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-rw-r--r--libcrystfel/src/symmetry.c175
1 files changed, 74 insertions, 101 deletions
diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c
index 06cc368c..69dada16 100644
--- a/libcrystfel/src/symmetry.c
+++ b/libcrystfel/src/symmetry.c
@@ -3,12 +3,12 @@
*
* Symmetry
*
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2019 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2014,2016 Thomas White <taw@physics.org>
- * 2014 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
+ * 2010-2019 Thomas White <taw@physics.org>
+ * 2014 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
*
* This file is part of CrystFEL.
*
@@ -41,6 +41,8 @@
#include "symmetry.h"
#include "utils.h"
#include "integer_matrix.h"
+#include "symop-parse.h"
+#include "symop-lex.h"
/**
@@ -195,9 +197,9 @@ static void add_symop_v(SymOpList *ops,
m = intmat_new(3, 3);
assert(m != NULL);
- for ( i=0; i<3; i++ ) intmat_set(m, 0, i, h[i]);
- for ( i=0; i<3; i++ ) intmat_set(m, 1, i, k[i]);
- for ( i=0; i<3; i++ ) intmat_set(m, 2, i, l[i]);
+ for ( i=0; i<3; i++ ) intmat_set(m, i, 0, h[i]);
+ for ( i=0; i<3; i++ ) intmat_set(m, i, 1, k[i]);
+ for ( i=0; i<3; i++ ) intmat_set(m, i, 2, l[i]);
free(h);
free(k);
@@ -369,13 +371,13 @@ static void expand_ops(SymOpList *s)
/* Transform all the operations in a SymOpList by a given matrix.
* The matrix must have a determinant of +/- 1 (otherwise its inverse would
* not also be an integer matrix). */
-static void transform_ops(SymOpList *s, IntegerMatrix *t)
+static void transform_ops(SymOpList *s, IntegerMatrix *P)
{
int n, i;
- IntegerMatrix *inv;
+ IntegerMatrix *Pi;
signed int det;
- det = intmat_det(t);
+ det = intmat_det(P);
if ( det == -1 ) {
ERROR("WARNING: mirrored SymOpList.\n");
} else if ( det != 1 ) {
@@ -383,8 +385,8 @@ static void transform_ops(SymOpList *s, IntegerMatrix *t)
return;
}
- inv = intmat_inverse(t);
- if ( inv == NULL ) {
+ Pi = intmat_inverse(P);
+ if ( Pi == NULL ) {
ERROR("Failed to invert matrix.\n");
return;
}
@@ -394,13 +396,13 @@ static void transform_ops(SymOpList *s, IntegerMatrix *t)
IntegerMatrix *r, *f;
- r = intmat_intmat_mult(s->ops[i], t);
+ r = intmat_intmat_mult(P, s->ops[i]);
if ( r == NULL ) {
ERROR("Matrix multiplication failed.\n");
return;
}
- f = intmat_intmat_mult(inv, r);
+ f = intmat_intmat_mult(r, Pi);
if ( f == NULL ) {
ERROR("Matrix multiplication failed.\n");
return;
@@ -413,7 +415,7 @@ static void transform_ops(SymOpList *s, IntegerMatrix *t)
}
- intmat_free(inv);
+ intmat_free(Pi);
}
@@ -1012,14 +1014,14 @@ static SymOpList *getpg_arbitrary_ua(const char *sym, size_t s)
case 'a' :
intmat_set(t, 0, 2, 1);
- intmat_set(t, 1, 1, 1);
- intmat_set(t, 2, 0, -1);
+ intmat_set(t, 1, 0, 1);
+ intmat_set(t, 2, 1, 1);
break;
case 'b' :
- intmat_set(t, 0, 0, 1);
+ intmat_set(t, 0, 1, 1);
intmat_set(t, 1, 2, 1);
- intmat_set(t, 2, 1, -1);
+ intmat_set(t, 2, 0, 1);
break;
@@ -1124,7 +1126,7 @@ static void do_op(const IntegerMatrix *op,
v[0] = h; v[1] = k; v[2] = l;
- ans = intmat_intvec_mult(op, v);
+ ans = transform_indices(op, v);
assert(ans != NULL);
*he = ans[0]; *ke = ans[1]; *le = ans[2];
@@ -1636,105 +1638,76 @@ SymOpList *get_ambiguities(const SymOpList *source, const SymOpList *target)
}
-static IntegerMatrix *parse_symmetry_operation(const char *s)
+/* Parse a single symmetry operation, e.g. 'h,-2k,(h+l)/3' */
+RationalMatrix *parse_symmetry_operation(const char *s)
{
- IntegerMatrix *m;
- char **els;
- int n, i;
+ YY_BUFFER_STATE b;
+ RationalMatrix *m;
+ int r;
+ m = rtnl_mtx_new(3, 3);
+ b = symop_scan_string(s);
+ r = symopparse(m, NULL);
+ symop_delete_buffer(b);
- n = assplode(s, ",", &els, ASSPLODE_NONE);
- if ( n != 3 ) {
- for ( i=0; i<n; i++ ) free(els[i]);
- free(els);
+ if ( r ) {
+ ERROR("Failed to parse '%s'\n", s);
+ rtnl_mtx_free(m);
return NULL;
}
- m = intmat_new(3, 3);
- if ( m == NULL ) return NULL;
-
- for ( i=0; i<n; i++ ) {
-
- int c;
- size_t cl;
- signed int nh = 0;
- signed int nk = 0;
- signed int nl = 0;
- signed int mult = 1;
- int ndigit = 0;
- signed int sign = +1;
-
- /* We have one expression something like "-2h+k" */
- cl = strlen(els[i]);
- for ( c=0; c<cl; c++ ) {
-
- if ( els[i][c] == '-' ) sign *= -1;
- if ( els[i][c] == 'h' ) {
- nh = mult*sign;
- mult = 1;
- ndigit = 0;
- sign = +1;
- }
- if ( els[i][c] == 'k' ) {
- nk = mult*sign;
- mult = 1;
- ndigit = 0;
- sign = +1;
- }
- if ( els[i][c] == 'l' ) {
- nl = mult*sign;
- mult = 1;
- ndigit = 0;
- sign = +1;
- }
- if ( isdigit(els[i][c]) ) {
- if ( ndigit > 0 ) {
- mult *= 10;
- mult += els[i][c] - '0';
- } else {
- mult *= els[i][c] - '0';
- }
- ndigit++;
- }
- }
-
- intmat_set(m, i, 0, nh);
- intmat_set(m, i, 1, nk);
- intmat_set(m, i, 2, nl);
-
- free(els[i]);
+ return m;
+}
- }
- free(els);
- return m;
+/**
+ * parse_cell_transformation
+ * @s: Textual representation of cell transformation
+ *
+ * Parses @s, for example 'a,(b+a)/2,c', and returns the corresponding
+ * %RationalMatrix.
+ *
+ * Returns: A %RationalMatrix describing the transformation, or NULL on error.
+ *
+ */
+RationalMatrix *parse_cell_transformation(const char *s)
+{
+ return parse_symmetry_operation(s);
}
+/**
+ * parse_symmetry_operations
+ * @s: Textual representation of a list of symmetry operations
+ *
+ * Parses @s, for example 'h,k,l;k,h,-l', and returns the corresponding
+ * %SymOpList
+ *
+ * Returns: A %SymOpList, or NULL on error.
+ *
+ */
SymOpList *parse_symmetry_operations(const char *s)
{
- SymOpList *sol;
- char **ops;
- int n, i;
+ YY_BUFFER_STATE b;
+ RationalMatrix *m;
+ SymOpList *list;
+ int r;
- sol = new_symoplist();
- if ( sol == NULL ) return NULL;
+ m = rtnl_mtx_new(3, 3); /* Scratch space for parser */
+ list = new_symoplist(); /* The result we want */
- n = assplode(s, ";:", &ops, ASSPLODE_NONE);
- for ( i=0; i<n; i++ ) {
- IntegerMatrix *m;
- m = parse_symmetry_operation(ops[i]);
- if ( m != NULL ) {
- add_symop(sol, m);
- } else {
- ERROR("Invalid symmetry operation '%s'\n", ops[i]);
- /* Try the next one */
- }
- free(ops[i]);
+ b = symop_scan_string(s);
+ r = symopparse(m, list);
+ symop_delete_buffer(b);
+ rtnl_mtx_free(m);
+
+ if ( r ) {
+ ERROR("Failed to parse '%s'\n", s);
+ free_symoplist(list);
+ return NULL;
}
- free(ops);
- return sol;
+ return list;
}
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