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-rw-r--r--src/indexamajig.c217
1 files changed, 1 insertions, 216 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 7fae3ea6..525fcfc3 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -29,15 +29,12 @@
#include "hdf5-file.h"
#include "index.h"
#include "peaks.h"
-#include "diffraction.h"
-#include "diffraction-gpu.h"
#include "detector.h"
#include "sfac.h"
#include "filters.h"
#include "reflections.h"
#include "thread-pool.h"
#include "beam-parameters.h"
-#include "symmetry.h"
#include "geometry.h"
@@ -50,16 +47,12 @@ enum {
/* Information about the indexing process which is common to all patterns */
struct static_index_args
{
- pthread_mutex_t *gpu_mutex; /* Protects "gctx" */
UnitCell *cell;
int config_cmfilter;
int config_noisefilter;
int config_dumpfound;
int config_verbose;
- int config_alternate;
int config_nearbragg;
- int config_gpu;
- int config_simulate;
int config_polar;
int config_satcorr;
int config_closer;
@@ -69,11 +62,6 @@ struct static_index_args
struct detector *det;
IndexingMethod *indm;
IndexingPrivate **ipriv;
- const double *intensities;
- const unsigned char *flags;
- const char *sym; /* Symmetry of "intensities" and "flags" */
- struct gpu_context *gctx;
- int gpu_dev;
int peaks;
int cellr;
struct beam_params *beam;
@@ -153,11 +141,6 @@ static void show_help(const char *s)
" was located by the initial peak search close to\n"
" the \"near Bragg\" location, its coordinates will\n"
" be taken as the centre instead.\n"
-" --simulate Simulate the diffraction pattern using the indexed\n"
-" unit cell. The simulated pattern will be saved\n"
-" as \"simulated.h5\". You can TRY to combine this\n"
-" with \"-j <n>\" with n greater than 1, but it's\n"
-" not a good idea.\n"
" --dump-peaks Write the results of the peak search to stdout.\n"
" The intensities in this list are from the\n"
" centroid/integration procedure.\n"
@@ -182,16 +165,8 @@ static void show_help(const char *s)
" --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n"
" Default: 100,000.\n"
"\n"
-"\nIf you used --simulate, you may also want:\n\n"
-" --intensities=<file> Specify file containing reflection intensities\n"
-" to use when simulating.\n"
-" -y, --symmetry=<sym> The symmetry of the intensities file.\n"
-"\n"
"\nOptions for greater performance or verbosity:\n\n"
" --verbose Be verbose about indexing.\n"
-" --gpu Use the GPU to speed up the simulation.\n"
-" --gpu-dev=<n> Use GPU device <n>. Omit this option to see the\n"
-" available devices.\n"
" -j <n> Run <n> analyses in parallel. Default 1.\n"
"\n"
"\nOptions you probably won't need:\n\n"
@@ -205,100 +180,11 @@ static void show_help(const char *s)
}
-static struct image *get_simage(struct image *template, int alternate)
-{
- struct image *image;
- struct panel panels[2];
-
- image = malloc(sizeof(*image));
-
- /* Simulate a diffraction pattern */
- image->twotheta = NULL;
- image->data = NULL;
- image->det = template->det;
- image->flags = NULL;
- image->f0_available = 0;
- image->f0 = 1.0;
-
- /* Detector geometry for the simulation
- * - not necessarily the same as the original. */
- image->width = 1024;
- image->height = 1024;
- image->det->n_panels = 2;
-
- if ( alternate ) {
-
- /* Upper */
- panels[0].min_fs = 0;
- panels[0].max_fs = 1023;
- panels[0].min_ss = 512;
- panels[0].max_ss = 1023;
- panels[0].cx = 523.6;
- panels[0].cy = 502.5;
- panels[0].clen = 56.4e-2; /* 56.4 cm */
- panels[0].res = 13333.3; /* 75 microns/pixel */
-
- /* Lower */
- panels[1].min_fs = 0;
- panels[1].max_fs = 1023;
- panels[1].min_ss = 0;
- panels[1].max_ss = 511;
- panels[1].cx = 520.8;
- panels[1].cy = 525.0;
- panels[1].clen = 56.7e-2; /* 56.7 cm */
- panels[1].res = 13333.3; /* 75 microns/pixel */
-
- image->det->panels = panels;
-
- } else {
-
- /* Copy pointer to old geometry */
- image->det->panels = template->det->panels;
-
- }
-
- image->lambda = ph_en_to_lambda(eV_to_J(1.8e3));
- image->features = template->features;
- image->filename = template->filename;
- image->indexed_cell = template->indexed_cell;
- image->f0 = template->f0;
-
- return image;
-}
-
-
-static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
- const double *intensities,
- const unsigned char *flags, UnitCell *cell,
- int gpu_dev, const char *sym)
-{
- /* Set up GPU if necessary.
- * Unfortunately, setup has to go here since until now we don't know
- * enough about the situation. */
- if ( (gctx != NULL) && (*gctx == NULL) ) {
- *gctx = setup_gpu(0, simage, intensities, flags, sym, gpu_dev);
- }
-
- if ( (gctx != NULL) && (*gctx != NULL) ) {
- get_diffraction_gpu(*gctx, simage, 24, 24, 40, cell);
- } else {
- get_diffraction(simage, 24, 24, 40,
- intensities, NULL, flags, cell, 0,
- GRADIENT_MOSAIC, sym);
- }
- record_image(simage, 0);
-
- hdf5_write("simulated.h5", simage->data, simage->width, simage->height,
- H5T_NATIVE_FLOAT);
-}
-
-
static void process_image(void *pp, int cookie)
{
struct index_args *pargs = pp;
struct hdfile *hdfile;
struct image image;
- struct image *simage;
float *data_for_measurement;
size_t data_size;
char *filename = pargs->filename;
@@ -307,16 +193,9 @@ static void process_image(void *pp, int cookie)
int config_noisefilter = pargs->static_args.config_noisefilter;
int config_dumpfound = pargs->static_args.config_dumpfound;
int config_verbose = pargs->static_args.config_verbose;
- int config_alternate = pargs->static_args.config_alternate;
int config_nearbragg = pargs->static_args.config_nearbragg;
- int config_gpu = pargs->static_args.config_gpu;
- int config_simulate = pargs->static_args.config_simulate;
int config_polar = pargs->static_args.config_polar;
IndexingMethod *indm = pargs->static_args.indm;
- const double *intensities = pargs->static_args.intensities;
- const unsigned char *flags = pargs->static_args.flags;
- struct gpu_context *gctx = pargs->static_args.gctx;
- const char *sym = pargs->static_args.sym;
const struct beam_params *beam = pargs->static_args.beam;
image.features = NULL;
@@ -417,27 +296,6 @@ static void process_image(void *pp, int cookie)
}
- simage = get_simage(&image, config_alternate);
-
- /* Simulate if requested */
- if ( config_simulate ) {
- if ( config_gpu ) {
- pthread_mutex_lock(pargs->static_args.gpu_mutex);
- simulate_and_write(simage, &gctx, intensities, flags,
- image.indexed_cell,
- pargs->static_args.gpu_dev, sym);
- pthread_mutex_unlock(pargs->static_args.gpu_mutex);
- } else {
- simulate_and_write(simage, NULL, intensities, flags,
- image.indexed_cell, 0, sym);
- }
- }
-
- /* Finished with alternate image */
- if ( simage->twotheta != NULL ) free(simage->twotheta);
- if ( simage->data != NULL ) free(simage->data);
- free(simage);
-
/* Only free cell if found */
cell_free(image.indexed_cell);
@@ -504,7 +362,6 @@ static void finalise_image(void *qp, void *pp)
int main(int argc, char *argv[])
{
int c;
- struct gpu_context *gctx = NULL;
char *filename = NULL;
char *outfile = NULL;
FILE *fh;
@@ -514,12 +371,9 @@ int main(int argc, char *argv[])
int config_noindex = 0;
int config_dumpfound = 0;
int config_nearbragg = 0;
- int config_simulate = 0;
int config_cmfilter = 0;
int config_noisefilter = 0;
- int config_gpu = 0;
int config_verbose = 0;
- int config_alternate = 0;
int config_polar = 1;
int config_satcorr = 1;
int config_checkprefix = 1;
@@ -535,9 +389,6 @@ int main(int argc, char *argv[])
int reduction_needs_cell;
char *indm_str = NULL;
UnitCell *cell;
- double *intensities = NULL;
- unsigned char *flags;
- char *intfile = NULL;
char *pdb = NULL;
char *prefix = NULL;
char *speaks = NULL;
@@ -547,21 +398,17 @@ int main(int argc, char *argv[])
int nthreads = 1;
int i;
pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
- pthread_mutex_t gpu_mutex = PTHREAD_MUTEX_INITIALIZER;
char prepare_line[1024];
char prepare_filename[1024];
struct queue_args qargs;
struct beam_params *beam = NULL;
double nominal_photon_energy;
- int gpu_dev = -1;
- char *sym = NULL;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
- {"gpu", 0, &config_gpu, 1},
{"no-index", 0, &config_noindex, 1},
{"dump-peaks", 0, &config_dumpfound, 1},
{"peaks", 1, NULL, 2},
@@ -570,13 +417,9 @@ int main(int argc, char *argv[])
{"indexing", 1, NULL, 'z'},
{"geometry", 1, NULL, 'g'},
{"beam", 1, NULL, 'b'},
- {"simulate", 0, &config_simulate, 1},
{"filter-cm", 0, &config_cmfilter, 1},
{"filter-noise", 0, &config_noisefilter, 1},
{"verbose", 0, &config_verbose, 1},
- {"alternate", 0, &config_alternate, 1},
- {"intensities", 1, NULL, 'q'},
- {"symmetry", 1, NULL, 'y'},
{"pdb", 1, NULL, 'p'},
{"prefix", 1, NULL, 'x'},
{"unpolarized", 0, &config_polar, 0},
@@ -586,13 +429,12 @@ int main(int argc, char *argv[])
{"min-gradient", 1, NULL, 4},
{"no-check-prefix", 0, &config_checkprefix, 0},
{"no-closer-peak", 0, &config_closer, 0},
- {"gpu-dev", 1, NULL, 5},
{"insane", 0, &config_insane, 1},
{0, 0, NULL, 0}
};
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:y:",
+ while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:",
longopts, NULL)) != -1) {
switch (c) {
@@ -612,10 +454,6 @@ int main(int argc, char *argv[])
indm_str = strdup(optarg);
break;
- case 'q' :
- intfile = strdup(optarg);
- break;
-
case 'p' :
pdb = strdup(optarg);
break;
@@ -636,10 +474,6 @@ int main(int argc, char *argv[])
threshold = strtof(optarg, NULL);
break;
- case 'y' :
- sym = strdup(optarg);
- break;
-
case 'b' :
beam = get_beam_parameters(optarg);
if ( beam == NULL ) {
@@ -661,10 +495,6 @@ int main(int argc, char *argv[])
min_gradient = strtof(optarg, NULL);
break;
- case 5 :
- gpu_dev = atoi(optarg);
- break;
-
case 0 :
break;
@@ -702,8 +532,6 @@ int main(int argc, char *argv[])
}
free(outfile);
- if ( sym == NULL ) sym = strdup("1");
-
if ( speaks == NULL ) {
speaks = strdup("zaef");
STATUS("You didn't specify a peak detection method.\n");
@@ -719,35 +547,6 @@ int main(int argc, char *argv[])
}
free(speaks);
- if ( intfile != NULL ) {
-
- ReflItemList *items;
- int i;
-
- items = read_reflections(intfile, intensities,
- NULL, NULL, NULL);
-
- flags = new_list_flag();
- for ( i=0; i<num_items(items); i++ ) {
- struct refl_item *it = get_item(items, i);
- set_flag(flags, it->h, it->k, it->l, 1);
- }
-
- if ( check_symmetry(items, sym) ) {
- ERROR("The input reflection list does not appear to"
- " have symmetry %s\n", sym);
- return 1;
- }
-
- delete_items(items);
-
- } else {
-
- intensities = NULL;
- flags = NULL;
-
- }
-
if ( pdb == NULL ) {
pdb = strdup("molecule.pdb");
}
@@ -869,16 +668,12 @@ int main(int argc, char *argv[])
gsl_set_error_handler_off();
- qargs.static_args.gpu_mutex = &gpu_mutex;
qargs.static_args.cell = cell;
qargs.static_args.config_cmfilter = config_cmfilter;
qargs.static_args.config_noisefilter = config_noisefilter;
qargs.static_args.config_dumpfound = config_dumpfound;
qargs.static_args.config_verbose = config_verbose;
- qargs.static_args.config_alternate = config_alternate;
qargs.static_args.config_nearbragg = config_nearbragg;
- qargs.static_args.config_gpu = config_gpu;
- qargs.static_args.config_simulate = config_simulate;
qargs.static_args.config_polar = config_polar;
qargs.static_args.config_satcorr = config_satcorr;
qargs.static_args.config_closer = config_closer;
@@ -889,11 +684,6 @@ int main(int argc, char *argv[])
qargs.static_args.det = det;
qargs.static_args.indm = indm;
qargs.static_args.ipriv = ipriv;
- qargs.static_args.intensities = intensities;
- qargs.static_args.flags = flags;
- qargs.static_args.sym = sym;
- qargs.static_args.gctx = gctx;
- qargs.static_args.gpu_dev = gpu_dev;
qargs.static_args.peaks = peaks;
qargs.static_args.output_mutex = &output_mutex;
qargs.static_args.ofh = ofh;
@@ -916,14 +706,9 @@ int main(int argc, char *argv[])
cell_free(cell);
if ( fh != stdin ) fclose(fh);
if ( ofh != stdout ) fclose(ofh);
- free(sym);
STATUS("There were %i images, of which %i could be indexed.\n",
n_images, qargs.n_indexable);
- if ( gctx != NULL ) {
- cleanup_gpu(gctx);
- }
-
return 0;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 08:23:18 +0000