aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--.gitignore1
-rw-r--r--doc/man/partial_sim.111
-rw-r--r--libcrystfel/src/cell.c2
-rw-r--r--libcrystfel/src/cell.h2
-rw-r--r--libcrystfel/src/index.c2
-rw-r--r--libcrystfel/src/index.h3
-rw-r--r--libcrystfel/src/mosflm.c7
-rw-r--r--libcrystfel/src/peaks.c7
-rw-r--r--src/indexamajig.c738
-rw-r--r--src/partial_sim.c4
-rw-r--r--tests/symmetry_check.c5
11 files changed, 473 insertions, 309 deletions
diff --git a/.gitignore b/.gitignore
index 219f0ec2..30a8bdee 100644
--- a/.gitignore
+++ b/.gitignore
@@ -46,6 +46,7 @@ build-aux/missing
build-aux/config.guess
build-aux/depcomp
build-aux/ltmain.sh
+/nbproject/private/
lib/.libs/
lib/dummy.lo
lib/libgnu.la
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1
index e41708ed..5b44d34f 100644
--- a/doc/man/partial_sim.1
+++ b/doc/man/partial_sim.1
@@ -71,17 +71,6 @@ When combined with with \fB-i\fR, specifies the symmetry of the input reflection
.PD
Add random values with a flat distribution to the components of the reciprocal lattice vectors written to the stream, simulating indexing errors. The maximum value that will be added is +/- \fIval\fR percent.
-.PD 0
-.B
-.IP "\fB--pgraph=\fR\fIfilename\fR
-.PD
-Write reflection statistics to \fifilename\fR. The file consists of a one-line
-header and has columns as follows: the centre of the resolution bin (in inverse
-nanometres), the number of reflections in that bin across the whole simulated
-data set, the mean partiality for the bin, and the maximum partiality which was
-encountered in the bin.
-
-
.SH AUTHOR
This page was written by Thomas White.
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 31d3b9b1..b6ea010b 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -694,7 +694,7 @@ static int same_vector(struct cvec a, struct cvec b)
/* Attempt to make 'cell' fit into 'template' somehow */
UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose,
- float *tols, int reduce)
+ const float *tols, int reduce)
{
signed int n1l, n2l, n3l;
double asx, asy, asz;
diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h
index cbe84772..bd2719dd 100644
--- a/libcrystfel/src/cell.h
+++ b/libcrystfel/src/cell.h
@@ -118,7 +118,7 @@ extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi,
extern void cell_print(UnitCell *cell);
extern UnitCell *match_cell(UnitCell *cell, UnitCell *tempcell, int verbose,
- float *ltl, int reduce);
+ const float *ltl, int reduce);
extern UnitCell *match_cell_ab(UnitCell *cell, UnitCell *tempcell);
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index f4bc9d6c..102a5312 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -167,7 +167,7 @@ void map_all_peaks(struct image *image)
void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
int cellr, int verbose, IndexingPrivate **ipriv,
- int config_insane, float *ltl)
+ int config_insane, const float *ltl)
{
int i;
int n = 0;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index c4e15f09..9d23f3fb 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -74,7 +74,8 @@ extern void map_all_peaks(struct image *image);
extern void index_pattern(struct image *image, UnitCell *cell,
IndexingMethod *indm, int cellr, int verbose,
- IndexingPrivate **priv, int config_insane, float *ltl);
+ IndexingPrivate **priv, int config_insane,
+ const float *ltl);
extern void cleanup_indexing(IndexingPrivate **priv);
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 410b779a..ed118aa4 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -379,7 +379,6 @@ static int mosflm_readable(struct image *image, struct mosflm_data *mosflm)
rval = read(mosflm->pty, mosflm->rbuffer+mosflm->rbufpos,
mosflm->rbuflen-mosflm->rbufpos);
-
if ( (rval == -1) || (rval == 0) ) return 1;
mosflm->rbufpos += rval;
@@ -436,7 +435,6 @@ static int mosflm_readable(struct image *image, struct mosflm_data *mosflm)
break;
case MOSFLM_INPUT_PROMPT :
-
mosflm_send_next(image, mosflm);
endbit_length = i+7;
break;
@@ -513,6 +511,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
remove(mosflm->newmatfile);
mosflm->pid = forkpty(&mosflm->pty, NULL, NULL, NULL);
+
if ( mosflm->pid == -1 ) {
ERROR("Failed to fork for MOSFLM\n");
free(mosflm);
@@ -545,6 +544,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
mosflm->step = 1; /* This starts the "initialisation" procedure */
mosflm->finished_ok = 0;
+
do {
fd_set fds;
@@ -559,7 +559,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
sval = select(mosflm->pty+1, &fds, NULL, NULL, &tv);
- if ( sval == -1 ) {
+ if ( sval == -1 ) {
int err = errno;
ERROR("select() failed: %s\n", strerror(err));
rval = 1;
@@ -570,6 +570,7 @@ void run_mosflm(struct image *image, UnitCell *cell)
rval = 1;
}
+
} while ( !rval );
close(mosflm->pty);
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 477d9345..583dff4c 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -148,10 +148,9 @@ static int cull_peaks(struct image *image)
/* Returns non-zero if peak has been vetoed.
* i.e. don't use result if return value is not zero. */
-static int integrate_peak(struct image *image, int cfs, int css,
- double *pfs, double *pss,
- double *intensity, double *sigma,
- double ir_inn, double ir_mid, double ir_out)
+int integrate_peak(struct image *image, int cfs, int css,
+ double *pfs, double *pss, double *intensity, double *sigma,
+ double ir_inn, double ir_mid, double ir_out)
{
signed int fs, ss;
double lim_sq, out_lim_sq, mid_lim_sq;
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 8c073e2c..223403ad 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -12,6 +12,7 @@
* 2010-2012 Thomas White <taw@physics.org>
* 2011 Richard Kirian
* 2012 Lorenzo Galli
+ * 2012 Chunhong Yoon
*
* This file is part of CrystFEL.
*
@@ -44,6 +45,8 @@
#include <hdf5.h>
#include <gsl/gsl_errno.h>
#include <pthread.h>
+#include <sys/wait.h>
+#include <fcntl.h>
#ifdef HAVE_CLOCK_GETTIME
#include <time.h>
@@ -67,7 +70,6 @@
/* Write statistics at APPROXIMATELY this interval */
#define STATS_EVERY_N_SECONDS (5)
-
enum {
PEAK_ZAEF,
PEAK_HDF5,
@@ -75,7 +77,7 @@ enum {
/* Information about the indexing process which is common to all patterns */
-struct static_index_args
+struct index_args
{
UnitCell *cell;
int config_cmfilter;
@@ -104,42 +106,23 @@ struct static_index_args
double ir_out;
/* Output stream */
- pthread_mutex_t *output_mutex; /* Protects the output stream */
FILE *ofh;
const struct copy_hdf5_field *copyme;
+ char *outfile;
};
/* Information about the indexing process for one pattern */
-struct index_args
+struct pattern_args
{
/* "Input" */
char *filename;
- struct static_index_args static_args;
/* "Output" */
int indexable;
};
-/* Information needed to choose the next task and dispatch it */
-struct queue_args
-{
- FILE *fh;
- char *prefix;
- int config_basename;
- struct static_index_args static_args;
-
- char *use_this_one_instead;
-
- int n_indexable;
- int n_processed;
- int n_indexable_last_stats;
- int n_processed_last_stats;
- int t_last_stats;
-};
-
-
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
@@ -234,80 +217,108 @@ static void show_help(const char *s)
" least 10%% of the located peaks.\n"
" --no-bg-sub Don't subtract local background estimates from\n"
" integrated intensities.\n"
-"\n"
-"\nYou can tune the CPU affinities for enhanced performance on NUMA machines:\n"
-"\n"
-" --cpus=<n> Specify number of CPUs. This is NOT the same as\n"
-" giving the number of analyses to run in parallel.\n"
-" --cpugroup=<n> Batch threads in groups of this size.\n"
-" --cpuoffset=<n> Start using CPUs at this group number.\n"
);
}
-static void process_image(void *pp, int cookie)
+static char *get_pattern(FILE *fh, char **use_this_one_instead,
+ int config_basename, const char *prefix)
+{
+ char *line;
+ char *filename;
+
+ /* Get the next filename */
+ if ( *use_this_one_instead != NULL ) {
+
+ line = *use_this_one_instead;
+ *use_this_one_instead = NULL;
+
+ } else {
+
+ char *rval;
+
+ line = malloc(1024*sizeof(char));
+ rval = fgets(line, 1023, fh);
+ if ( rval == NULL ) {
+ free(line);
+ return NULL;
+ }
+
+ }
+
+ chomp(line);
+
+ if ( config_basename ) {
+ char *tmp;
+ tmp = safe_basename(line);
+ free(line);
+ line = tmp;
+ }
+
+ filename = malloc(strlen(prefix)+strlen(line)+1);
+
+ snprintf(filename, 1023, "%s%s", prefix, line);
+
+ free(line);
+
+ return filename;
+}
+
+
+static void process_image(const struct index_args *iargs,
+ struct pattern_args *pargs, int cookie)
{
- struct index_args *pargs = pp;
- struct hdfile *hdfile;
- struct image image;
float *data_for_measurement;
size_t data_size;
- char *filename = pargs->filename;
- UnitCell *cell = pargs->static_args.cell;
- int config_cmfilter = pargs->static_args.config_cmfilter;
- int config_noisefilter = pargs->static_args.config_noisefilter;
- int config_verbose = pargs->static_args.config_verbose;
- IndexingMethod *indm = pargs->static_args.indm;
- struct beam_params *beam = pargs->static_args.beam;
+ UnitCell *cell = iargs->cell;
+ int config_cmfilter = iargs->config_cmfilter;
+ int config_noisefilter = iargs->config_noisefilter;
+ int config_verbose = iargs->config_verbose;
+ IndexingMethod *indm = iargs->indm;
+ struct beam_params *beam = iargs->beam;
+ int r, check;
+ struct hdfile *hdfile;
+ char *outfile = iargs->outfile;
+ struct image image;
+ char *outfilename = iargs->outfile;
+ int fd;
+ FILE *fh;
+ struct flock fl = {F_WRLCK, SEEK_SET, 0, 0, 0};
image.features = NULL;
image.data = NULL;
image.flags = NULL;
image.indexed_cell = NULL;
- image.id = cookie;
- image.filename = filename;
- image.det = copy_geom(pargs->static_args.det);
- image.copyme = pargs->static_args.copyme;
+ image.det = copy_geom(iargs->det);
+ image.copyme = iargs->copyme;
image.beam = beam;
+ image.id = cookie;
+ image.filename = pargs->filename;
- pargs->indexable = 0;
-
- hdfile = hdfile_open(filename);
+ hdfile = hdfile_open(image.filename);
if ( hdfile == NULL ) return;
- if ( pargs->static_args.element != NULL ) {
-
- int r;
- r = hdfile_set_image(hdfile, pargs->static_args.element);
- if ( r ) {
- ERROR("Couldn't select path '%s'\n",
- pargs->static_args.element);
- hdfile_close(hdfile);
- return;
- }
-
- } else {
-
- int r;
- r = hdfile_set_first_image(hdfile, "/");
- if ( r ) {
- ERROR("Couldn't select first path\n");
- hdfile_close(hdfile);
- return;
- }
-
+ r = hdfile_set_first_image(hdfile, "/");
+ if ( r ) {
+ ERROR("Couldn't select first path\n");
+ hdfile_close(hdfile);
+ return;
}
- hdf5_read(hdfile, &image, pargs->static_args.config_satcorr);
+ check = hdf5_read(hdfile, &image, 1);
+ if ( check ) {
+ hdfile_close(hdfile);
+ return;
+ }
- if ( (image.width != image.det->max_fs+1)
- || (image.height != image.det->max_ss+1) )
+ if ( (image.width != image.det->max_fs + 1 )
+ || (image.height != image.det->max_ss + 1))
{
ERROR("Image size doesn't match geometry size"
- " - rejecting image.\n");
+ " - rejecting image.\n");
ERROR("Image size: %i,%i. Geometry size: %i,%i\n",
- image.width, image.height,
- image.det->max_fs+1, image.det->max_ss+1);
+ image.width, image.height,
+ image.det->max_fs + 1, image.det->max_ss + 1);
hdfile_close(hdfile);
free_detector_geometry(image.det);
return;
@@ -316,12 +327,12 @@ static void process_image(void *pp, int cookie)
if ( image.lambda < 0.0 ) {
if ( beam != NULL ) {
ERROR("Using nominal photon energy of %.2f eV\n",
- beam->photon_energy);
+ beam->photon_energy);
image.lambda = ph_en_to_lambda(
- eV_to_J(beam->photon_energy));
+ eV_to_J(beam->photon_energy));
} else {
ERROR("No wavelength in file, so you need to give "
- "a beam parameters file with -b.\n");
+ "a beam parameters file with -b.\n");
hdfile_close(hdfile);
free_detector_geometry(image.det);
return;
@@ -335,7 +346,7 @@ static void process_image(void *pp, int cookie)
/* Take snapshot of image after CM subtraction but before
* the aggressive noise filter. */
- data_size = image.width*image.height*sizeof(float);
+ data_size = image.width * image.height * sizeof(float);
data_for_measurement = malloc(data_size);
if ( config_noisefilter ) {
@@ -344,25 +355,25 @@ static void process_image(void *pp, int cookie)
memcpy(data_for_measurement, image.data, data_size);
}
- switch ( pargs->static_args.peaks )
- {
- case PEAK_HDF5 :
- /* Get peaks from HDF5 */
- if ( get_peaks(&image, hdfile,
- pargs->static_args.hdf5_peak_path) )
- {
+ switch ( iargs->peaks ) {
+
+ case PEAK_HDF5:
+ // Get peaks from HDF5
+ if (get_peaks(&image, hdfile,
+ iargs->hdf5_peak_path)) {
ERROR("Failed to get peaks from HDF5 file.\n");
}
break;
- case PEAK_ZAEF :
- search_peaks(&image, pargs->static_args.threshold,
- pargs->static_args.min_gradient,
- pargs->static_args.min_snr,
- pargs->static_args.ir_inn,
- pargs->static_args.ir_mid,
- pargs->static_args.ir_out);
+ case PEAK_ZAEF:
+ search_peaks(&image, iargs->threshold,
+ iargs->min_gradient,
+ iargs->min_snr,
+ iargs->ir_inn,
+ iargs->ir_mid,
+ iargs->ir_out);
break;
+
}
/* Get rid of noise-filtered version at this point
@@ -374,40 +385,55 @@ static void process_image(void *pp, int cookie)
image.div = beam->divergence;
image.bw = beam->bandwidth;
image.profile_radius = 0.0001e9;
- index_pattern(&image, cell, indm, pargs->static_args.cellr,
- config_verbose, pargs->static_args.ipriv,
- pargs->static_args.config_insane,
- pargs->static_args.tols);
- if ( image.indexed_cell != NULL ) {
+ index_pattern(&image, cell, indm, iargs->cellr,
+ config_verbose, iargs->ipriv,
+ iargs->config_insane, iargs->tols);
+ if ( image.indexed_cell != NULL ) {
pargs->indexable = 1;
-
image.reflections = find_intersections(&image,
- image.indexed_cell);
-
- if ( image.reflections != NULL ) {
-
+ image.indexed_cell);
+ if (image.reflections != NULL) {
integrate_reflections(&image,
- pargs->static_args.config_closer,
- pargs->static_args.config_bgsub,
- pargs->static_args.min_int_snr,
- pargs->static_args.ir_inn,
- pargs->static_args.ir_mid,
- pargs->static_args.ir_out);
-
+ iargs->config_closer,
+ iargs->config_bgsub,
+ iargs->min_int_snr,
+ iargs->ir_inn,
+ iargs->ir_mid,
+ iargs->ir_out);
}
-
} else {
-
image.reflections = NULL;
+ }
+ /* Write Lock */
+ fl.l_pid = getpid();
+
+ fd = open(outfile, O_WRONLY);
+ if ( fd == -1) {
+ ERROR("Error on opening\n");
+ exit(1);
+ }
+ if (fcntl(fd, F_SETLKW, &fl) == -1) {
+ ERROR("Error on setting lock wait\n");
+ exit(1);
}
- pthread_mutex_lock(pargs->static_args.output_mutex);
- write_chunk(pargs->static_args.ofh, &image, hdfile,
- pargs->static_args.stream_flags);
- pthread_mutex_unlock(pargs->static_args.output_mutex);
+ fh = fopen(outfilename, "a");
+ if ( fh == NULL ) {
+ ERROR("Couldn't open stream '%s'.\n", outfilename);
+ }
+ write_chunk(fh, &image, hdfile, iargs->stream_flags);
+ fclose(fh);
+
+ /* Unlock stream for other processes */
+ fl.l_type = F_UNLCK; /* set to unlock same region */
+ if ( fcntl(fd, F_SETLK, &fl) == -1 ) {
+ ERROR("fcntl");
+ exit(1);
+ }
+ close(fd);
/* Only free cell if found */
cell_free(image.indexed_cell);
@@ -421,51 +447,60 @@ static void process_image(void *pp, int cookie)
}
-static void *get_image(void *qp)
+static void run_work(const struct index_args *iargs,
+ int filename_pipe, int results_pipe, int cookie)
{
- char *line;
- struct index_args *pargs;
- char *rval;
- struct queue_args *qargs = qp;
-
- /* Initialise new task arguments */
- pargs = malloc(sizeof(struct index_args));
- memcpy(&pargs->static_args, &qargs->static_args,
- sizeof(struct static_index_args));
+ int allDone = 0;
+ FILE *fh;
- /* Get the next filename */
- if ( qargs->use_this_one_instead != NULL ) {
+ fh = fdopen(filename_pipe, "r");
+ if ( fh == NULL ) {
+ ERROR("Failed to fdopen() the filename pipe!\n");
+ close(filename_pipe);
+ close(results_pipe);
+ return;
+ }
- line = qargs->use_this_one_instead;
- qargs->use_this_one_instead = NULL;
+ while ( !allDone ) {
- } else {
+ struct pattern_args pargs;
+ int w, c;
+ char buf[1024];
+ char *line;
+ char *rval;
line = malloc(1024*sizeof(char));
- rval = fgets(line, 1023, qargs->fh);
+ rval = fgets(line, 1023, fh);
if ( rval == NULL ) {
- free(pargs);
free(line);
- return NULL;
+ if ( feof(fh) ) {
+ allDone = 1;
+ continue;
+ } else {
+ ERROR("Read error!\n");
+ return;
+ }
}
- chomp(line);
- }
-
- if ( qargs->config_basename ) {
- char *tmp;
- tmp = safe_basename(line);
- free(line);
- line = tmp;
- }
+ chomp(line);
+ pargs.filename = line;
+ pargs.indexable = 0;
- pargs->filename = malloc(strlen(qargs->prefix)+strlen(line)+1);
+ process_image(iargs, &pargs, cookie);
- snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, line);
+ /* Request another image */
+ c = sprintf(buf, "%i\n", pargs.indexable);
+ w = write(results_pipe, buf, c);
+ if ( w < 0 ) {
+ ERROR("write P0\n");
+ }
- free(line);
+ free(line);
- return pargs;
+ }
+ /* close my pipes */
+ fclose(fh);
+ close(results_pipe);
}
@@ -492,34 +527,6 @@ static time_t get_monotonic_seconds()
#endif
-static void finalise_image(void *qp, void *pp)
-{
- struct queue_args *qargs = qp;
- struct index_args *pargs = pp;
- time_t monotonic_seconds;
-
- qargs->n_indexable += pargs->indexable;
- qargs->n_processed++;
-
- monotonic_seconds = get_monotonic_seconds();
- if ( monotonic_seconds >= qargs->t_last_stats+STATS_EVERY_N_SECONDS ) {
-
- STATUS("%i out of %i indexed so far,"
- " %i out of %i since the last message.\n",
- qargs->n_indexable, qargs->n_processed,
- qargs->n_indexable - qargs->n_indexable_last_stats,
- qargs->n_processed - qargs->n_processed_last_stats);
-
- qargs->n_processed_last_stats = qargs->n_processed;
- qargs->n_indexable_last_stats = qargs->n_indexable;
- qargs->t_last_stats = monotonic_seconds;
-
- }
-
- free(pargs->filename);
- free(pargs);
-}
-
static int parse_cell_reduction(const char *scellr, int *err,
int *reduction_needs_cell)
@@ -553,7 +560,6 @@ int main(int argc, char *argv[])
FILE *fh;
FILE *ofh;
char *rval = NULL;
- int n_images;
int config_noindex = 0;
int config_cmfilter = 0;
int config_noisefilter = 0;
@@ -584,25 +590,31 @@ int main(int argc, char *argv[])
float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */
int cellr;
int peaks;
- int nthreads = 1;
- pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
+ int n_proc = 1;
char *prepare_line;
char prepare_filename[1024];
- struct queue_args qargs;
+ char *use_this_one_instead;
+ struct index_args iargs;
struct beam_params *beam = NULL;
char *element = NULL;
double nominal_photon_energy;
int stream_flags = STREAM_INTEGRATED;
- int cpu_num = 0;
- int cpu_groupsize = 1;
- int cpu_offset = 0;
- char *endptr;
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 n_indexable, n_processed, n_indexable_last_stats;
+ int n_processed_last_stats;
+ int t_last_stats;
+ pid_t *pids;
+ int *filename_pipes;
+ FILE **result_fhs;
+ fd_set fds;
+ int i;
+ int allDone;
+ int *finished;
copyme = new_copy_hdf5_field_list();
if ( copyme == NULL ) {
@@ -653,7 +665,7 @@ int main(int argc, char *argv[])
};
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:e:",
+ while ((c = getopt_long(argc, argv, "hi:o:z:p:x:j:g:t:b:e:",
longopts, NULL)) != -1)
{
switch (c) {
@@ -683,7 +695,7 @@ int main(int argc, char *argv[])
break;
case 'j' :
- nthreads = atoi(optarg);
+ n_proc = atoi(optarg);
break;
case 'g' :
@@ -725,39 +737,10 @@ int main(int argc, char *argv[])
break;
case 6 :
- cpu_num = strtol(optarg, &endptr, 10);
- if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
- ERROR("Invalid number of CPUs ('%s')\n",
- optarg);
- return 1;
- }
- break;
-
case 7 :
- cpu_groupsize = strtol(optarg, &endptr, 10);
- if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
- ERROR("Invalid CPU group size ('%s')\n",
- optarg);
- return 1;
- }
- if ( cpu_groupsize < 1 ) {
- ERROR("CPU group size cannot be"
- " less than 1.\n");
- return 1;
- }
- break;
-
case 8 :
- cpu_offset = strtol(optarg, &endptr, 10);
- if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
- ERROR("Invalid CPU offset ('%s')\n",
- optarg);
- return 1;
- }
- if ( cpu_offset < 0 ) {
- ERROR("CPU offset must be positive.\n");
- return 1;
- }
+ ERROR("The options --cpus, --cpugroup and --cpuoffset"
+ " are no longer used by indexamajig.\n");
break;
case 9 :
@@ -794,12 +777,6 @@ int main(int argc, char *argv[])
}
- if ( (cpu_num > 0) && (cpu_num % cpu_groupsize != 0) ) {
- ERROR("Number of CPUs must be divisible by"
- " the CPU group size.\n");
- return 1;
- }
-
if ( filename == NULL ) {
filename = strdup("-");
}
@@ -826,7 +803,6 @@ int main(int argc, char *argv[])
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");
@@ -859,8 +835,8 @@ int main(int argc, char *argv[])
}
}
- if ( nthreads == 0 ) {
- ERROR("Invalid number of threads.\n");
+ if ( n_proc == 0 ) {
+ ERROR("Invalid number of processes.\n");
return 1;
}
@@ -966,22 +942,20 @@ int main(int argc, char *argv[])
} else {
STATUS("No beam parameters file was given, so I'm taking the"
" nominal photon energy to be 2 keV.\n");
+ ERROR("I'm also going to assume 1 ADU per photon, which is");
+ ERROR(" almost certainly wrong. Peak sigmas will be"
+ " incorrect.\n");
nominal_photon_energy = 2000.0;
}
- if ( beam == NULL ) {
- ERROR("Warning: no beam parameters file.\n");
- ERROR("I'm going to assume 1 ADU per photon, which is almost");
- ERROR(" certainly wrong. Peak sigmas will be incorrect.\n");
- }
-
/* Get first filename and use it to set up the indexing */
- prepare_line = malloc(1024*sizeof(char));
+ prepare_line = malloc(1024);
rval = fgets(prepare_line, 1023, fh);
if ( rval == NULL ) {
ERROR("Failed to get filename to prepare indexing.\n");
return 1;
}
+ use_this_one_instead = strdup(prepare_line);
chomp(prepare_line);
if ( config_basename ) {
char *tmp;
@@ -990,7 +964,6 @@ int main(int argc, char *argv[])
prepare_line = tmp;
}
snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line);
- qargs.use_this_one_instead = prepare_line;
/* Prepare the indexer */
if ( indm != NULL ) {
@@ -1006,50 +979,258 @@ int main(int argc, char *argv[])
gsl_set_error_handler_off();
- qargs.static_args.cell = cell;
- qargs.static_args.config_cmfilter = config_cmfilter;
- qargs.static_args.config_noisefilter = config_noisefilter;
- qargs.static_args.config_verbose = config_verbose;
- qargs.static_args.config_satcorr = config_satcorr;
- qargs.static_args.config_closer = config_closer;
- qargs.static_args.config_insane = config_insane;
- qargs.static_args.config_bgsub = config_bgsub;
- qargs.static_args.cellr = cellr;
- qargs.static_args.tols[0] = tols[0];
- qargs.static_args.tols[1] = tols[1];
- qargs.static_args.tols[2] = tols[2];
- qargs.static_args.tols[3] = tols[3];
- qargs.static_args.threshold = threshold;
- qargs.static_args.min_gradient = min_gradient;
- qargs.static_args.min_snr = min_snr;
- qargs.static_args.min_int_snr = min_int_snr;
- qargs.static_args.det = det;
- qargs.static_args.indm = indm;
- qargs.static_args.ipriv = ipriv;
- qargs.static_args.peaks = peaks;
- qargs.static_args.output_mutex = &output_mutex;
- qargs.static_args.ofh = ofh;
- qargs.static_args.beam = beam;
- qargs.static_args.element = element;
- qargs.static_args.stream_flags = stream_flags;
- qargs.static_args.hdf5_peak_path = hdf5_peak_path;
- qargs.static_args.copyme = copyme;
- qargs.static_args.ir_inn = ir_inn;
- qargs.static_args.ir_mid = ir_mid;
- qargs.static_args.ir_out = ir_out;
-
- qargs.fh = fh;
- qargs.prefix = prefix;
- qargs.config_basename = config_basename;
- qargs.n_indexable = 0;
- qargs.n_processed = 0;
- qargs.n_indexable_last_stats = 0;
- qargs.n_processed_last_stats = 0;
- qargs.t_last_stats = get_monotonic_seconds();
-
- n_images = run_threads(nthreads, process_image, get_image,
- finalise_image, &qargs, 0,
- cpu_num, cpu_groupsize, cpu_offset);
+ /* 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_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];
+ 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.ofh = ofh;
+ 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;
+ iargs.ir_mid = ir_mid;
+ iargs.ir_out = ir_out;
+ iargs.outfile = outfile;
+
+ n_indexable = 0;
+ n_processed = 0;
+ n_indexable_last_stats = 0;
+ n_processed_last_stats = 0;
+ t_last_stats = get_monotonic_seconds();
+
+ FD_ZERO(&fds);
+ filename_pipes = calloc(n_proc, sizeof(int));
+ result_fhs = calloc(n_proc, sizeof(FILE *));
+ if ( filename_pipes == NULL ) {
+ ERROR("Couldn't allocate memory for pipes.\n");
+ return 1;
+ }
+ if ( result_fhs == NULL ) {
+ ERROR("Couldn't allocate memory for pipe file handles.\n");
+ return 1;
+ }
+
+ pids = calloc(n_proc, sizeof(pid_t));
+ if ( pids == NULL ) {
+ ERROR("Couldn't allocate memory for PIDs.\n");
+ return 1;
+ }
+
+ finished = calloc(n_proc, sizeof(int));
+ if ( finished == NULL ) {
+ ERROR("Couldn't allocate memory for process flags.\n");
+ return 1;
+ }
+
+ /* Fork the right number of times */
+ for ( i=0; i<n_proc; i++ ) {
+
+ pid_t p;
+ int filename_pipe[2];
+ int result_pipe[2];
+
+ if ( pipe(filename_pipe) == - 1 ) {
+ ERROR("pipe() failed!\n");
+ return 1;
+ }
+
+ if ( pipe(result_pipe) == - 1 ) {
+ ERROR("pipe() failed!\n");
+ return 1;
+ }
+
+ p = fork();
+ if ( p == -1 ) {
+ ERROR("fork() failed!\n");
+ return 1;
+ }
+
+ if ( p == 0 ) {
+ /* Child process gets the 'read' end of the filename
+ * pipe, and the 'write' end of the result pipe. */
+ close(filename_pipe[1]);
+ close(result_pipe[0]);
+ run_work(&iargs, filename_pipe[0], result_pipe[1], i);
+ exit(0);
+ }
+
+ /* Parent process gets the 'write' end of the filename pipe
+ * and the 'read' end of the result pipe. */
+ pids[i] = p;
+ close(filename_pipe[0]);
+ close(result_pipe[1]);
+ filename_pipes[i] = filename_pipe[1];
+
+ result_fhs[i] = fdopen(result_pipe[0], "r");
+ if ( result_fhs[i] == NULL ) {
+ ERROR("fdopen() failed.\n");
+ return 1;
+ }
+
+ }
+
+ /* Send first image to all children */
+ for ( i=0; i<n_proc; i++ ) {
+
+ char *nextImage;
+
+ nextImage = get_pattern(fh, &use_this_one_instead,
+ config_basename, prefix);
+
+ if ( nextImage != NULL ) {
+
+ write(filename_pipes[i], nextImage, strlen(nextImage));
+ write(filename_pipes[i], "\n", 1);
+
+ free(nextImage);
+
+ } else {
+
+ /* No more files to process.. already? */
+ close(filename_pipes[i]);
+
+ }
+
+ }
+
+ allDone = 0;
+ while ( !allDone ) {
+
+ int r, i;
+ struct timeval tv;
+ fd_set fds;
+ double tNow;
+ int fdmax;
+
+ tv.tv_sec = 5;
+ tv.tv_usec = 0;
+
+ FD_ZERO(&fds);
+ fdmax = 0;
+ for ( i=0; i<n_proc; i++ ) {
+
+ int fd;
+
+ if ( finished[i] ) continue;
+
+ fd = fileno(result_fhs[i]);
+ FD_SET(fd, &fds);
+ if ( fd > fdmax ) fdmax = fd;
+
+ }
+
+ r = select(fdmax+1, &fds, NULL, NULL, &tv);
+
+ if ( r == -1 ) {
+ ERROR("select() failed: %s\n", strerror(errno));
+ continue;
+ }
+
+ if ( r == 0 ) {
+ STATUS("Timeout\n");
+ continue;
+ }
+
+ for ( i=0; i<n_proc; i++ ) {
+
+ char *nextImage;
+ char results[1024];
+ char *rval;
+ int fd;
+
+ if ( finished[i] ) continue;
+
+ fd = fileno(result_fhs[i]);
+ if ( !FD_ISSET(fd, &fds) ) continue;
+
+ rval = fgets(results, 1024, result_fhs[i]);
+ if ( rval == NULL ) {
+ if ( feof(result_fhs[i]) ) {
+ /* Process died */
+ finished[i] = 1;
+ } else {
+ ERROR("fgets() failed: %s\n",
+ strerror(errno));
+ }
+ continue;
+ }
+
+ chomp(results);
+ n_indexable += atoi(results);
+ n_processed++;
+
+ /* Send next filename */
+ nextImage = get_pattern(fh,
+ &use_this_one_instead,
+ config_basename,
+ prefix);
+
+ if ( nextImage == NULL ) {
+ /* No more images */
+ finished[i] = 1;
+ } else {
+
+ r = write(filename_pipes[i], nextImage,
+ strlen(nextImage));
+ r -= write(filename_pipes[i], "\n", 1);
+ if ( r < 0 ) {
+ ERROR("write pipe\n");
+ }
+ }
+
+ }
+
+ /* Update progress */
+ tNow = get_monotonic_seconds();
+ if ( tNow >= t_last_stats+STATS_EVERY_N_SECONDS ) {
+
+ STATUS("%i out of %i indexed so far,"
+ " %i out of %i since the last message.\n",
+ n_indexable, n_processed,
+ n_indexable - n_indexable_last_stats,
+ n_processed - n_processed_last_stats);
+
+ n_indexable_last_stats = n_indexable;
+ n_processed_last_stats = n_processed;
+ t_last_stats = tNow;
+
+ }
+
+ allDone = 1;
+ for ( i=0; i<n_proc; i++ ) {
+ if ( !finished[i] ) allDone = 0;
+ }
+
+ }
+
+ for ( i=0; i<n_proc; i++ ) {
+ close(filename_pipes[i]);
+ fclose(result_fhs[i]);
+ }
+ free(filename_pipes);
+ free(result_fhs);
+ free(pids);
+ free(finished);
cleanup_indexing(ipriv);
@@ -1062,11 +1243,12 @@ int main(int argc, char *argv[])
free(hdf5_peak_path);
free_copy_hdf5_field_list(copyme);
cell_free(cell);
+ free(use_this_one_instead);
if ( fh != stdin ) fclose(fh);
if ( ofh != stdout ) fclose(ofh);
STATUS("There were %i images, of which %i could be indexed.\n",
- n_images, qargs.n_indexable);
+ n_processed, n_indexable);
return 0;
}
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 6b99864e..9e054675 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -178,8 +178,6 @@ static void show_help(const char *s)
" -c, --cnoise=<val> Add random noise, with a flat distribution, to the\n"
" reciprocal lattice vector components given in the\n"
" stream, with maximum error +/- <val> percent.\n"
-" --pgraph=<file> Write reflection counts and partiality statistics\n"
-" to <file>.\n"
"\n"
);
}
@@ -542,8 +540,6 @@ int main(int argc, char *argv[])
if ( fh != NULL ) {
- fprintf(fh, "1/d_nm #refl pmean pmax\n");
-
for ( i=0; i<NBINS; i++ ) {
double rcen;
diff --git a/tests/symmetry_check.c b/tests/symmetry_check.c
index 7c06dfc8..edbacbf1 100644
--- a/tests/symmetry_check.c
+++ b/tests/symmetry_check.c
@@ -324,11 +324,6 @@ int main(int argc, char *argv[])
check_subgroup("4/m", "-4", 1, 1, 2, &fail);
check_subgroup("622", "321_H", 1, 1, 2, &fail);
- check_subgroup("4/mmm", "-42m", 1, 1, 2, &fail);
- check_subgroup("4/mmm", "-4m2", 1, 1, 2, &fail);
- check_subgroup("4/mmm", "4/m", 1, 1, 2, &fail);
- check_subgroup("4/mmm", "4mm", 1, 1, 2, &fail);
-
/* Tetartohedral */
check_subgroup("6/mmm", "-3_H", 1, 1, 4, &fail);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 20:13:53 +0000