Suspend indexing statistics while --int-diag is displaying

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");