From 1e6cb84f7ae14cb39b4ca5c0bc768399462ad2d0 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 11 Jul 2023 16:08:46 +0200
Subject: partialator: Add --unmerged-output

---
 src/merge.c       | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 src/merge.h       |  2 ++
 src/partialator.c | 11 ++++++++++
 3 files changed, 74 insertions(+)

(limited to 'src')

diff --git a/src/merge.c b/src/merge.c
index 20981ff8..0a5c5f14 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -484,3 +484,64 @@ double log_residual(Crystal *cr, const RefList *full, int free,
 	if ( pn_used != NULL ) *pn_used = n_used;
 	return dev;
 }
+
+
+/* Has to match run_merge_job to be useful */
+void write_unmerged(const char *fn, Crystal **crystals, int n_crystals)
+{
+	FILE *fh;
+	int i;
+
+	fh = fopen(fn, "w");
+	if ( fh == NULL ) {
+		ERROR("Failed to open %s\n", fn);
+		return;
+	}
+
+	for ( i=0; i<n_crystals; i++ ) {
+
+		Reflection *refl;
+		RefListIterator *iter;
+		double G, B;
+		UnitCell *cell;
+
+		fprintf(fh, "Crystal %i\n", i);
+		if ( crystal_get_user_flag(crystals[i]) ) {
+			fprintf(fh, "Flagged: yes\n");
+		} else {
+			fprintf(fh, "Flagged: no\n");
+		}
+
+		G = crystal_get_osf(crystals[i]);
+		B = crystal_get_Bfac(crystals[i]);
+		cell = crystal_get_cell(crystals[i]);
+
+		for ( refl = first_refl(crystal_get_reflections(crystals[i]), &iter);
+		      refl != NULL;
+		      refl = next_refl(refl, iter) )
+		{
+			signed int h, k, l;
+			double res;
+
+			get_indices(refl, &h, &k, &l);
+			res = resolution(cell, h, k, l);
+			fprintf(fh, "%4i %4i %4i %10.2f %10.2f", h, k, l,
+			        correct_reflection(get_intensity(refl), refl, G,  B, res),
+			        get_partiality(refl) / correct_reflection_nopart(1.0, refl, G, B, res));
+
+			if ( get_partiality(refl) < MIN_PART_MERGE ) {
+				fprintf(fh, " partiality_too_small");
+			}
+			if ( isnan(get_esd_intensity(refl)) ) {
+				fprintf(fh, " nan_esd");
+			}
+			fprintf(fh, "\n");
+
+		}
+
+		fprintf(fh, "\n");
+
+	}
+
+	fclose(fh);
+}
diff --git a/src/merge.h b/src/merge.h
index 1e193b62..5f7e0e64 100644
--- a/src/merge.h
+++ b/src/merge.h
@@ -59,4 +59,6 @@ extern double residual(Crystal *cr, const RefList *full, int free,
 extern double log_residual(Crystal *cr, const RefList *full, int free,
                            int *pn_used, const char *filename);
 
+extern void write_unmerged(const char *fn, Crystal **crystals, int n_crystals);
+
 #endif	/* MERGE */
diff --git a/src/partialator.c b/src/partialator.c
index 39e8f8a3..9b1803b0 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -332,6 +332,7 @@ static void show_help(const char *s)
 "  -i, --input=<filename>     Specify the name of the input 'stream'.\n"
 "  -o, --output=<filename>    Output filename.  Default: partialator.hkl.\n"
 "      --output-every-cycle   Write .hkl* and .params files in every cycle.\n"
+"      --unmerged-output=<f>  Write unmerged (but scaled and corrected) intensities.\n"
 "  -y, --symmetry=<sym>       Merge according to symmetry <sym>.\n"
 "      --start-after=<n>      Skip <n> crystals at the start of the stream.\n"
 "      --stop-after=<n>       Stop after merging <n> crystals.\n"
@@ -1068,6 +1069,7 @@ int main(int argc, char *argv[])
 	                                  .streams = NULL};
 	char *outfile = NULL;
 	char *sym_str = NULL;
+	char *unmerged_filename = NULL;
 	SymOpList *sym;
 	SymOpList *amb;
 	SymOpList *w_sym;
@@ -1151,6 +1153,7 @@ int main(int argc, char *argv[])
 		{"no-polarization",    0, NULL,               15}, /* compat */
 		{"harvest-file",       1, NULL,               16},
 		{"log-folder",         1, NULL,               17},
+		{"unmerged-output",    1, NULL,               18},
 
 		{"no-scale",           0, &no_scale,           1},
 		{"no-Bscale",          0, &no_Bscale,          1},
@@ -1344,6 +1347,10 @@ int main(int argc, char *argv[])
 			log_folder = strdup(optarg);
 			break;
 
+			case 18 :
+			unmerged_filename = strdup(optarg);
+			break;
+
 			case 0 :
 			break;
 
@@ -1790,6 +1797,10 @@ int main(int argc, char *argv[])
 		                         min_measurements, push_res, 1, 0);
 	}
 
+	if ( unmerged_filename != NULL ) {
+		write_unmerged(unmerged_filename, crystals, n_crystals);
+	}
+
 	/* Write final figures of merit (no rejection any more) */
 	show_all_residuals(crystals, n_crystals, full, no_free);
 	if ( do_write_logs ) {
-- 
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