Implement parse_symmetry_operations

6 files changed, 117 insertions, 82 deletions

diff --git a/libcrystfel/src/rational.c b/libcrystfel/src/rational.c
index b6ca5dd4..5db83165 100644
--- a/libcrystfel/src/rational.c
+++ b/libcrystfel/src/rational.c
@@ -326,6 +326,31 @@ RationalMatrix *rtnl_mtx_from_intmat(const IntegerMatrix *m)
 }
 
 
+IntegerMatrix *intmat_from_rtnl_mtx(const RationalMatrix *m)
+{
+	IntegerMatrix *n;
+	int i, j;
+
+	n = intmat_new(m->rows, m->cols);
+	if ( n == NULL ) return NULL;
+
+	for ( i=0; i<m->rows; i++ ) {
+		for ( j=0; j<m->cols; j++ ) {
+			Rational v = rtnl_mtx_get(m, i, j);
+			squish(&v);
+			if ( v.den != 1 ) {
+				ERROR("Rational matrix can't be converted to integers\n");
+				intmat_free(n);
+				return NULL;
+			}
+			intmat_set(n, i, j, v.num);
+		}
+	}
+
+	return n;
+}
+
+
 void rtnl_mtx_free(RationalMatrix *mtx)
 {
 	if ( mtx == NULL ) return;
diff --git a/libcrystfel/src/rational.h b/libcrystfel/src/rational.h
index e2d3e5bf..925f9be1 100644
--- a/libcrystfel/src/rational.h
+++ b/libcrystfel/src/rational.h
@@ -82,6 +82,7 @@ extern RationalMatrix *rtnl_mtx_copy(const RationalMatrix *m);
 extern Rational rtnl_mtx_get(const RationalMatrix *m, int i, int j);
 extern void rtnl_mtx_set(const RationalMatrix *m, int i, int j, Rational v);
 extern RationalMatrix *rtnl_mtx_from_intmat(const IntegerMatrix *m);
+extern IntegerMatrix *intmat_from_rtnl_mtx(const RationalMatrix *m);
 extern void rtnl_mtx_free(RationalMatrix *mtx);
 extern void rtnl_mtx_mult(const RationalMatrix *m, const Rational *vec,
                           Rational *ans);
diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c
index 19c754ea..9ee80a16 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.
  *
@@ -1638,102 +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)
 {
 	YY_BUFFER_STATE b;
 	RationalMatrix *m;
+	SymOpList *list;
 	int r;
 
-	m = rtnl_mtx_new(3, 3);
+	m = rtnl_mtx_new(3, 3); /* Scratch space for parser */
+	list = new_symoplist(); /* The result we want */
+
 	b = symop_scan_string(s);
-	r = symopparse(m);
+	r = symopparse(m, list);
 	symop_delete_buffer(b);
+	rtnl_mtx_free(m);
 
 	if ( r ) {
 		ERROR("Failed to parse '%s'\n", s);
-		rtnl_mtx_free(m);
+		free_symoplist(list);
 		return NULL;
 	}
 
-	STATUS("Parsed OK\n");
-	rtnl_mtx_print(m);
-
-	return NULL;
+	return list;
 }
 
 
diff --git a/libcrystfel/src/symmetry.h b/libcrystfel/src/symmetry.h
index a61ca96f..ab2aa934 100644
--- a/libcrystfel/src/symmetry.h
+++ b/libcrystfel/src/symmetry.h
@@ -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.
  *
@@ -36,6 +36,7 @@
 
 
 #include "integer_matrix.h"
+#include "rational.h"
 
 /**
  * SymOpList
@@ -93,7 +94,9 @@ extern int is_centric(signed int h, signed int k, signed int l,
 extern void pointgroup_warning(const char *sym);
 
 extern void add_symop(SymOpList *ops, IntegerMatrix *m);
+extern RationalMatrix *parse_symmetry_operation(const char *s);
 extern SymOpList *parse_symmetry_operations(const char *s);
+extern RationalMatrix *parse_cell_transformation(const char *s);
 extern char *get_matrix_name(const IntegerMatrix *m, int row);
 
 #ifdef __cplusplus
diff --git a/libcrystfel/src/symop.l b/libcrystfel/src/symop.l
index b00b35b4..ed38a65e 100644
--- a/libcrystfel/src/symop.l
+++ b/libcrystfel/src/symop.l
@@ -47,5 +47,6 @@
 [clz]      { return L; }
 [(]        { return OPENB; }
 [)]        { return CLOSEB; }
+[;]        { return SEMICOLON; }
 
 %%
diff --git a/libcrystfel/src/symop.y b/libcrystfel/src/symop.y
index 4aec791a..a304ea37 100644
--- a/libcrystfel/src/symop.y
+++ b/libcrystfel/src/symop.y
@@ -30,15 +30,20 @@
   #include <stdio.h>
 
   #include "rational.h"
+  #include "symmetry.h"
 
   extern int symoplex();
-  extern int symopparse(RationalMatrix *m);
-  void symoperror(RationalMatrix *m, const char *s);
+  extern int symopparse(RationalMatrix *m, SymOpList *list);
+  void symoperror(RationalMatrix *m, SymOpList *list, const char *s);
 %}
 
 %define api.prefix {symop}
 
-%parse-param {RationalMatrix *m}
+%parse-param {RationalMatrix *m} {SymOpList *list}
+
+%code requires {
+  #include "symmetry.h"
+}
 
 %union {
   RationalMatrix *m;  /* Full rational matrix */
@@ -47,6 +52,7 @@
   int n;              /* Just a number */
 }
 
+%token SEMICOLON
 %token COMMA
 %token NUMBER
 %token OPENB CLOSEB
@@ -63,8 +69,33 @@
 %type <n> NUMBER
 %type <r> fraction
 
+%{
+static int try_add_symop(SymOpList *list, RationalMatrix *m)
+{
+	if ( list == NULL ) {
+		yyerror(m, list, "Must be a single symmetry operation");
+		return 1;
+	} else {
+		IntegerMatrix *im;
+		im = intmat_from_rtnl_mtx(m);
+		if ( im == NULL ) {
+			yyerror(m, list, "Symmetry operations must all be integer");
+			return 1;
+		} else {
+			add_symop(list, im);
+		}
+	}
+	return 0;
+}
+%}
+
 %%
 
+symoplist:
+  symop                       { if ( try_add_symop(list, m) ) YYERROR; }
+| symoplist SEMICOLON symop   { if ( try_add_symop(list, m) ) YYERROR; }
+;
+
 symop:
   axexpr COMMA axexpr COMMA axexpr { rtnl_mtx_set(m, 0, 0, $1[0]);
                                      rtnl_mtx_set(m, 0, 1, $1[1]);
@@ -101,6 +132,6 @@ fraction:
 
 %%
 
-void symoperror(RationalMatrix *m, const char *s) {
-	printf("Error\n");
+void symoperror(RationalMatrix *m, SymOpList *list, const char *s) {
+	printf("Error: %s\n", s);
 }