Tidy up / fussiness

4 files changed, 22 insertions, 51 deletions

diff --git a/AUTHORS b/AUTHORS
index 20be21df..5add4577 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -3,6 +3,7 @@
 
 * Kenneth Beyerlein <kenneth.beyerlein@desy.de>
   Peak integration improvements
+  General bug finding and fixing
 
 * Richard Kirian <rkirian@asu.edu>
   MOSFLM auto-indexing, bug fixing.
@@ -21,9 +22,7 @@
 * Chun Hong Yoon <chun.hong.yoon@desy.de>
   Speed improvements to indexamajig
   pattern_sim overhaul and SASE spectrum simulation
-
-* Kenneth Beyerlein <kenneth.beyerlein@desy.de>
-  General bug finding and fixing
+  C++ compatibility
 
 * Nadia Zatsepin <nadia.zatsepin@asu.edu>
   General bug finding and fixing
@@ -48,3 +47,8 @@
 
 * Valerio Mariani <<alerio.mariani@desy.de>
   Packaging and general bug fixing
+  hdfsee calibration mode
+  --version options
+
+* Parker de Waal <Parker.deWaal@vai.org>
+  A small (but important) bug fix
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
index 82e393d9..035ab935 100644
--- a/doc/reference/libcrystfel/CrystFEL-sections.txt
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -26,8 +26,6 @@ get_partial
 get_indices
 get_symmetric_indices
 get_intensity
-get_scalable
-get_refinable
 get_redundancy
 get_esd_intensity
 get_phase
@@ -41,8 +39,6 @@ set_partiality
 set_lorentz
 set_partial
 set_intensity
-set_scalable
-set_refinable
 set_redundancy
 set_esd_intensity
 set_phase
@@ -291,6 +287,7 @@ get_pointgroup
 parse_symmetry_operations
 add_symop
 get_equiv
+get_symop
 special_position
 get_asymm
 get_ambiguities
@@ -455,12 +452,14 @@ IntegrationMethod
 IntDiag
 integrate_all
 integrate_all_2
+integrate_all_3
 integration_method
 </SECTION>
 
 <SECTION>
 <FILE>stream</FILE>
 Stream
+StreamReadFlags
 CHUNK_END_MARKER
 CHUNK_START_MARKER
 CRYSTAL_END_MARKER
@@ -472,11 +471,12 @@ REFLECTION_START_MARKER
 open_stream_fd_for_write
 open_stream_for_read
 open_stream_for_write
+get_stream_fd
 close_stream
 read_chunk
+read_chunk_2
 write_chunk
 rewind_stream
 is_stream
 write_command
-write_line
 </SECTION>
diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c
index 14b108b7..1a4fee1e 100644
--- a/libcrystfel/src/symmetry.c
+++ b/libcrystfel/src/symmetry.c
@@ -8,6 +8,7 @@
  *
  * Authors:
  *   2010-2014 Thomas White <taw@physics.org>
+ *   2014      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
  *
  * This file is part of CrystFEL.
  *
@@ -215,7 +216,7 @@ static void add_symop_v(SymOpList *ops,
  * contained in the symmetry operator list, and identified by the specified
  * index.
  **/
-IntegerMatrix* get_symop(const SymOpList *ops, const SymOpMask *m, int idx)
+IntegerMatrix *get_symop(const SymOpList *ops, const SymOpMask *m, int idx)
 {
 	const int n = num_ops(ops);
 
@@ -255,6 +256,7 @@ IntegerMatrix* get_symop(const SymOpList *ops, const SymOpMask *m, int idx)
 	return ops->ops[idx];
 }
 
+
 static signed int *v(signed int h, signed int k, signed int i, signed int l)
 {
 	signed int *vec = malloc(3*sizeof(signed int));
@@ -1130,47 +1132,10 @@ void get_equiv(const SymOpList *ops, const SymOpMask *m, int idx,
                signed int h, signed int k, signed int l,
                signed int *he, signed int *ke, signed int *le)
 {
-	const int n = num_ops(ops);
-
-	if ( m != NULL ) {
-
-		int i, c;
-
-		c = 0;
-		for ( i=0; i<n; i++ ) {
-
-			if ( (c == idx) && m->mask[i] ) {
-				do_op(ops->ops[i], h, k, l, he, ke, le);
-				return;
-			}
-
-			if ( m->mask[i] ) {
-				c++;
-			}
-
-		}
-
-		ERROR("Index %i out of range for point group '%s' with"
-		      " reflection %i %i %i\n",
-		      idx, symmetry_name(ops), h, k, l);
-
-		*he = 0;  *ke = 0;  *le = 0;
-
-		return;
-
-	}
-
-	if ( idx >= n ) {
-
-		ERROR("Index %i out of range for point group '%s'\n", idx,
-		      symmetry_name(ops));
-
-		*he = 0;  *ke = 0;  *le = 0;
-		return;
-
-	}
-
-	do_op(ops->ops[idx], h, k, l, he, ke, le);
+	IntegerMatrix *op;
+	op = get_symop(ops, m, idx);
+	if ( op == NULL ) return;
+	do_op(op, h, k, l, he, ke, le);
 }
 
 
diff --git a/libcrystfel/src/symmetry.h b/libcrystfel/src/symmetry.h
index 42cbd9b3..d7373ba2 100644
--- a/libcrystfel/src/symmetry.h
+++ b/libcrystfel/src/symmetry.h
@@ -8,6 +8,7 @@
  *
  * Authors:
  *   2010-2014 Thomas White <taw@physics.org>
+ *   2014      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
  *
  * This file is part of CrystFEL.
  *
@@ -61,7 +62,6 @@ extern "C" {
 
 extern void free_symoplist(SymOpList *ops);
 extern SymOpList *get_pointgroup(const char *sym);
-extern IntegerMatrix* get_symop(const SymOpList *ops, const SymOpMask *m, int idx);
 
 extern SymOpMask *new_symopmask(const SymOpList *list);
 extern void free_symopmask(SymOpMask *m);
@@ -75,6 +75,8 @@ extern int num_equivs(const SymOpList *ops, const SymOpMask *m);
 extern void get_equiv(const SymOpList *ops, const SymOpMask *m, int idx,
                       signed int h, signed int k, signed int l,
                       signed int *he, signed int *ke, signed int *le);
+extern IntegerMatrix *get_symop(const SymOpList *ops, const SymOpMask *m,
+                                int idx);
 
 extern SymOpList *get_ambiguities(const SymOpList *source,
                                   const SymOpList *target);