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-rw-r--r--doc/man/partialator.15
-rw-r--r--src/partialator.c58
-rw-r--r--src/post-refinement.c52
-rw-r--r--src/post-refinement.h12
4 files changed, 84 insertions, 43 deletions
diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index 9808c64b..7cd8df03 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -162,6 +162,11 @@ Write out the per-crystal parameters and reflection lists after every cycle of r
Do not write the extensive log files needed for plotting contour maps and spectrum graphs. This makes the process a lot faster, but you probably do want these logs to check that post-refinement is working reasonably.
.PD 0
+.IP \fB--log-folder=\fIfolder\fR
+.PD
+Specify the location of the log folder (see \fB--no-logs\fR). The default is \fB--log-folder=pr-logs\fR.
+
+.PD 0
.IP "\fB-w\fR \fIpg\fR"
.PD
Set the apparent symmetry of the crystals. The ambiguity operator will be determined by comparing this to the actual symmetry.
diff --git a/src/partialator.c b/src/partialator.c
index ca0249ce..35d1ff95 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -334,6 +334,7 @@ static void show_help(const char *s)
" --custom-split List of files for custom dataset splitting.\n"
" --max-rel-B Maximum allowable relative |B| factor.\n"
" --no-logs Do not write extensive log files.\n"
+" --log-folder=<fn> Location for log folder.\n"
" -w <pg> Apparent point group for resolving ambiguities.\n"
" --operator=<op> Indexing ambiguity operator for resolving.\n"
" --force-bandwidth=<n> Set all bandwidths to <n> (fraction).\n"
@@ -686,13 +687,14 @@ static void write_to_pgraph(FILE *fh, RefList *list, RefList *full, Crystal *cr,
static void write_pgraph(RefList *full, Crystal **crystals, int n_crystals,
- signed int iter, const char *suff)
+ signed int iter, const char *suff,
+ const char *log_folder)
{
FILE *fh;
char tmp[256];
int i;
- snprintf(tmp, 256, "pr-logs/pgraph%s.dat", suff);
+ snprintf(tmp, 256, "%s/pgraph%s.dat", log_folder, suff);
if ( iter == 0 ) {
fh = fopen(tmp, "w");
@@ -850,6 +852,7 @@ struct log_qargs
int scaleflags;
PartialityModel pmodel;
int n_done;
+ const char *log_folder;
};
@@ -861,6 +864,7 @@ struct log_args
PartialityModel pmodel;
int iter;
int cnum;
+ const char *log_folder;
};
@@ -880,6 +884,7 @@ static void *get_log_task(void *vp)
task->cnum = qargs->next;
task->scaleflags = qargs->scaleflags;
task->pmodel = qargs->pmodel;
+ task->log_folder = qargs->log_folder;
qargs->next += 20;
return task;
@@ -889,10 +894,12 @@ static void *get_log_task(void *vp)
static void write_logs(void *vp, int cookie)
{
struct log_args *args = vp;
- write_specgraph(args->cr, args->full, args->iter, args->cnum);
+ write_specgraph(args->cr, args->full, args->iter, args->cnum,
+ args->log_folder);
write_gridscan(args->cr, args->full, args->iter, args->cnum,
- args->scaleflags, args->pmodel);
- write_test_logs(args->cr, args->full, args->iter, args->cnum);
+ args->scaleflags, args->pmodel, args->log_folder);
+ write_test_logs(args->cr, args->full, args->iter, args->cnum,
+ args->log_folder);
}
@@ -908,7 +915,8 @@ static void done_log(void *vqargs, void *vp)
static void write_logs_parallel(Crystal **crystals, int n_crystals,
RefList *full, int iter, int n_threads,
- int scaleflags, PartialityModel pmodel)
+ int scaleflags, PartialityModel pmodel,
+ const char *log_folder)
{
struct log_qargs qargs;
@@ -920,6 +928,7 @@ static void write_logs_parallel(Crystal **crystals, int n_crystals,
qargs.n_crystals = n_crystals;
qargs.scaleflags = scaleflags;
qargs.pmodel = pmodel;
+ qargs.log_folder = log_folder;
run_threads(n_threads, write_logs, get_log_task, done_log, &qargs,
n_crystals/20, 0, 0, 0);
@@ -1058,6 +1067,7 @@ int main(int argc, char *argv[])
int do_write_logs = 0;
int no_deltacchalf = 0;
char *harvest_file = NULL;
+ char *log_folder = "pr-logs";
/* Long options */
const struct option longopts[] = {
@@ -1091,6 +1101,7 @@ int main(int argc, char *argv[])
{"no-polarisation", 0, NULL, 15},
{"no-polarization", 0, NULL, 15}, /* compat */
{"harvest-file", 1, NULL, 16},
+ {"log-folder", 1, NULL, 17},
{"no-scale", 0, &no_scale, 1},
{"no-Bscale", 0, &no_Bscale, 1},
@@ -1280,6 +1291,10 @@ int main(int argc, char *argv[])
harvest_file = strdup(optarg);
break;
+ case 17 :
+ log_folder = strdup(optarg);
+ break;
+
case 0 :
break;
@@ -1391,21 +1406,24 @@ int main(int argc, char *argv[])
}
if ( do_write_logs ) {
- int r = mkdir("pr-logs", S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+ int r = mkdir(log_folder, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
if ( r ) {
if ( errno == EEXIST ) {
- ERROR("WARNING: pr-logs folder already exists. "
- "Beware of mixing old and new log files!\n");
+ ERROR("WARNING: Log folder (%s) already exists. "
+ "Beware of mixing old and new log files!\n",
+ log_folder);
} else {
- ERROR("Failed to create pr-logs folder.\n");
+ ERROR("Failed to create log folder (%s).\n",
+ log_folder);
return 1;
}
}
} else {
struct stat s;
- if ( stat("pr-logs", &s) != -1 ) {
- ERROR("WARNING: pr-logs folder exists, but I will not "
- "write anything in it with these settings.\n");
+ if ( stat(log_folder, &s) != -1 ) {
+ ERROR("WARNING: Log folder (%s) exists, but I will not "
+ "write anything in it with these settings.\n",
+ log_folder);
}
}
@@ -1641,9 +1659,9 @@ int main(int argc, char *argv[])
show_all_residuals(crystals, n_crystals, full, no_free);
if ( do_write_logs ) {
- write_pgraph(full, crystals, n_crystals, 0, "");
+ write_pgraph(full, crystals, n_crystals, 0, "", log_folder);
write_logs_parallel(crystals, n_crystals, full, 0, nthreads,
- scaleflags, pmodel);
+ scaleflags, pmodel, log_folder);
}
/* Iterate */
@@ -1653,7 +1671,8 @@ int main(int argc, char *argv[])
if ( !no_pr ) {
refine_all(crystals, n_crystals, full, nthreads, pmodel,
- itn+1, no_logs, sym, amb, scaleflags);
+ itn+1, no_logs, sym, amb, scaleflags,
+ log_folder);
}
/* Create new reference if needed */
@@ -1674,7 +1693,8 @@ int main(int argc, char *argv[])
show_all_residuals(crystals, n_crystals, full, no_free);
if ( do_write_logs ) {
- write_pgraph(full, crystals, n_crystals, itn+1, "");
+ write_pgraph(full, crystals, n_crystals, itn+1, "",
+ log_folder);
}
if ( output_everycycle ) {
@@ -1724,9 +1744,9 @@ int main(int argc, char *argv[])
/* Write final figures of merit (no rejection any more) */
show_all_residuals(crystals, n_crystals, full, no_free);
if ( do_write_logs ) {
- write_pgraph(full, crystals, n_crystals, -1, "");
+ write_pgraph(full, crystals, n_crystals, -1, "", log_folder);
write_logs_parallel(crystals, n_crystals, full, -1, nthreads,
- scaleflags, pmodel);
+ scaleflags, pmodel, log_folder);
}
/* Output results */
diff --git a/src/post-refinement.c b/src/post-refinement.c
index e5218094..70b14a0f 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -317,14 +317,15 @@ static void try_reindex(Crystal *crin, const RefList *full,
void write_test_logs(Crystal *crystal, const RefList *full,
- signed int cycle, int serial)
+ signed int cycle, int serial,
+ const char *log_folder)
{
FILE *fh;
struct image *image = crystal_get_image(crystal);
char tmp[256];
char ins[16];
- snprintf(tmp, 256, "pr-logs/parameters-crystal%i.dat", serial);
+ snprintf(tmp, 256, "%s/parameters-crystal%i.dat", log_folder, serial);
if ( cycle == 0 ) {
fh = fopen(tmp, "w");
@@ -367,7 +368,8 @@ void write_test_logs(Crystal *crystal, const RefList *full,
void write_specgraph(Crystal *crystal, const RefList *full,
- signed int cycle, int serial)
+ signed int cycle, int serial,
+ const char *log_folder)
{
FILE *fh;
char tmp[256];
@@ -379,7 +381,7 @@ void write_specgraph(Crystal *crystal, const RefList *full,
struct image *image = crystal_get_image(crystal);
char ins[16];
- snprintf(tmp, 256, "pr-logs/specgraph-crystal%i.dat", serial);
+ snprintf(tmp, 256, "%s/specgraph-crystal%i.dat", log_folder, serial);
if ( cycle == 0 ) {
fh = fopen(tmp, "w");
@@ -443,7 +445,8 @@ void write_specgraph(Crystal *crystal, const RefList *full,
static void write_angle_grid(Crystal *cr, const RefList *full,
signed int cycle, int serial, int scaleflags,
- PartialityModel pmodel)
+ PartialityModel pmodel,
+ const char *log_folder)
{
FILE *fh;
char fn[64];
@@ -475,8 +478,8 @@ static void write_angle_grid(Crystal *cr, const RefList *full,
ins[1] = '\0';
}
- snprintf(fn, 64, "pr-logs/grid-crystal%i-cycle%s-ang1-ang2.dat",
- serial, ins);
+ snprintf(fn, 64, "%s/grid-crystal%i-cycle%s-ang1-ang2.dat",
+ log_folder, serial, ins);
fh = fopen(fn, "w");
if ( fh != NULL ) {
double v1, v2;
@@ -509,7 +512,8 @@ static void write_angle_grid(Crystal *cr, const RefList *full,
static void write_radius_grid(Crystal *cr, const RefList *full,
signed int cycle, int serial, int scaleflags,
- PartialityModel pmodel)
+ PartialityModel pmodel,
+ const char *log_folder)
{
FILE *fh;
char fn[64];
@@ -541,8 +545,8 @@ static void write_radius_grid(Crystal *cr, const RefList *full,
ins[1] = '\0';
}
- snprintf(fn, 64, "pr-logs/grid-crystal%i-cycle%s-R-wave.dat",
- serial, ins);
+ snprintf(fn, 64, "%s/grid-crystal%i-cycle%s-R-wave.dat",
+ log_folder, serial, ins);
fh = fopen(fn, "w");
if ( fh != NULL ) {
double v1, v2;
@@ -575,10 +579,11 @@ static void write_radius_grid(Crystal *cr, const RefList *full,
void write_gridscan(Crystal *cr, const RefList *full,
signed int cycle, int serial, int scaleflags,
- PartialityModel pmodel)
+ PartialityModel pmodel,
+ const char *log_folder)
{
- write_angle_grid(cr, full, cycle, serial, scaleflags, pmodel);
- write_radius_grid(cr, full, cycle, serial, scaleflags, pmodel);
+ write_angle_grid(cr, full, cycle, serial, scaleflags, pmodel, log_folder);
+ write_radius_grid(cr, full, cycle, serial, scaleflags, pmodel, log_folder);
}
@@ -647,7 +652,8 @@ static void zero_alter(struct rf_alteration *alter)
static void do_pr_refine(Crystal *cr, const RefList *full,
PartialityModel pmodel, int serial,
int cycle, int write_logs,
- SymOpList *sym, SymOpList *amb, int scaleflags)
+ SymOpList *sym, SymOpList *amb, int scaleflags,
+ const char *log_folder)
{
struct rf_priv priv;
struct rf_alteration alter;
@@ -684,7 +690,8 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
char fn[64];
- snprintf(fn, 63, "pr-logs/crystal%i-cycle%i.log", serial, cycle);
+ snprintf(fn, 63, "%s/crystal%i-cycle%i.log",
+ log_folder, serial, cycle);
fh = fopen(fn, "w");
if ( fh != NULL ) {
fprintf(fh, "iter FoM FreeFoM rotx/rad "
@@ -722,9 +729,10 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
calculate_partialities(cr, pmodel);
if ( write_logs ) {
- write_gridscan(cr, full, cycle, serial, scaleflags, pmodel);
- write_specgraph(cr, full, cycle, serial);
- write_test_logs(cr, full, cycle, serial);
+ write_gridscan(cr, full, cycle, serial, scaleflags,
+ pmodel, log_folder);
+ write_specgraph(cr, full, cycle, serial, log_folder);
+ write_test_logs(cr, full, cycle, serial, log_folder);
}
if ( crystal_get_profile_radius(cr) > 5e9 ) {
@@ -752,6 +760,7 @@ struct refine_args
SymOpList *sym;
SymOpList *amb;
int scaleflags;
+ const char *log_folder;
};
@@ -775,7 +784,8 @@ static void refine_image(void *task, int id)
do_pr_refine(cr, pargs->full, pargs->pmodel,
pargs->serial, pargs->cycle, write_logs,
- pargs->sym, pargs->amb, pargs->scaleflags);
+ pargs->sym, pargs->amb, pargs->scaleflags,
+ pargs->log_folder);
}
@@ -810,7 +820,8 @@ static void done_image(void *vqargs, void *task)
void refine_all(Crystal **crystals, int n_crystals,
RefList *full, int nthreads, PartialityModel pmodel,
int cycle, int no_logs,
- SymOpList *sym, SymOpList *amb, int scaleflags)
+ SymOpList *sym, SymOpList *amb, int scaleflags,
+ const char *log_folder)
{
struct refine_args task_defaults;
struct pr_queue_args qargs;
@@ -824,6 +835,7 @@ void refine_all(Crystal **crystals, int n_crystals,
task_defaults.amb = amb;
task_defaults.scaleflags = scaleflags;
task_defaults.serial = 0;
+ task_defaults.log_folder = log_folder;
qargs.task_defaults = task_defaults;
qargs.n_started = 0;
diff --git a/src/post-refinement.h b/src/post-refinement.h
index a15d0396..546050a4 100644
--- a/src/post-refinement.h
+++ b/src/post-refinement.h
@@ -61,20 +61,24 @@ extern const char *str_prflag(enum prflag flag);
extern void refine_all(Crystal **crystals, int n_crystals,
RefList *full, int nthreads, PartialityModel pmodel,
int cycle, int no_logs,
- SymOpList *sym, SymOpList *amb, int scaleflags);
+ SymOpList *sym, SymOpList *amb, int scaleflags,
+ const char *log_folder);
extern void write_gridscan(Crystal *cr, const RefList *full,
int cycle, int serial, int scaleflags,
- PartialityModel model);
+ PartialityModel model,
+ const char *log_folder);
extern void write_specgraph(Crystal *crystal, const RefList *full,
- signed int cycle, int serial);
+ signed int cycle, int serial,
+ const char *log_folder);
/* Exported so it can be poked by tests/pr_p_gradient_check */
extern double gradient(Crystal *cr, int k, Reflection *refl,
PartialityModel pmodel);
extern void write_test_logs(Crystal *crystal, const RefList *full,
- signed int cycle, int serial);
+ signed int cycle, int serial,
+ const char *log_folder);
#endif /* POST_REFINEMENT_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-11 02:31:53 +0000