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-rw-r--r--libcrystfel/src/integration.c51
-rw-r--r--libcrystfel/src/integration.h8
-rw-r--r--src/im-sandbox.c44
-rw-r--r--src/process_image.c6
-rw-r--r--src/process_image.h6
-rw-r--r--tests/integration_check.c2
-rw-r--r--tests/prof2d_check.c2
7 files changed, 85 insertions, 34 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index a0d23d2d..f42da36f 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -33,6 +33,7 @@
#include <stdlib.h>
#include <assert.h>
+#include <unistd.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_linalg.h>
@@ -337,13 +338,16 @@ static void show_reference_profile(struct intcontext *ic, int i)
}
-static void show_peak_box(struct intcontext *ic, struct peak_box *bx)
+static void show_peak_box(struct intcontext *ic, struct peak_box *bx,
+ int results_pipe)
{
#ifdef HAVE_CURSES_COLOR
int q;
signed int h, k, l;
double fs, ss;
+ if ( results_pipe != 0 ) write(results_pipe, "SUSPEND\n", 8);
+
initscr();
clear();
start_color();
@@ -402,6 +406,8 @@ static void show_peak_box(struct intcontext *ic, struct peak_box *bx)
refresh();
getch();
endwin();
+
+ if ( results_pipe != 0 ) write(results_pipe, "RELEASE\n", 8);
#endif
}
@@ -1345,7 +1351,8 @@ static int get_int_diag(struct intcontext *ic, Reflection *refl)
-static void integrate_prof2d_once(struct intcontext *ic, struct peak_box *bx)
+static void integrate_prof2d_once(struct intcontext *ic, struct peak_box *bx,
+ int results_pipe)
{
bx->intensity = fit_intensity(ic, bx);
bx->sigma = calc_sigma(ic, bx);
@@ -1375,7 +1382,8 @@ static void integrate_prof2d_once(struct intcontext *ic, struct peak_box *bx)
set_redundancy(bx->refl, 0);
}
- if ( get_int_diag(ic, bx->refl) ) show_peak_box(ic, bx);
+ if ( get_int_diag(ic, bx->refl) ) show_peak_box(ic, bx,
+ results_pipe);
} else {
@@ -1467,7 +1475,8 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list)
static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
Crystal *cr, struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
- double ir_inn, double ir_mid, double ir_out)
+ double ir_inn, double ir_mid, double ir_out,
+ int results_pipe)
{
RefList *list;
UnitCell *cell;
@@ -1512,7 +1521,7 @@ static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
for ( i=0; i<ic.n_boxes; i++ ) {
struct peak_box *bx;
bx = &ic.boxes[i];
- integrate_prof2d_once(&ic, bx);
+ integrate_prof2d_once(&ic, bx, results_pipe);
}
//refine_rigid_groups(&ic);
@@ -1526,7 +1535,8 @@ static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
static void integrate_rings_once(Reflection *refl, struct image *image,
- struct intcontext *ic, UnitCell *cell)
+ struct intcontext *ic, UnitCell *cell,
+ int results_pipe)
{
double pfs, pss;
struct peak_box *bx;
@@ -1623,7 +1633,7 @@ static void integrate_rings_once(Reflection *refl, struct image *image,
pss += bx->offs_ss;
set_detector_pos(refl, 0.0, pfs, pss);
- if ( get_int_diag(ic, refl) ) show_peak_box(ic, bx);
+ if ( get_int_diag(ic, refl) ) show_peak_box(ic, bx, results_pipe);
if ( intensity < -5.0*sigma ) {
ic->n_implausible++;
@@ -1722,7 +1732,8 @@ static double estimate_resolution(UnitCell *cell, ImageFeatureList *flist)
static void integrate_rings(IntegrationMethod meth, PartialityModel pmodel,
Crystal *cr, struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
- double ir_inn, double ir_mid, double ir_out)
+ double ir_inn, double ir_mid, double ir_out,
+ int results_pipe)
{
RefList *list;
Reflection *refl;
@@ -1761,7 +1772,7 @@ static void integrate_rings(IntegrationMethod meth, PartialityModel pmodel,
refl != NULL;
refl = next_refl(refl, iter) )
{
- integrate_rings_once(refl, image, &ic, cell);
+ integrate_rings_once(refl, image, &ic, cell, results_pipe);
}
//refine_rigid_groups(&ic);
@@ -1799,11 +1810,12 @@ static void apply_resolution_cutoff(Crystal *cr, double res)
}
-void integrate_all_3(struct image *image, IntegrationMethod meth,
+void integrate_all_4(struct image *image, IntegrationMethod meth,
PartialityModel pmodel, double push_res,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
- signed int idh, signed int idk, signed int idl)
+ signed int idh, signed int idk, signed int idl,
+ int results_pipe)
{
int i;
@@ -1820,7 +1832,8 @@ void integrate_all_3(struct image *image, IntegrationMethod meth,
case INTEGRATION_RINGS :
integrate_rings(meth, pmodel, cr, image,
int_diag, idh, idk, idl,
- ir_inn, ir_mid, ir_out);
+ ir_inn, ir_mid, ir_out,
+ results_pipe);
res = estimate_resolution(crystal_get_cell(cr),
image->features);
break;
@@ -1828,7 +1841,8 @@ void integrate_all_3(struct image *image, IntegrationMethod meth,
case INTEGRATION_PROF2D :
integrate_prof2d(meth, pmodel, cr, image,
int_diag, idh, idk, idl,
- ir_inn, ir_mid, ir_out);
+ ir_inn, ir_mid, ir_out,
+ results_pipe);
res = estimate_resolution(crystal_get_cell(cr),
image->features);
break;
@@ -1848,6 +1862,17 @@ void integrate_all_3(struct image *image, IntegrationMethod meth,
}
+void integrate_all_3(struct image *image, IntegrationMethod meth,
+ PartialityModel pmodel, double push_res,
+ double ir_inn, double ir_mid, double ir_out,
+ IntDiag int_diag,
+ signed int idh, signed int idk, signed int idl)
+{
+ integrate_all_4(image, meth, pmodel, 0.0, ir_inn, ir_mid, ir_out,
+ int_diag, idh, idk, idl, 0);
+}
+
+
void integrate_all_2(struct image *image, IntegrationMethod meth,
double push_res,
double ir_inn, double ir_mid, double ir_out,
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index f077be32..9e1c8ee1 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -105,6 +105,14 @@ extern void integrate_all_3(struct image *image, IntegrationMethod meth,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl);
+extern void integrate_all_4(struct image *image, IntegrationMethod meth,
+ PartialityModel pmodel, double push_res,
+ double ir_inn, double ir_mid, double ir_out,
+ IntDiag int_diag,
+ signed int idh, signed int idk, signed int idl,
+ int results_pipe);
+
+
#ifdef __cplusplus
}
#endif
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 3e2ab2b3..7305dfd4 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -3,13 +3,13 @@
*
* Sandbox for indexing
*
- * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
* Copyright © 2012 Lorenzo Galli
*
* Authors:
- * 2010-2013 Thomas White <taw@physics.org>
+ * 2010-2014 Thomas White <taw@physics.org>
* 2011 Richard Kirian
* 2012 Lorenzo Galli
* 2012 Chunhong Yoon
@@ -90,6 +90,7 @@ struct sandbox
int n_hadcrystals_last_stats;
int n_crystals_last_stats;
int t_last_stats;
+ int suspend_stats;
struct index_args *iargs;
@@ -218,7 +219,8 @@ static void run_work(const struct index_args *iargs,
pargs.filename = line;
pargs.n_crystals = 0;
- process_image(iargs, &pargs, st, cookie, tmpdir);
+ process_image(iargs, &pargs, st, cookie, tmpdir,
+ results_pipe);
/* Request another image */
c = sprintf(buf, "%i\n", pargs.n_crystals);
@@ -650,6 +652,7 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
sb->n_hadcrystals_last_stats = 0;
sb->n_crystals_last_stats = 0;
sb->t_last_stats = get_monotonic_seconds();
+ sb->suspend_stats = 0;
sb->n_proc = n_proc;
sb->iargs = iargs;
@@ -824,19 +827,32 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
chomp(results);
- strtol(results, &eptr, 10);
- if ( eptr == results ) {
- if ( strlen(results) > 0 ) {
- ERROR("Invalid result '%s'\n", results);
+ if ( strcmp(results, "SUSPEND") == 0 ) {
+ sb->suspend_stats++;
+ } else if ( strcmp(results, "RELEASE") == 0 ) {
+ if ( sb->suspend_stats > 0 ) {
+ sb->suspend_stats--;
+ } else {
+ ERROR("RELEASE before SUSPEND.\n");
}
} else {
- int nc = atoi(results);
- sb->n_crystals += nc;
- if ( nc > 0 ) {
- sb->n_hadcrystals++;
+ strtol(results, &eptr, 10);
+ if ( eptr == results ) {
+ if ( strlen(results) > 0 ) {
+ ERROR("Invalid result '%s'\n",
+ results);
+ }
+ } else {
+
+ int nc = atoi(results);
+ sb->n_crystals += nc;
+ if ( nc > 0 ) {
+ sb->n_hadcrystals++;
+ }
+ sb->n_processed++;
+
}
- sb->n_processed++;
}
@@ -867,7 +883,9 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
/* Update progress */
lock_sandbox(sb);
tNow = get_monotonic_seconds();
- if ( tNow >= sb->t_last_stats+STATS_EVERY_N_SECONDS ) {
+ if ( !sb->suspend_stats
+ && (tNow >= sb->t_last_stats+STATS_EVERY_N_SECONDS) )
+ {
STATUS("%4i indexable out of %4i processed (%4.1f%%), "
"%4i crystals so far. "
diff --git a/src/process_image.c b/src/process_image.c
index 4751073b..0ec058ac 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -51,7 +51,7 @@
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
- Stream *st, int cookie, const char *tmpdir)
+ Stream *st, int cookie, const char *tmpdir, int results_pipe)
{
float *data_for_measurement;
size_t data_size;
@@ -184,10 +184,10 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Integrate all the crystals at once - need all the crystals so that
* overlaps can be detected. */
- integrate_all_2(&image, iargs->int_meth, iargs->push_res,
+ integrate_all_4(&image, iargs->int_meth, PMODEL_SPHERE, iargs->push_res,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
iargs->int_diag, iargs->int_diag_h,
- iargs->int_diag_k, iargs->int_diag_l);
+ iargs->int_diag_k, iargs->int_diag_l, results_pipe);
write_chunk(st, &image, hdfile,
iargs->stream_peaks, iargs->stream_refls);
diff --git a/src/process_image.h b/src/process_image.h
index 1a8a9ff3..98228f6f 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -3,11 +3,11 @@
*
* The processing pipeline for one image
*
- * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2013 Thomas White <taw@physics.org>
+ * 2010-2014 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -97,7 +97,7 @@ struct pattern_args
extern void process_image(const struct index_args *iargs,
struct pattern_args *pargs, Stream *st,
- int cookie, const char *tmpdir);
+ int cookie, const char *tmpdir, int results_pipe);
#endif /* PROCESS_IMAGEs_H */
diff --git a/tests/integration_check.c b/tests/integration_check.c
index 701d8be7..b5dbea67 100644
--- a/tests/integration_check.c
+++ b/tests/integration_check.c
@@ -146,7 +146,7 @@ int main(int argc, char *argv[])
}
setup_ring_masks(&ic, ir_inn, ir_mid, ir_out);
- integrate_rings_once(refl, &image, &ic, cell);
+ integrate_rings_once(refl, &image, &ic, cell, 0);
cell_free(cell);
diff --git a/tests/prof2d_check.c b/tests/prof2d_check.c
index 75b9748e..a1c89d36 100644
--- a/tests/prof2d_check.c
+++ b/tests/prof2d_check.c
@@ -177,7 +177,7 @@ int main(int argc, char *argv[])
reflist_free(list); /* integrate_prof2d() will predict again */
integrate_prof2d(INTEGRATION_PROF2D, PMODEL_SPHERE, cr, &image,
- INTDIAG_NONE, 0, 0, 0, ir_inn, ir_mid, ir_out);
+ INTDIAG_NONE, 0, 0, 0, ir_inn, ir_mid, ir_out, 0);
list = crystal_get_reflections(cr);
printf("Weak reflections:\n");
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-26 19:13:55 +0000