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-rw-r--r--src/im-sandbox.c2
-rw-r--r--src/im-sandbox.h10
-rw-r--r--src/indexamajig.c226
3 files changed, 101 insertions, 137 deletions
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 7494a527..cefdeeb9 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -344,7 +344,7 @@ static void process_image(const struct index_args *iargs,
iargs->res_cutoff);
write_chunk(st, &image, hdfile,
- iargs->include_peaks, iargs->include_reflections);
+ iargs->stream_peaks, iargs->stream_refls);
for ( i=0; i<image.n_crystals; i++ ) {
crystal_free(image.crystals[i]);
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 80ffc0ad..f7951c04 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -61,16 +61,16 @@ struct index_args
struct beam_params *beam;
char *element;
char *hdf5_peak_path;
- double ir_inn;
- double ir_mid;
- double ir_out;
+ float ir_inn;
+ float ir_mid;
+ float ir_out;
struct copy_hdf5_field *copyme;
int integrate_saturated;
int use_saturated;
int no_revalidate;
int integrate_found;
- int include_peaks;
- int include_reflections;
+ int stream_peaks;
+ int stream_refls;
int res_cutoff;
};
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 908c1b6e..980f23f1 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -161,87 +161,85 @@ int main(int argc, char *argv[])
FILE *fh;
FILE *ofh;
char *rval = NULL;
- int config_noindex = 0;
- int config_cmfilter = 0;
- int config_noisefilter = 0;
- int config_verbose = 0;
- int config_satcorr = 1;
int config_checkprefix = 1;
- int config_closer = 0;
- int config_bgsub = 1;
int config_basename = 0;
- float threshold = 800.0;
- float min_gradient = 100000.0;
- float min_snr = 5.0;
- double min_int_snr = -INFINITY;
- struct detector *det;
- char *geometry = NULL;
IndexingMethod *indm;
IndexingPrivate **ipriv;
char *indm_str = NULL;
- UnitCell *cell;
char *pdb = NULL;
char *prefix = NULL;
char *speaks = NULL;
char *toler = NULL;
- float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */
- int peaks;
int n_proc = 1;
char *prepare_line;
char prepare_filename[1024];
char *use_this_one_instead;
struct index_args iargs;
- struct beam_params *beam = NULL;
- char *element = NULL;
- char *hdf5_peak_path = NULL;
- struct copy_hdf5_field *copyme;
char *intrad = NULL;
- float ir_inn = 4.0;
- float ir_mid = 5.0;
- float ir_out = 7.0;
- int integrate_saturated = 0;
- int use_saturated = 0;
- int no_revalidate = 0;
- int integrate_found = 0;
- int config_nopeaks = 0;
- int config_norefls = 0;
- int config_rescutoff = 0;
-
- /* For ease of upgrading from old method */
- char *scellr = NULL;
- int config_insane = 0;
-
- copyme = new_copy_hdf5_field_list();
- if ( copyme == NULL ) {
+
+ /* Defaults */
+ iargs.cell = NULL;
+ iargs.config_cmfilter = 0;
+ iargs.config_noisefilter = 0;
+ iargs.config_verbose = 0;
+ iargs.config_satcorr = 1;
+ iargs.config_closer = 0;
+ iargs.config_bgsub = 1;
+ iargs.tols[0] = 5.0;
+ iargs.tols[1] = 5.0;
+ iargs.tols[2] = 5.0;
+ iargs.tols[3] = 1.5;
+ iargs.threshold = 800.0;
+ iargs.min_gradient = 100000.0;
+ iargs.min_snr = 5.0;
+ iargs.min_int_snr = -INFINITY;
+ iargs.det = NULL;
+ iargs.peaks = PEAK_ZAEF;
+ iargs.beam = NULL;
+ iargs.element = NULL;
+ iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
+ iargs.copyme = NULL;
+ iargs.ir_inn = 4.0;
+ iargs.ir_mid = 5.0;
+ iargs.ir_out = 7.0;
+ iargs.use_saturated = 0;
+ iargs.integrate_saturated = 1;
+ iargs.no_revalidate = 0;
+ iargs.integrate_found = 0;
+ iargs.stream_peaks = 1;
+ iargs.stream_refls = 1;
+ iargs.res_cutoff = 0;
+ iargs.copyme = new_copy_hdf5_field_list();
+ if ( iargs.copyme == NULL ) {
ERROR("Couldn't allocate HDF5 field list.\n");
return 1;
}
+ iargs.indm = NULL; /* No default */
+ iargs.ipriv = NULL; /* No default */
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
- {"no-index", 0, &config_noindex, 1},
{"indexing", 1, NULL, 'z'},
{"geometry", 1, NULL, 'g'},
{"beam", 1, NULL, 'b'},
- {"filter-cm", 0, &config_cmfilter, 1},
- {"filter-noise", 0, &config_noisefilter, 1},
- {"verbose", 0, &config_verbose, 1},
+ {"filter-cm", 0, &iargs.config_cmfilter, 1},
+ {"filter-noise", 0, &iargs.config_noisefilter, 1},
+ {"verbose", 0, &iargs.config_verbose, 1},
{"pdb", 1, NULL, 'p'},
{"prefix", 1, NULL, 'x'},
- {"no-sat-corr", 0, &config_satcorr, 0},
- {"sat-corr", 0, &config_satcorr, 1}, /* Compat */
+ {"no-sat-corr", 0, &iargs.config_satcorr, 0},
+ {"sat-corr", 0, &iargs.config_satcorr, 1},
{"threshold", 1, NULL, 't'},
{"no-check-prefix", 0, &config_checkprefix, 0},
- {"no-closer-peak", 0, &config_closer, 0},
- {"closer-peak", 0, &config_closer, 1},
- {"insane", 0, &config_insane, 1},
+ {"no-closer-peak", 0, &iargs.config_closer, 0},
+ {"closer-peak", 0, &iargs.config_closer, 1},
{"image", 1, NULL, 'e'},
{"basename", 0, &config_basename, 1},
- {"bg-sub", 0, &config_bgsub, 1}, /* Compat */
- {"no-bg-sub", 0, &config_bgsub, 0},
+ {"bg-sub", 0, &iargs.config_bgsub, 1},
+ {"no-bg-sub", 0, &iargs.config_bgsub, 0},
{"peaks", 1, NULL, 2},
{"cell-reduction", 1, NULL, 3},
@@ -256,16 +254,16 @@ int main(int argc, char *argv[])
{"min-integration-snr",1, NULL, 12},
{"tolerance", 1, NULL, 13},
{"int-radius", 1, NULL, 14},
- {"no-peaks-in-stream", 1, &config_nopeaks, 1},
- {"no-refls-in-stream", 1, &config_norefls, 1},
- {"res-cutoff", 1, &config_rescutoff, 1},
+ {"no-peaks-in-stream", 1, &iargs.stream_peaks, 0},
+ {"no-refls-in-stream", 1, &iargs.stream_refls, 0},
+ {"res-cutoff", 1, &iargs.res_cutoff, 1},
/* 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},
- {"integrate-found", 0, &integrate_found, 1},
+ {"integrate-saturated",0, &iargs.integrate_saturated,1},
+ {"use-saturated", 0, &iargs.use_saturated, 1},
+ {"no-revalidate", 0, &iargs.no_revalidate, 1},
+ {"integrate-found", 0, &iargs.integrate_found, 1},
{0, 0, NULL, 0}
};
@@ -304,16 +302,21 @@ int main(int argc, char *argv[])
break;
case 'g' :
- geometry = strdup(optarg);
+ iargs.det = get_detector_geometry(optarg);
+ if ( iargs.det == NULL ) {
+ ERROR("Failed to read detector geometry from "
+ "'%s'\n", optarg);
+ return 1;
+ }
break;
case 't' :
- threshold = strtof(optarg, NULL);
+ iargs.threshold = strtof(optarg, NULL);
break;
case 'b' :
- beam = get_beam_parameters(optarg);
- if ( beam == NULL ) {
+ iargs.beam = get_beam_parameters(optarg);
+ if ( iargs.beam == NULL ) {
ERROR("Failed to load beam parameters"
" from '%s'\n", optarg);
return 1;
@@ -321,7 +324,7 @@ int main(int argc, char *argv[])
break;
case 'e' :
- element = strdup(optarg);
+ iargs.element = strdup(optarg);
break;
case 2 :
@@ -329,17 +332,24 @@ int main(int argc, char *argv[])
break;
case 3 :
- scellr = strdup(optarg);
- break;
+ ERROR("The option '--cell-reduction' is no longer "
+ "used.\n"
+ "The complete indexing behaviour is now "
+ "controlled using '--indexing'.\n"
+ "See 'man indexamajig' for details of the "
+ "available methods.\n");
+ return 1;
case 4 :
- min_gradient = strtof(optarg, NULL);
+ iargs.min_gradient = strtof(optarg, NULL);
break;
case 5 :
- ERROR("The option '--record' is no longer used.\n");
- /* FIXME: Translate to new style */
- break;
+ ERROR("The option '--record' is no longer used.\n"
+ "Use '--no-peaks-in-stream' and"
+ "'--no-refls-in-stream' if you need to control"
+ "the contents of the stream.\n");
+ return 1;
case 6 :
case 7 :
@@ -349,19 +359,20 @@ int main(int argc, char *argv[])
break;
case 9 :
- hdf5_peak_path = strdup(optarg);
+ free(iargs.hdf5_peak_path);
+ iargs.hdf5_peak_path = strdup(optarg);
break;
case 10 :
- add_copy_hdf5_field(copyme, optarg);
+ add_copy_hdf5_field(iargs.copyme, optarg);
break;
case 11 :
- min_snr = strtof(optarg, NULL);
+ iargs.min_snr = strtof(optarg, NULL);
break;
case 12 :
- min_int_snr = strtof(optarg, NULL);
+ iargs.min_int_snr = strtof(optarg, NULL);
break;
case 13 :
@@ -386,12 +397,6 @@ 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("-");
}
@@ -406,19 +411,15 @@ int main(int argc, char *argv[])
}
free(filename);
- if ( hdf5_peak_path == NULL ) {
- hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
- }
-
if ( speaks == NULL ) {
speaks = strdup("zaef");
STATUS("You didn't specify a peak detection method.\n");
STATUS("I'm using 'zaef' for you.\n");
}
if ( strcmp(speaks, "zaef") == 0 ) {
- peaks = PEAK_ZAEF;
+ iargs.peaks = PEAK_ZAEF;
} else if ( strcmp(speaks, "hdf5") == 0 ) {
- peaks = PEAK_HDF5;
+ iargs.peaks = PEAK_HDF5;
} else {
ERROR("Unrecognised peak detection method '%s'\n", speaks);
return 1;
@@ -459,7 +460,8 @@ int main(int argc, char *argv[])
if ( toler != NULL ) {
int ttt;
ttt = sscanf(toler, "%f,%f,%f,%f",
- &tols[0], &tols[1], &tols[2], &tols[3] );
+ &iargs.tols[0], &iargs.tols[1],
+ &iargs.tols[2], &iargs.tols[3]);
if ( ttt != 4 ) {
ERROR("Invalid parameters for '--tolerance'\n");
return 1;
@@ -469,7 +471,8 @@ int main(int argc, char *argv[])
if ( intrad != NULL ) {
int r;
- r = sscanf(intrad, "%f,%f,%f", &ir_inn, &ir_mid, &ir_out);
+ r = sscanf(intrad, "%f,%f,%f",
+ &iargs.ir_inn, &iargs.ir_mid, &iargs.ir_out);
if ( r != 3 ) {
ERROR("Invalid parameters for '--int-radius'\n");
return 1;
@@ -481,37 +484,30 @@ int main(int argc, char *argv[])
" probably not appropriate for your patterns.\n");
}
- if ( geometry == NULL ) {
+ if ( iargs.det == NULL ) {
ERROR("You need to provide a geometry file (please read the"
" manual for more details).\n");
return 1;
}
- if ( beam == NULL ) {
+ if ( iargs.beam == NULL ) {
ERROR("You need to provide a beam parameters file (please read"
" the manual for more details).\n");
return 1;
}
- det = get_detector_geometry(geometry);
- if ( det == NULL ) {
- ERROR("Failed to read detector geometry from '%s'\n", geometry);
- return 1;
- }
- free(geometry);
-
if ( pdb != NULL ) {
- cell = load_cell_from_pdb(pdb);
- if ( cell == NULL ) {
+ iargs.cell = load_cell_from_pdb(pdb);
+ if ( iargs.cell == NULL ) {
ERROR("Couldn't read unit cell (from %s)\n", pdb);
return 1;
}
free(pdb);
STATUS("This is what I understood your unit cell to be:\n");
- cell_print(cell);
+ cell_print(iargs.cell);
} else {
STATUS("No unit cell given.\n");
- cell = NULL;
+ iargs.cell = NULL;
}
ofh = fopen(outfile, "w");
@@ -541,8 +537,8 @@ int main(int argc, char *argv[])
/* Prepare the indexer */
if ( indm != NULL ) {
- ipriv = prepare_indexing(indm, cell, prepare_filename,
- det, beam, tols);
+ ipriv = prepare_indexing(indm, iargs.cell, prepare_filename,
+ iargs.det, iargs.beam, iargs.tols);
if ( ipriv == NULL ) {
ERROR("Failed to prepare indexing.\n");
return 1;
@@ -553,40 +549,8 @@ int main(int argc, char *argv[])
gsl_set_error_handler_off();
- /* Static worker args */
- iargs.cell = cell;
- iargs.config_cmfilter = config_cmfilter;
- iargs.config_noisefilter = config_noisefilter;
- iargs.config_verbose = config_verbose;
- iargs.config_satcorr = config_satcorr;
- iargs.config_closer = config_closer;
- iargs.config_bgsub = config_bgsub;
- iargs.tols[0] = tols[0];
- iargs.tols[1] = tols[1];
- iargs.tols[2] = tols[2];
- iargs.tols[3] = tols[3];
- iargs.threshold = threshold;
- iargs.min_gradient = min_gradient;
- iargs.min_snr = min_snr;
- iargs.min_int_snr = min_int_snr;
- iargs.det = det;
iargs.indm = indm;
iargs.ipriv = ipriv;
- iargs.peaks = peaks;
- iargs.beam = beam;
- iargs.element = element;
- iargs.hdf5_peak_path = hdf5_peak_path;
- iargs.copyme = copyme;
- iargs.ir_inn = ir_inn;
- iargs.ir_mid = ir_mid;
- iargs.ir_out = ir_out;
- iargs.use_saturated = use_saturated;
- iargs.integrate_saturated = integrate_saturated;
- iargs.no_revalidate = no_revalidate;
- iargs.integrate_found = integrate_found;
- iargs.include_peaks = !config_nopeaks;
- iargs.include_reflections = !config_norefls;
- iargs.res_cutoff = config_rescutoff;
create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
use_this_one_instead, ofh, argc, argv);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 01:59:21 +0000