Don't include 1/d in reflection lists, because it's pointless

9 files changed, 24 insertions, 60 deletions

diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index 8f445ff4..f8d14d7a 100644
--- a/libcrystfel/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
@@ -152,23 +152,20 @@ int find_equiv_in_list(RefList *list, signed int h, signed int k,
  * write_reflections_to_file:
  * @fh: File handle to write to
  * @list: The reflection list to write
- * @cell: Unit cell to use for generating 1/d values, or NULL.
  *
- * This function writes the contents of @list to @fh, using @cell to generate
- * 1/d values to ease later processing.  If @cell is NULL, 1/d values will not
- * be included ('-' will be written in their place).
+ * This function writes the contents of @list to @fh,
  *
  * Reflections which have a redundancy of zero will not be written.
  *
  * The resulting list can be read back with read_reflections_from_file().
  **/
-void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
+void write_reflections_to_file(FILE *fh, RefList *list)
 {
 	Reflection *refl;
 	RefListIterator *iter;
 
 	fprintf(fh, "  h   k   l          I    phase   sigma(I) "
-		     " 1/d(nm^-1)  counts  fs/px  ss/px\n");
+		     " counts  fs/px  ss/px\n");
 
 	for ( refl = first_refl(list, &iter);
 	      refl != NULL;
@@ -193,13 +190,6 @@ void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
 		/* Reflections with redundancy = 0 are not written */
 		if ( red == 0 ) continue;
 
-		if ( cell != NULL ) {
-			s = 2.0 * resolution(cell, h, k, l);
-			snprintf(res, 16, "%10.2f", s/1e9);
-		} else {
-			strcpy(res, "         -");
-		}
-
 		if ( have_phase ) {
 			snprintf(phs, 16, "%8.2f", rad2deg(ph));
 		} else {
@@ -207,9 +197,8 @@ void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
 		}
 
 		fprintf(fh,
-		       "%3i %3i %3i %10.2f %s %10.2f  %s %7i %6.1f %6.1f\n",
-		       h, k, l, intensity, phs, esd_i, res, red,
-		       fs, ss);
+		       "%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f\n",
+		       h, k, l, intensity, phs, esd_i, red,  fs, ss);
 
 	}
 }
@@ -219,11 +208,8 @@ void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
  * write_reflist:
  * @filename: Filename
  * @list: The reflection list to write
- * @cell: Unit cell to use for generating 1/d values, or NULL.
  *
- * This function writes the contents of @list to @file, using @cell to generate
- * 1/d values to ease later processing.  If @cell is NULL, 1/d values will not
- * be included ('-' will be written in their place).
+ * This function writes the contents of @list to @file,
  *
  * Reflections which have a redundancy of zero will not be written.
  *
@@ -235,7 +221,7 @@ void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell)
  *
  * Returns: zero on success, non-zero on failure.
  **/
-int write_reflist(const char *filename, RefList *list, UnitCell *cell)
+int write_reflist(const char *filename, RefList *list)
 {
 	FILE *fh;
 
@@ -250,7 +236,7 @@ int write_reflist(const char *filename, RefList *list, UnitCell *cell)
 		return 1;
 	}
 
-	write_reflections_to_file(fh, list, cell);
+	write_reflections_to_file(fh, list);
 	fprintf(fh, REFLECTION_END_MARKER"\n");
 
 	fclose(fh);
@@ -284,10 +270,9 @@ RefList *read_reflections_from_file(FILE *fh)
 
 		if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
 
-		r = sscanf(line, "%i %i %i %f %s %f %s %i %f %f",
-		           &h, &k, &l, &intensity, phs, &sigma, ress, &cts,
-		           &fs, &ss);
-		if ( (r != 10) && (!first) ) {
+		r = sscanf(line, "%i %i %i %f %s %f %i %f %f",
+		           &h, &k, &l, &intensity, phs, &sigma, &cts, &fs, &ss);
+		if ( (r != 9) && (!first) ) {
 			reflist_free(out);
 			return NULL;
 		}
diff --git a/libcrystfel/src/reflist-utils.h b/libcrystfel/src/reflist-utils.h
index f03be906..b12b8dfa 100644
--- a/libcrystfel/src/reflist-utils.h
+++ b/libcrystfel/src/reflist-utils.h
@@ -38,9 +38,9 @@
 #define REFLECTION_END_MARKER "End of reflections"
 
 
-extern void write_reflections_to_file(FILE *fh, RefList *list, UnitCell *cell);
+extern void write_reflections_to_file(FILE *fh, RefList *list);
 
-extern int write_reflist(const char *filename, RefList *list, UnitCell *cell);
+extern int write_reflist(const char *filename, RefList *list);
 
 extern RefList *read_reflections_from_file(FILE *fh);
 
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 7f2e341e..486049bf 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -285,8 +285,7 @@ void write_chunk(FILE *ofh, struct image *i, struct hdfile *hdfile, int f)
 		if ( i->reflections != NULL ) {
 
 			fprintf(ofh, REFLECTION_START_MARKER"\n");
-			write_reflections_to_file(ofh, i->reflections,
-			                               i->indexed_cell);
+			write_reflections_to_file(ofh, i->reflections);
 			fprintf(ofh, REFLECTION_END_MARKER"\n");
 
 		} else {
diff --git a/scripts/gen-sfs b/scripts/gen-sfs
index bf86fb01..619ac08f 100755
--- a/scripts/gen-sfs
+++ b/scripts/gen-sfs
@@ -50,8 +50,7 @@ use strict;
 my \$line;
 open(FILE, "${PDB}-temp.hkl");
 
-printf("  h   k   l          I    phase   sigma(I)  1/d(nm^-1)  ".
-       "counts  fs/px  ss/px\\n");
+printf("  h   k   l          I    phase   sigma(I)  counts  fs/px  ss/px\\n");
 
 while ( \$line = <FILE> ) {
 
@@ -63,9 +62,8 @@ while ( \$line = <FILE> ) {
                 my \$intensity = \$4*\$4;  # Square to convert F->I
                 my \$phase = \$5;
 
-                printf("%3i %3i %3i %10.2f %8.2f %10.2f  %s %7i %6.1f %6.1f\n",
-                       \$h, \$k, \$l, \$intensity, \$phase, 0.0,
-                       "         -", 1, 0.0, 0.0);
+                printf("%3i %3i %3i %10.2f %8.2f %10.2f %7i %6.1f %6.1f\n",
+                       \$h, \$k, \$l, \$intensity, \$phase, 0.0, 1, 0.0, 0.0);
 
         } else {
         	printf(STDERR "Couldn't understand line '%s'\n", \$line);
diff --git a/scripts/gen-sfs-ano b/scripts/gen-sfs-ano
index 522e0a6d..05eb69d2 100755
--- a/scripts/gen-sfs-ano
+++ b/scripts/gen-sfs-ano
@@ -48,8 +48,7 @@ use strict;
 my \$line;
 open(FILE, "${PDB}-temp1.hkl");
 
-printf("  h   k   l          I    phase   sigma(I)  1/d(nm^-1)  ".
-       "counts  fs/px  ss/px\\n");
+printf("  h   k   l          I    phase   sigma(I)   counts  fs/px  ss/px\\n");
 
 while ( \$line = <FILE> ) {
 
@@ -62,10 +61,10 @@ while ( \$line = <FILE> ) {
                 my \$iminus = \$5*\$5;
 
                 printf("%3i %3i %3i %10.2f -     0.0  %s %7i %6.1f %6.1f\n",
-                       \$h, \$k, \$l, \$iplus, "         -", 1, 0.0, 0.0);
+                       \$h, \$k, \$l, \$iplus, 1, 0.0, 0.0);
 
                 printf("%3i %3i %3i %10.2f -     0.0  %s %7i %6.1f %6.1f\n",
-                       -\$h, -\$k, -\$l, \$iminus, "         -", 1, 0.0, 0.0);
+                       -\$h, -\$k, -\$l, \$iminus, 1, 0.0, 0.0);
 
         } else {
         	printf(STDERR "Couldn't understand line '%s'\n", \$line);
diff --git a/src/get_hkl.c b/src/get_hkl.c
index c1310418..905da569 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -77,8 +77,6 @@ static void show_help(const char *s)
 "\n"
 "Don't forget to specify the output filename:\n"
 "  -o, --output=<filename>    Output filename (default: stdout).\n"
-"  -p, --pdb=<filename>       Use unit cell parameters from this PDB file to\n"
-"                              generate resolution values in the output file.\n"
 );
 }
 
@@ -364,7 +362,6 @@ int main(int argc, char *argv[])
 	char *beamfile = NULL;
 	struct beam_params *beam = NULL;
 	RefList *input;
-	UnitCell *cell = NULL;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -379,7 +376,6 @@ int main(int argc, char *argv[])
 		{"intensities",        1, NULL,               'i'},
 		{"multiplicity",       0, &config_multi,       1},
 		{"beam",               1, NULL,               'b'},
-		{"pdb",                1, NULL,               'p'},
 		{"trim-centrics",      0, &config_trimc,       1},
 		{0, 0, NULL, 0}
 	};
@@ -421,14 +417,6 @@ int main(int argc, char *argv[])
 			beamfile = strdup(optarg);
 			break;
 
-		case 'p' :
-			cell = load_cell_from_pdb(optarg);
-			if ( cell == NULL ) {
-				ERROR("Failed to get cell from '%s'\n", optarg);
-				return 1;
-			}
-			break;
-
 		case 0 :
 			break;
 
@@ -453,11 +441,6 @@ int main(int argc, char *argv[])
 		}
 	}
 
-	if ( cell == NULL ) {
-		ERROR("You need to give a PDB file with the unit cell.\n");
-		return 1;
-	}
-
 	if ( holo_str != NULL ) {
 		holo = get_pointgroup(holo_str);
 		free(holo_str);
@@ -583,7 +566,7 @@ int main(int argc, char *argv[])
 
 	}
 
-	write_reflist(output, input, cell);
+	write_reflist(output, input);
 
 	reflist_free(input);
 
diff --git a/src/partial_sim.c b/src/partial_sim.c
index b9cb69e5..90e29ce4 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -525,7 +525,7 @@ int main(int argc, char *argv[])
 
 	if ( random_intensities ) {
 		STATUS("Writing full intensities to %s\n", save_file);
-		write_reflist(save_file, full, cell);
+		write_reflist(save_file, full);
 	}
 
 	if ( phist_file != NULL ) {
diff --git a/src/partialator.c b/src/partialator.c
index a834aeb3..eb2a8e52 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -556,7 +556,7 @@ int main(int argc, char *argv[])
 	STATUS("%i images could not be refined on the last cycle.\n", n_dud);
 
 	/* Output results */
-	write_reflist(outfile, full, images[0].indexed_cell);
+	write_reflist(outfile, full);
 
 	/* Clean up */
 	for ( i=0; i<n_usable_patterns; i++ ) {
diff --git a/src/process_hkl.c b/src/process_hkl.c
index fb0f7fa4..05c5e059 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -617,7 +617,7 @@ int main(int argc, char *argv[])
 		               hist_nbins);
 	}
 
-	write_reflist(output, model, NULL);
+	write_reflist(output, model);
 
 	fclose(fh);