0)) ) {
- STATUS("Not indexing anything.\n");
- indexer_needs_cell = 0;
- reduction_needs_cell = 0;
+ if ( indm_str == NULL ) {
+
+ STATUS("You didn't specify an indexing method, so I won't try "
+ " to index anything.\n"
+ "If that isn't what you wanted, re-run with"
+ " --indexing=<methods>.\n");
indm = NULL;
- cellr = CELLR_NONE;
+
} else {
- if ( indm_str == NULL ) {
- STATUS("You didn't specify an indexing method, so I "
- " won't try to index anything.\n"
- "If that isn't what you wanted, re-run with"
- " --indexing=<method>.\n");
- indm = NULL;
- indexer_needs_cell = 0;
- } else {
- indm = build_indexer_list(indm_str,
- &indexer_needs_cell);
- if ( indm == NULL ) {
- ERROR("Invalid indexer list '%s'\n", indm_str);
- return 1;
- }
- free(indm_str);
- }
- reduction_needs_cell = 0;
- if ( scellr == NULL ) {
- STATUS("You didn't specify a cell reduction method, so"
- " I'm going to use 'reduce'.\n");
- cellr = CELLR_REDUCE;
- reduction_needs_cell = 1;
- } else {
- int err;
- cellr = parse_cell_reduction(scellr, &err,
- &reduction_needs_cell);
- if ( err ) {
- ERROR("Unrecognised cell reduction '%s'\n",
- scellr);
- return 1;
- }
- free(scellr);
+ indm = build_indexer_list(indm_str);
+ if ( indm == NULL ) {
+ ERROR("Invalid indexer list '%s'\n", indm_str);
+ return 1;
}
+ free(indm_str);
}
- /* No indexing -> no reduction */
- if ( indm == NULL ) reduction_needs_cell = 0;
-
if ( toler != NULL ) {
int ttt;
ttt = sscanf(toler, "%f,%f,%f,%f",
@@ -586,7 +526,12 @@ int main(int argc, char *argv[])
cell = NULL;
}
- write_stream_header(ofh, argc, argv);
+ st = open_stream_for_write(outfile);
+ if ( st == NULL ) {
+ ERROR("Failed to open stream '%s'\n", outfile);
+ return 1;
+ }
+ free(outfile);
/* Get first filename and use it to set up the indexing */
prepare_line = malloc(1024);
@@ -609,7 +554,7 @@ int main(int argc, char *argv[])
/* Prepare the indexer */
if ( indm != NULL ) {
ipriv = prepare_indexing(indm, cell, prepare_filename,
- det, beam);
+ det, beam, tols);
if ( ipriv == NULL ) {
ERROR("Failed to prepare indexing.\n");
return 1;
@@ -627,9 +572,7 @@ int main(int argc, char *argv[])
iargs.config_verbose = config_verbose;
iargs.config_satcorr = config_satcorr;
iargs.config_closer = config_closer;
- iargs.config_insane = config_insane;
iargs.config_bgsub = config_bgsub;
- iargs.cellr = cellr;
iargs.tols[0] = tols[0];
iargs.tols[1] = tols[1];
iargs.tols[2] = tols[2];
@@ -644,7 +587,6 @@ int main(int argc, char *argv[])
iargs.peaks = peaks;
iargs.beam = beam;
iargs.element = element;
- iargs.stream_flags = stream_flags;
iargs.hdf5_peak_path = hdf5_peak_path;
iargs.copyme = copyme;
iargs.ir_inn = ir_inn;
@@ -654,9 +596,11 @@ int main(int argc, char *argv[])
iargs.integrate_saturated = integrate_saturated;
iargs.no_revalidate = no_revalidate;
iargs.integrate_found = integrate_found;
+ iargs.include_peaks = 1;
+ iargs.include_reflections = 1; /* FIXME! */
create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
- use_this_one_instead, ofh);
+ use_this_one_instead, st);
free(prefix);
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-30 12:44:47 +0000