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-rw-r--r--libcrystfel/Makefile.am4
-rw-r--r--libcrystfel/src/cell-utils.c44
-rw-r--r--libcrystfel/src/cell-utils.h3
-rw-r--r--libcrystfel/src/index.c22
-rw-r--r--libcrystfel/src/index.h7
-rw-r--r--libcrystfel/src/taketwo.c1624
-rw-r--r--libcrystfel/src/taketwo.h41
7 files changed, 1742 insertions, 3 deletions
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 8af82552..fef2e11f 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -11,7 +11,7 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
src/cell-utils.c src/integer_matrix.c src/crystal.c \
src/xds.c src/integration.c src/predict-refine.c \
src/histogram.c src/events.c src/felix.c \
- src/peakfinder8.c
+ src/taketwo.c src/peakfinder8.c
if HAVE_FFTW
libcrystfel_la_SOURCES += src/asdf.c
@@ -32,7 +32,7 @@ libcrystfel_la_include_HEADERS = ${top_srcdir}/version.h \
src/xds.h src/predict-refine.h \
src/integration.h src/histogram.h \
src/events.h src/asdf.h src/felix.h \
- src/peakfinder8.h
+ src/taketwo.h src/peakfinder8.h
AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -Wall
AM_CPPFLAGS += -I$(top_srcdir)/lib @LIBCRYSTFEL_CFLAGS@
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 84a14b5c..6610abc3 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -38,7 +38,6 @@
#include <string.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_blas.h>
-#include <gsl/gsl_linalg.h>
#include <assert.h>
#include "cell.h"
@@ -1438,6 +1437,49 @@ void cell_fudge_gslcblas()
}
+UnitCell *transform_cell_gsl(UnitCell *in, gsl_matrix *m)
+{
+ gsl_matrix *c;
+ double asx, asy, asz;
+ double bsx, bsy, bsz;
+ double csx, csy, csz;
+ gsl_matrix *res;
+ UnitCell *out;
+
+ cell_get_reciprocal(in, &asx, &asy, &asz, &bsx, &bsy,
+ &bsz, &csx, &csy, &csz);
+
+ c = gsl_matrix_alloc(3, 3);
+ gsl_matrix_set(c, 0, 0, asx);
+ gsl_matrix_set(c, 1, 0, asy);
+ gsl_matrix_set(c, 2, 0, asz);
+ gsl_matrix_set(c, 0, 1, bsx);
+ gsl_matrix_set(c, 1, 1, bsy);
+ gsl_matrix_set(c, 2, 1, bsz);
+ gsl_matrix_set(c, 0, 2, csx);
+ gsl_matrix_set(c, 1, 2, csy);
+ gsl_matrix_set(c, 2, 2, csz);
+
+ res = gsl_matrix_calloc(3, 3);
+ gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, m, c, 0.0, res);
+
+ out = cell_new_from_cell(in);
+ cell_set_reciprocal(out, gsl_matrix_get(res, 0, 0),
+ gsl_matrix_get(res, 1, 0),
+ gsl_matrix_get(res, 2, 0),
+ gsl_matrix_get(res, 0, 1),
+ gsl_matrix_get(res, 1, 1),
+ gsl_matrix_get(res, 2, 1),
+ gsl_matrix_get(res, 0, 2),
+ gsl_matrix_get(res, 1, 2),
+ gsl_matrix_get(res, 2, 2));
+
+ gsl_matrix_free(res);
+ gsl_matrix_free(c);
+ return out;
+}
+
+
/**
* rotate_cell:
* @in: A %UnitCell to rotate
diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h
index 000c863a..efb4b25b 100644
--- a/libcrystfel/src/cell-utils.h
+++ b/libcrystfel/src/cell-utils.h
@@ -35,6 +35,8 @@
#include <config.h>
#endif
+#include <gsl/gsl_matrix.h>
+
#include "cell.h"
#ifdef __cplusplus
@@ -47,6 +49,7 @@ extern double resolution(UnitCell *cell,
extern UnitCell *cell_rotate(UnitCell *in, struct quaternion quat);
extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi,
double rot);
+extern UnitCell *transform_cell_gsl(UnitCell *in, gsl_matrix *m);
extern void cell_print(UnitCell *cell);
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 446f57a3..bdabb062 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -56,6 +56,7 @@
#include "cell-utils.h"
#include "felix.h"
#include "predict-refine.h"
+#include "taketwo.h"
struct _indexingprivate
@@ -120,6 +121,10 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
priv = felix_prepare(m, cell, det, ltl, options);
break;
+ case INDEXING_TAKETWO :
+ priv = taketwo_prepare(m, cell, det, ltl);
+ break;
+
default :
ERROR("Don't know how to prepare indexing method %i\n", *m);
break;
@@ -252,6 +257,10 @@ void cleanup_indexing(IndexingPrivate *ipriv)
free(ipriv->engine_private[n]);
break;
+ case INDEXING_TAKETWO :
+ taketwo_cleanup(ipriv->engine_private[n]);
+ break;
+
default :
ERROR("Don't know how to clean up indexing method %i\n",
ipriv->methods[n]);
@@ -329,6 +338,10 @@ static int try_indexer(struct image *image, IndexingMethod indm,
r = felix_index(image, mpriv);
break;
+ case INDEXING_TAKETWO :
+ r = taketwo_index(image, mpriv);
+ break;
+
default :
ERROR("Unrecognised indexing method: %i\n", indm);
return 0;
@@ -662,6 +675,10 @@ char *indexer_str(IndexingMethod indm)
strcpy(str, "xds");
break;
+ case INDEXING_TAKETWO :
+ strcpy(str, "taketwo");
+ break;
+
case INDEXING_SIMULATION :
strcpy(str, "simulation");
break;
@@ -770,6 +787,11 @@ IndexingMethod get_indm_from_string(const char *str)
method = INDEXING_DEFAULTS_FELIX;
have_method = 1;
+ } else if ( strcmp(bits[i], "taketwo") == 0) {
+ if ( have_method ) return warn_method(str);
+ method = INDEXING_DEFAULTS_TAKETWO;
+ have_method = 1;
+
} else if ( strcmp(bits[i], "none") == 0) {
if ( have_method ) return warn_method(str);
method = INDEXING_NONE;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 8dd7de21..2107ed80 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -58,6 +58,11 @@
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_RETRY | INDEXING_REFINE)
+#define INDEXING_DEFAULTS_TAKETWO (INDEXING_TAKETWO | INDEXING_CHECK_PEAKS \
+ | INDEXING_USE_CELL_PARAMETERS \
+ | INDEXING_USE_LATTICE_TYPE \
+ | INDEXING_RETRY | INDEXING_REFINE)
+
/* Axis check is needed for XDS, because it likes to permute the axes */
#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS \
@@ -75,6 +80,7 @@
* @INDEXING_SIMULATION: Dummy value
* @INDEXING_DEBUG: Results injector for debugging
* @INDEXING_ASDF: Use in-built "asdf" indexer
+ * @INDEXING_TAKETWO: Use in-built "taketwo" indexer
* @INDEXING_ERROR: Special value for unrecognised indexing engine name
* @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell
* axes for agreement with given cell.
@@ -108,6 +114,7 @@ typedef enum {
INDEXING_SIMULATION = 6,
INDEXING_DEBUG = 7,
INDEXING_ASDF = 8,
+ INDEXING_TAKETWO = 9,
INDEXING_ERROR = 255, /* Unrecognised indexing engine */
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c
new file mode 100644
index 00000000..605ced7f
--- /dev/null
+++ b/libcrystfel/src/taketwo.c
@@ -0,0 +1,1624 @@
+/*
+ * taketwo.c
+ *
+ * Rewrite of TakeTwo algorithm (Acta D72 (8) 956-965) for CrystFEL
+ *
+ * Copyright © 2016 Helen Ginn
+ * Copyright © 2016 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2016 Helen Ginn <helen@strubi.ox.ac.uk>
+ * 2016 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_blas.h>
+#include <float.h>
+#include <math.h>
+#include <assert.h>
+#include <time.h>
+
+#include "cell-utils.h"
+#include "index.h"
+#include "taketwo.h"
+#include "peaks.h"
+#include "symmetry.h"
+
+/**
+ * spotvec
+ * @obsvec: an observed vector between two spots
+ * @matches: array of matching theoretical vectors from unit cell
+ * @match_num: number of matches
+ * @distance: length of obsvec (do I need this?)
+ * @her_rlp: pointer to first rlp position for difference vec
+ * @his_rlp: pointer to second rlp position for difference vec
+ *
+ * Structure representing 3D vector between two potential Bragg peaks
+ * in reciprocal space, and an array of potential matching theoretical
+ * vectors from unit cell/centering considerations.
+ **/
+struct SpotVec
+{
+ struct rvec obsvec;
+ struct rvec *matches;
+ int match_num;
+ struct rvec *asym_matches;
+ int asym_match_num;
+ double distance;
+ struct rvec *her_rlp;
+ struct rvec *his_rlp;
+};
+
+
+struct taketwo_private
+{
+ IndexingMethod indm;
+ float *ltl;
+ UnitCell *cell;
+};
+
+// These rotation symmetry operators
+struct TakeTwoCell
+{
+ UnitCell *cell;
+ gsl_matrix **rotSymOps;
+ unsigned int numOps;
+ struct SpotVec **obs_vecs; // Pointer to an array
+ int obs_vec_count;
+ gsl_matrix *twiz1Tmp;
+ gsl_matrix *twiz2Tmp;
+ gsl_vector *vec1Tmp;
+ gsl_vector *vec2Tmp;
+};
+
+
+/* Maximum distance between two rlp sizes to consider info for indexing */
+#define MAX_RECIP_DISTANCE (0.15*1e10)
+
+/* Tolerance for two lengths in reciprocal space to be considered the same */
+#define RECIP_TOLERANCE (0.0010*1e10)
+
+/* Threshold for network members to consider a potential solution */
+#define NETWORK_MEMBER_THRESHOLD (20)
+
+/* Maximum network members (obviously a solution so should stop) */
+#define MAX_NETWORK_MEMBERS (NETWORK_MEMBER_THRESHOLD + 3)
+
+/* Maximum dead ends for a single branch extension during indexing */
+#define MAX_DEAD_ENDS (10)
+
+/* Maximum observed vectors before TakeTwo gives up and deals with
+ * what is already there. */
+#define MAX_OBS_VECTORS 100000
+
+/* Tolerance for two angles to be considered the same */
+#define ANGLE_TOLERANCE (deg2rad(0.6))
+
+/* Tolerance for rot_mats_are_similar */
+#define TRACE_TOLERANCE (deg2rad(3.0))
+
+/** TODO:
+ *
+ * - May need to be capable of playing with the tolerances/#defined stuff.
+ * - Multiple lattices
+ */
+
+
+/* ------------------------------------------------------------------------
+ * apologetic function
+ * ------------------------------------------------------------------------*/
+
+void apologise()
+{
+ printf("Error - could not allocate memory for indexing.\n");
+}
+
+/* ------------------------------------------------------------------------
+ * functions concerning aspects of rvec which are very likely to be
+ * incorporated somewhere else in CrystFEL and therefore may need to be
+ * deleted and references connected to a pre-existing function. (Lowest level)
+ * ------------------------------------------------------------------------*/
+
+static struct rvec new_rvec(double new_u, double new_v, double new_w)
+{
+ struct rvec new_rvector;
+ new_rvector.u = new_u;
+ new_rvector.v = new_v;
+ new_rvector.w = new_w;
+
+ return new_rvector;
+}
+
+
+static struct rvec diff_vec(struct rvec from, struct rvec to)
+{
+ struct rvec diff = new_rvec(to.u - from.u,
+ to.v - from.v,
+ to.w - from.w);
+
+ return diff;
+}
+
+static double sq_length(struct rvec vec)
+{
+ double sqlength = (vec.u * vec.u + vec.v * vec.v + vec.w * vec.w);
+
+ return sqlength;
+}
+
+
+static double rvec_length(struct rvec vec)
+{
+ return sqrt(sq_length(vec));
+}
+
+
+static void normalise_rvec(struct rvec *vec)
+{
+ double length = rvec_length(*vec);
+ vec->u /= length;
+ vec->v /= length;
+ vec->w /= length;
+}
+
+
+static double rvec_cosine(struct rvec v1, struct rvec v2)
+{
+ double dot_prod = v1.u * v2.u + v1.v * v2.v + v1.w * v2.w;
+ double v1_length = rvec_length(v1);
+ double v2_length = rvec_length(v2);
+
+ double cos_theta = dot_prod / (v1_length * v2_length);
+
+ return cos_theta;
+}
+
+
+static double rvec_angle(struct rvec v1, struct rvec v2)
+{
+ double cos_theta = rvec_cosine(v1, v2);
+ double angle = acos(cos_theta);
+
+ return angle;
+}
+
+
+static struct rvec rvec_cross(struct rvec a, struct rvec b)
+{
+ struct rvec c;
+
+ c.u = a.v*b.w - a.w*b.v;
+ c.v = -(a.u*b.w - a.w*b.u);
+ c.w = a.u*b.v - a.v*b.u;
+
+ return c;
+}
+
+/*
+static void show_rvec(struct rvec r2)
+{
+ struct rvec r = r2;
+ normalise_rvec(&r);
+ STATUS("[ %.3f %.3f %.3f ]\n", r.u, r.v, r.w);
+}
+*/
+
+
+/* ------------------------------------------------------------------------
+ * functions called under the core functions, still specialised (Level 3)
+ * ------------------------------------------------------------------------*/
+
+static void rotation_around_axis(struct rvec c, double th,
+ gsl_matrix *res)
+{
+ double omc = 1.0 - cos(th);
+ double s = sin(th);
+ gsl_matrix_set(res, 0, 0, cos(th) + c.u*c.u*omc);
+ gsl_matrix_set(res, 0, 1, c.u*c.v*omc - c.w*s);
+ gsl_matrix_set(res, 0, 2, c.u*c.w*omc + c.v*s);
+ gsl_matrix_set(res, 1, 0, c.u*c.v*omc + c.w*s);
+ gsl_matrix_set(res, 1, 1, cos(th) + c.v*c.v*omc);
+ gsl_matrix_set(res, 1, 2, c.v*c.w*omc - c.u*s);
+ gsl_matrix_set(res, 2, 0, c.w*c.u*omc - c.v*s);
+ gsl_matrix_set(res, 2, 1, c.w*c.v*omc + c.u*s);
+ gsl_matrix_set(res, 2, 2, cos(th) + c.w*c.w*omc);
+}
+
+
+/* Rotate vector (vec1) around axis (axis) by angle theta. Find value of
+ * theta for which the angle between (vec1) and (vec2) is minimised. */
+static void closest_rot_mat(struct rvec vec1, struct rvec vec2,
+ struct rvec axis, gsl_matrix *twizzle)
+{
+ /* Let's have unit vectors */
+ normalise_rvec(&vec1);
+ normalise_rvec(&vec2);
+ normalise_rvec(&axis);
+
+ /* Redeclaring these to try and maintain readability and
+ * check-ability against the maths I wrote down */
+ double a = vec2.u; double b = vec2.v; double c = vec2.w;
+ double p = vec1.u; double q = vec1.v; double r = vec1.w;
+ double x = axis.u; double y = axis.v; double z = axis.w;
+
+ /* Components in handwritten maths online when I upload it */
+ double A = a*(p*x*x - p + x*y*q + x*z*r) +
+ b*(p*x*y + q*y*y - q + r*y*z) +
+ c*(p*x*z + q*y*z + r*z*z - r);
+
+ double B = a*(y*r - z*q) + b*(p*z - r*x) + c*(q*x - p*y);
+
+ double tan_theta = - B / A;
+ double theta = atan(tan_theta);
+
+ /* Now we have two possible solutions, theta or theta+pi
+ * and we need to work out which one. This could potentially be
+ * simplified - do we really need so many cos/sins? maybe check
+ * the 2nd derivative instead? */
+ double cc = cos(theta);
+ double C = 1 - cc;
+ double s = sin(theta);
+ double occ = -cc;
+ double oC = 1 - occ;
+ double os = -s;
+
+ double pPrime = (x*x*C+cc)*p + (x*y*C-z*s)*q + (x*z*C+y*s)*r;
+ double qPrime = (y*x*C+z*s)*p + (y*y*C+cc)*q + (y*z*C-x*s)*r;
+ double rPrime = (z*x*C-y*s)*p + (z*y*C+x*s)*q + (z*z*C+cc)*r;
+
+ double pDbPrime = (x*x*oC+occ)*p + (x*y*oC-z*os)*q + (x*z*oC+y*os)*r;
+ double qDbPrime = (y*x*oC+z*os)*p + (y*y*oC+occ)*q + (y*z*oC-x*os)*r;
+ double rDbPrime = (z*x*oC-y*os)*p + (z*y*oC+x*os)*q + (z*z*oC+occ)*r;
+
+ double cosAlpha = pPrime * a + qPrime * b + rPrime * c;
+ double cosAlphaOther = pDbPrime * a + qDbPrime * b + rDbPrime * c;
+
+ int addPi = (cosAlphaOther > cosAlpha);
+ double bestAngle = theta + addPi * M_PI;
+
+ /* Don't return an identity matrix which has been rotated by
+ * theta around "axis", but do assign it to twizzle. */
+ rotation_around_axis(axis, bestAngle, twizzle);
+}
+
+
+static double matrix_trace(gsl_matrix *a)
+{
+ int i;
+ double tr = 0.0;
+
+ assert(a->size1 == a->size2);
+ for ( i=0; i<a->size1; i++ ) {
+ tr += gsl_matrix_get(a, i, i);
+ }
+ return tr;
+}
+
+static char *add_ua(const char *inp, char ua)
+{
+ char *pg = malloc(64);
+ if ( pg == NULL ) return NULL;
+ snprintf(pg, 63, "%s_ua%c", inp, ua);
+ return pg;
+}
+
+
+static char *get_chiral_holohedry(UnitCell *cell)
+{
+ LatticeType lattice = cell_get_lattice_type(cell);
+ char *pg = malloc(64);
+ char *pgout = 0;
+
+ if ( pg == NULL ) return NULL;
+
+ switch (lattice)
+ {
+ case L_TRICLINIC:
+ pg = "1";
+ break;
+
+ case L_MONOCLINIC:
+ pg = "2";
+ break;
+
+ case L_ORTHORHOMBIC:
+ pg = "222";
+ break;
+
+ case L_TETRAGONAL:
+ pg = "422";
+ break;
+
+ case L_RHOMBOHEDRAL:
+ pg = "3_R";
+ break;
+
+ case L_HEXAGONAL:
+ if ( cell_get_centering(cell) == 'H' ) {
+ pg = "3_H";
+ } else {
+ pg = "622";
+ }
+ break;
+
+ case L_CUBIC:
+ pg = "432";
+ break;
+
+ default:
+ pg = "error";
+ break;
+ }
+
+ switch (lattice)
+ {
+ case L_TRICLINIC:
+ case L_ORTHORHOMBIC:
+ case L_RHOMBOHEDRAL:
+ case L_CUBIC:
+ pgout = strdup(pg);
+ break;
+
+ case L_MONOCLINIC:
+ case L_TETRAGONAL:
+ case L_HEXAGONAL:
+ pgout = add_ua(pg, cell_get_unique_axis(cell));
+ break;
+
+ default:
+ break;
+ }
+
+ return pgout;
+}
+
+
+static SymOpList *sym_ops_for_cell(UnitCell *cell)
+{
+ SymOpList *rawList;
+
+ char *pg = get_chiral_holohedry(cell);
+ rawList = get_pointgroup(pg);
+ free(pg);
+
+ return rawList;
+}
+
+static int rot_mats_are_similar(gsl_matrix *rot1, gsl_matrix *rot2,
+ gsl_matrix *sub, gsl_matrix *mul,
+ double *score)
+{
+ double tr;
+
+ gsl_matrix_memcpy(sub, rot1);
+ gsl_matrix_sub(sub, rot2); /* sub = rot1 - rot2 */
+
+ gsl_blas_dgemm(CblasNoTrans, CblasTrans, 1.0, sub, sub, 0.0, mul);
+
+ tr = matrix_trace(mul);
+ if (score != NULL) *score = tr;
+
+ double max = sqrt(4.0*(1.0-cos(TRACE_TOLERANCE)));
+
+ return (tr < max);
+}
+
+static int symm_rot_mats_are_similar(gsl_matrix *rot1, gsl_matrix *rot2,
+ struct TakeTwoCell *cell)
+{
+ int i;
+
+ gsl_matrix *sub = gsl_matrix_calloc(3, 3);
+ gsl_matrix *mul = gsl_matrix_calloc(3, 3);
+
+ for (i = 0; i < cell->numOps; i++) {
+ gsl_matrix *testRot = gsl_matrix_alloc(3, 3);
+ gsl_matrix *symOp = cell->rotSymOps[i];
+
+ gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, rot1, symOp,
+ 0.0, testRot);
+
+ if (rot_mats_are_similar(testRot, rot2, sub, mul, NULL)) {
+ gsl_matrix_free(testRot);
+ gsl_matrix_free(sub);
+ gsl_matrix_free(mul);
+ return 1;
+ }
+
+ gsl_matrix_free(testRot);
+ }
+
+ gsl_matrix_free(sub);
+ gsl_matrix_free(mul);
+
+ return 0;
+}
+
+static void rotation_between_vectors(struct rvec a, struct rvec b,
+ gsl_matrix *twizzle)
+{
+ double th = rvec_angle(a, b);
+ struct rvec c = rvec_cross(a, b);
+ normalise_rvec(&c);
+ rotation_around_axis(c, th, twizzle);
+}
+
+
+static void rvec_to_gsl(gsl_vector *newVec, struct rvec v)
+{
+ gsl_vector_set(newVec, 0, v.u);
+ gsl_vector_set(newVec, 1, v.v);
+ gsl_vector_set(newVec, 2, v.w);
+}
+
+
+struct rvec gsl_to_rvec(gsl_vector *a)
+{
+ struct rvec v;
+ v.u = gsl_vector_get(a, 0);
+ v.v = gsl_vector_get(a, 1);
+ v.w = gsl_vector_get(a, 2);
+ return v;
+}
+
+
+/* Code me in gsl_matrix language to copy the contents of the function
+ * in cppxfel (IndexingSolution::createSolution). This function is quite
+ * intensive on the number crunching side so simple angle checks are used
+ * to 'pre-scan' vectors beforehand. */
+static gsl_matrix *generate_rot_mat(struct rvec obs1, struct rvec obs2,
+ struct rvec cell1, struct rvec cell2,
+ struct TakeTwoCell *cell)
+{
+ gsl_matrix *fullMat;
+ rvec_to_gsl(cell->vec1Tmp, cell2);
+
+// gsl_vector *cell2v = rvec_to_gsl(cell2);
+// gsl_vector *cell2vr = gsl_vector_calloc(3);
+
+ normalise_rvec(&obs1);
+ normalise_rvec(&obs2);
+ normalise_rvec(&cell1);
+ normalise_rvec(&cell2);
+
+ /* Rotate reciprocal space so that the first simulated vector lines up
+ * with the observed vector. */
+ rotation_between_vectors(cell1, obs1, cell->twiz1Tmp);
+
+ normalise_rvec(&obs1);
+
+ /* Multiply cell2 by rotateSpotDiffMatrix --> cell2vr */
+ gsl_blas_dgemv(CblasNoTrans, 1.0, cell->twiz1Tmp, cell->vec1Tmp,
+ 0.0, cell->vec2Tmp);
+
+ /* Now we twirl around the firstAxisUnit until the rotated simulated
+ * vector matches the second observed vector as closely as possible. */
+
+ closest_rot_mat(gsl_to_rvec(cell->vec2Tmp), obs2, obs1, cell->twiz2Tmp);
+
+ /* We want to apply the first matrix and then the second matrix,
+ * so we multiply these. */
+ fullMat = gsl_matrix_calloc(3, 3);
+ gsl_blas_dgemm(CblasTrans, CblasTrans, 1.0,
+ cell->twiz1Tmp, cell->twiz2Tmp, 0.0, fullMat);
+ gsl_matrix_transpose(fullMat);
+
+ return fullMat;
+}
+
+
+static int obs_vecs_share_spot(struct SpotVec *her_obs, struct SpotVec *his_obs)
+{
+ if ( (her_obs->her_rlp == his_obs->her_rlp) ||
+ (her_obs->her_rlp == his_obs->his_rlp) ||
+ (her_obs->his_rlp == his_obs->her_rlp) ||
+ (her_obs->his_rlp == his_obs->his_rlp) ) {
+ return 1;
+ }
+
+ return 0;
+}
+
+
+static int obs_shares_spot_w_array(struct SpotVec *obs_vecs, int test_idx,
+ int *members, int num)
+{
+ int i;
+
+ struct SpotVec *her_obs = &obs_vecs[test_idx];
+
+ for ( i=0; i<num; i++ ) {
+ struct SpotVec *his_obs = &obs_vecs[members[i]];
+
+ int shares = obs_vecs_share_spot(her_obs, his_obs);
+
+ if ( shares ) return 1;
+ }
+
+ return 0;
+}
+
+
+static int obs_vecs_match_angles(struct SpotVec *her_obs,
+ struct SpotVec *his_obs,
+ int **her_match_idxs, int **his_match_idxs,
+ int *match_count)
+{
+ int i, j;
+ *match_count = 0;
+
+ double min_angle = deg2rad(2.5);
+ double max_angle = deg2rad(187.5);
+
+ /* calculate angle between observed vectors */
+ double obs_angle = rvec_angle(her_obs->obsvec, his_obs->obsvec);
+
+ /* calculate angle between all potential theoretical vectors */
+
+ for ( i=0; i<her_obs->match_num; i++ ) {
+ for ( j=0; j<his_obs->match_num; j++ ) {
+
+ struct rvec *her_match = &her_obs->matches[i];
+ struct rvec *his_match = &his_obs->matches[j];
+
+ double theory_angle = rvec_angle(*her_match,
+ *his_match);
+
+ /* is this angle a match? */
+
+ double angle_diff = fabs(theory_angle - obs_angle);
+
+ if ( angle_diff < ANGLE_TOLERANCE ) {
+ // in the case of a brief check only
+ if (!her_match_idxs || !his_match_idxs) {
+ return 1;
+ }
+
+ /* If the angles are too close to 0
+ or 180, one axis ill-determined */
+ if (theory_angle < min_angle ||
+ theory_angle > max_angle) {
+ continue;
+ }
+
+ // check the third vector
+
+ struct rvec theory_diff = diff_vec(*his_match, *her_match);
+ struct rvec obs_diff = diff_vec(his_obs->obsvec,
+ her_obs->obsvec);
+
+ theory_angle = rvec_angle(*her_match,
+ theory_diff);
+ obs_angle = rvec_angle(her_obs->obsvec, obs_diff);
+
+ if (fabs(obs_angle - theory_angle) > ANGLE_TOLERANCE) {
+ continue;
+ }
+
+ theory_angle = rvec_angle(*his_match,
+ theory_diff);
+ obs_angle = rvec_angle(his_obs->obsvec, obs_diff);
+
+ if (fabs(obs_angle - theory_angle) > ANGLE_TOLERANCE) {
+ continue;
+ }
+
+ size_t new_size = (*match_count + 1) *
+ sizeof(int);
+ if (her_match_idxs && his_match_idxs)
+ {
+ /* Reallocate the array to fit in another match */
+ int *temp_hers;
+ int *temp_his;
+ temp_hers = realloc(*her_match_idxs, new_size);
+ temp_his = realloc(*his_match_idxs, new_size);
+
+ if ( temp_hers == NULL || temp_his == NULL ) {
+ apologise();
+ }
+
+ (*her_match_idxs) = temp_hers;
+ (*his_match_idxs) = temp_his;
+
+ (*her_match_idxs)[*match_count] = i;
+ (*his_match_idxs)[*match_count] = j;
+ }
+
+ (*match_count)++;
+ }
+ }
+ }
+
+ return (*match_count > 0);
+}
+
+/* ------------------------------------------------------------------------
+ * core functions regarding the meat of the TakeTwo algorithm (Level 2)
+ * ------------------------------------------------------------------------*/
+
+static signed int finish_solution(gsl_matrix *rot, struct SpotVec *obs_vecs,
+ int *obs_members, int *match_members,
+ int member_num, struct TakeTwoCell *cell)
+{
+ gsl_matrix *sub = gsl_matrix_calloc(3, 3);
+ gsl_matrix *mul = gsl_matrix_calloc(3, 3);
+
+ gsl_matrix **rotations = malloc(sizeof(*rotations)* pow(member_num, 2)
+ - member_num);
+
+ int i, j, count;
+
+ count = 0;
+ for ( i=0; i<1; i++ ) {
+ for ( j=0; j<member_num; j++ ) {
+ if (i == j) continue;
+ struct SpotVec i_vec = obs_vecs[obs_members[i]];
+ struct SpotVec j_vec = obs_vecs[obs_members[j]];
+
+ struct rvec i_obsvec = i_vec.obsvec;
+ struct rvec j_obsvec = j_vec.obsvec;
+ struct rvec i_cellvec = i_vec.matches[match_members[i]];
+ struct rvec j_cellvec = j_vec.matches[match_members[j]];
+
+ rotations[count] = generate_rot_mat(i_obsvec, j_obsvec,
+ i_cellvec, j_cellvec,
+ cell);
+
+ count++;
+ }
+ }
+
+ double min_score = FLT_MAX;
+ int min_rot_index = 0;
+
+ for (i=0; i<count; i++) {
+ double current_score = 0;
+ for (j=0; j<count; j++) {
+ double addition;
+ rot_mats_are_similar(rotations[i], rotations[j],
+ sub, mul,
+ &addition);
+
+ current_score += addition;
+ }
+
+ if (current_score < min_score) {
+ min_score = current_score;
+ min_rot_index = i;
+ }
+ }
+
+ gsl_matrix_memcpy(rot, rotations[min_rot_index]);
+
+ for (i=0; i<count; i++) {
+ gsl_matrix_free(rotations[i]);
+ }
+
+ free(rotations);
+ gsl_matrix_free(sub);
+ gsl_matrix_free(mul);
+
+ return 1;
+}
+
+static int weed_duplicate_matches(struct SpotVec *her_obs,
+ struct SpotVec *his_obs,
+ int **her_match_idxs, int **his_match_idxs,
+ int *match_count, struct TakeTwoCell *cell)
+{
+ int num_occupied = 0;
+ gsl_matrix **old_mats = calloc(*match_count, sizeof(gsl_matrix *));
+
+ if (old_mats == NULL)
+ {
+ apologise();
+ return 0;
+ }
+
+ signed int i, j;
+ int duplicates = 0;
+
+ for (i = *match_count - 1; i >= 0; i--) {
+ int her_match = (*her_match_idxs)[i];
+ int his_match = (*his_match_idxs)[i];
+
+ struct rvec i_obsvec = her_obs->obsvec;
+ struct rvec j_obsvec = his_obs->obsvec;
+ struct rvec i_cellvec = her_obs->matches[her_match];
+ struct rvec j_cellvec = his_obs->matches[his_match];
+
+ gsl_matrix *mat = generate_rot_mat(i_obsvec, j_obsvec,
+ i_cellvec, j_cellvec, cell);
+
+ int found = 0;
+
+ for (j = 0; j < num_occupied; j++) {
+ if (old_mats[j] && mat &&
+ symm_rot_mats_are_similar(old_mats[j], mat, cell))
+ {
+ // we have found a duplicate, so flag as bad.
+ (*her_match_idxs)[i] = -1;
+ (*his_match_idxs)[i] = -1;
+ found = 1;
+
+ duplicates++;
+
+ gsl_matrix_free(mat);
+ break;
+ }
+ }
+
+ if (!found) {
+ // we have not found a duplicate, add to list.
+ old_mats[num_occupied] = mat;
+ num_occupied++;
+ }
+ }
+
+ for (i = 0; i < num_occupied; i++) {
+ if (old_mats[i]) {
+ gsl_matrix_free(old_mats[i]);
+ }
+ }
+
+ free(old_mats);
+
+ return 1;
+}
+
+static signed int find_next_index(gsl_matrix *rot, int *obs_members,
+ int *match_members, int start, int member_num,
+ int *match_found, struct TakeTwoCell *cell)
+{
+ struct SpotVec *obs_vecs = *(cell->obs_vecs);
+ int obs_vec_count = cell->obs_vec_count;
+ gsl_matrix *sub = gsl_matrix_calloc(3, 3);
+ gsl_matrix *mul = gsl_matrix_calloc(3, 3);
+
+ int i, j, k;
+
+ for ( i=start; i<obs_vec_count; i++ ) {
+
+ /* first we check for a shared spot - harshest condition */
+ int shared = obs_shares_spot_w_array(obs_vecs, i, obs_members,
+ member_num);
+
+ if ( !shared ) continue;
+
+ int skip = 0;
+ for ( j=0; j<member_num && skip == 0; j++ ) {
+ if (i == obs_members[j]) {
+ skip = 1;
+ }
+ }
+
+ if (skip) {
+ continue;
+ }
+
+ int all_ok = 1;
+ int matched = -1;
+
+ for ( j=0; j<member_num && all_ok; j++ ) {
+
+ struct SpotVec *me = &obs_vecs[i];
+ struct SpotVec *you = &obs_vecs[obs_members[j]];
+ struct rvec you_cell = you->matches[match_members[j]];
+
+ struct rvec me_obs = me->obsvec;
+ struct rvec you_obs = you->obsvec;
+
+ int one_is_okay = 0;
+
+ for ( k=0; k<me->match_num; k++ ) {
+
+ gsl_matrix *test_rot;
+
+ struct rvec me_cell = me->matches[k];
+
+ test_rot = generate_rot_mat(me_obs,
+ you_obs, me_cell, you_cell,
+ cell);
+
+ double trace = 0;
+ int ok = rot_mats_are_similar(rot, test_rot,
+ sub, mul, &trace);
+
+ gsl_matrix_free(test_rot);
+
+ if (ok) {
+ one_is_okay = 1;
+
+ if (matched >= 0 && k == matched) {
+ *match_found = k;
+ } else if (matched < 0) {
+ matched = k;
+ } else {
+ one_is_okay = 0;
+ break;
+ }
+ }
+ }
+
+ if (!one_is_okay) {
+ all_ok = 0;
+ break;
+ }
+ }
+
+
+ if (all_ok) {
+
+ for ( j=0; j<member_num; j++ ) {
+ // STATUS("%i ", obs_members[j]);
+ }
+ //STATUS("%i\n", i);
+
+ return i;
+ }
+ }
+
+ /* give up. */
+
+ return -1;
+}
+
+
+static int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2,
+ int match_idx1, int match_idx2, int *max_members,
+ struct TakeTwoCell *cell)
+{
+ struct SpotVec *obs_vecs = *(cell->obs_vecs);
+ int obs_vec_count = cell->obs_vec_count;
+
+ /* indices of members of the self-consistent network of vectors */
+ int obs_members[MAX_NETWORK_MEMBERS];
+ int match_members[MAX_NETWORK_MEMBERS];
+
+ /* initialise the ones we know already */
+ obs_members[0] = obs_idx1;
+ obs_members[1] = obs_idx2;
+ match_members[0] = match_idx1;
+ match_members[1] = match_idx2;
+ int member_num = 2;
+ *max_members = 2;
+
+ /* counter for dead ends which must not exceed MAX_DEAD_ENDS
+ * before it is reset in an additional branch */
+ int dead_ends = 0;
+
+ /* we start from 0 */
+ int start = 0;
+
+ while ( 1 ) {
+
+ if (start > obs_vec_count) {
+ return 0;
+ }
+
+ int match_found = -1;
+
+ signed int next_index = find_next_index(rot, obs_members,
+ match_members,
+ start, member_num,
+ &match_found, cell);
+
+ if ( member_num < 2 ) {
+ return 0;
+ }
+
+ if ( next_index < 0 ) {
+ /* If there have been too many dead ends, give up
+ * on indexing altogether.
+ **/
+ if ( dead_ends > MAX_DEAD_ENDS ) {
+ break;
+ }
+
+ /* We have not had too many dead ends. Try removing
+ the last member and continue. */
+ start = obs_members[member_num - 1] + 1;
+ member_num--;
+ dead_ends++;
+
+ continue;
+ }
+
+ /* we have elongated membership - so reset dead_ends counter */
+ // dead_ends = 0;
+
+ obs_members[member_num] = next_index;
+ match_members[member_num] = match_found;
+
+ member_num++;
+
+ if (member_num > *max_members) {
+ *max_members = member_num;
+ }
+
+ /* If member_num is high enough, we want to return a yes */
+ if ( member_num > NETWORK_MEMBER_THRESHOLD ) break;
+ }
+
+ finish_solution(rot, obs_vecs, obs_members,
+ match_members, member_num, cell);
+
+ return ( member_num > NETWORK_MEMBER_THRESHOLD );
+}
+
+
+static int start_seed(int i, int j, int i_match, int j_match,
+ gsl_matrix **rotation, int *max_members,
+ struct TakeTwoCell *cell)
+{
+ struct SpotVec *obs_vecs = *(cell->obs_vecs);
+
+ gsl_matrix *rot_mat;
+
+ rot_mat = generate_rot_mat(obs_vecs[i].obsvec,
+ obs_vecs[j].obsvec,
+ obs_vecs[i].matches[i_match],
+ obs_vecs[j].matches[j_match],
+ cell);
+
+ /* Try to expand this rotation matrix to a larger network */
+
+ int success = grow_network(rot_mat, i, j, i_match, j_match, max_members,
+ cell);
+
+ /* return this matrix and if it was immediately successful */
+ *rotation = rot_mat;
+
+ return success;
+}
+
+static int find_seed(gsl_matrix **rotation, struct TakeTwoCell *cell)
+{
+ struct SpotVec *obs_vecs = *(cell->obs_vecs);
+ int obs_vec_count = cell->obs_vec_count;
+
+ /* META: Maximum achieved maximum network membership */
+ int max_max_members = 0;
+ gsl_matrix *best_rotation = NULL;
+
+// unsigned long start_time = time(NULL);
+
+ /* loop round pairs of vectors to try and find a suitable
+ * seed to start building a self-consistent network of vectors
+ */
+ int i, j;
+
+ for ( i=0; i<obs_vec_count; i++ ) {
+ for ( j=0; j<i; j++ ) {
+
+ /** Check to see if there is a shared spot - opportunity
+ * for optimisation by generating a look-up table
+ * by spot instead of by vector.
+ */
+ int shared = obs_vecs_share_spot(&obs_vecs[i], &obs_vecs[j]);
+
+ if ( !shared ) continue;
+
+ /* cell vector index matches stored in i, j and total number
+ * stored in int matches.
+ */
+ int *i_idx = 0;
+ int *j_idx = 0;
+ int matches;
+
+ // double dist1Pc = 100 * obs_vecs[i].distance / MAX_RECIP_DISTANCE;
+// double dist2Pc = 100 * obs_vecs[j].distance / MAX_RECIP_DISTANCE;
+
+ /* Check to see if any angles match from the cell vectors */
+ obs_vecs_match_angles(&obs_vecs[i], &obs_vecs[j],
+ &i_idx, &j_idx, &matches);
+ if ( matches == 0 ) {
+ free(i_idx);
+ free(j_idx);
+ continue;
+ }
+
+ /* Weed out the duplicate seeds (from symmetric
+ * reflection pairs)
+ */
+
+ weed_duplicate_matches(&obs_vecs[i], &obs_vecs[j],
+ &i_idx, &j_idx, &matches, cell);
+
+ /* We have seeds! Pass each of them through the seed-starter */
+ /* If a seed has the highest achieved membership, make note...*/
+ int k;
+ for ( k=0; k<matches; k++ ) {
+ if (i_idx[k] < 0 || j_idx[k] < 0) {
+ continue;
+ }
+
+ int max_members = 0;
+
+ int success = start_seed(i, j,
+ i_idx[k], j_idx[k],
+ rotation, &max_members,
+ cell);
+
+ if (success) {
+ free(i_idx); free(j_idx);
+ gsl_matrix_free(best_rotation);
+ return success;
+ } else {
+ if (max_members > max_max_members) {
+ max_max_members = max_members;
+ gsl_matrix_free(best_rotation);
+ best_rotation = *rotation;
+ *rotation = NULL;
+ } else {
+ gsl_matrix_free(*rotation);
+ *rotation = NULL;
+ }
+ }
+ }
+
+ free(i_idx);
+ free(j_idx);
+ }
+ } /* yes this } is meant to be here */
+
+ *rotation = best_rotation;
+ return (best_rotation != NULL);
+}
+
+static void set_gsl_matrix(gsl_matrix *mat, double asx, double asy, double asz,
+ double bsx, double bsy, double bsz,
+ double csx, double csy, double csz)
+{
+ gsl_matrix_set(mat, 0, 0, asx);
+ gsl_matrix_set(mat, 0, 1, asy);
+ gsl_matrix_set(mat, 0, 2, asz);
+ gsl_matrix_set(mat, 1, 0, bsx);
+ gsl_matrix_set(mat, 1, 1, bsy);
+ gsl_matrix_set(mat, 1, 2, bsz);
+ gsl_matrix_set(mat, 2, 0, csx);
+ gsl_matrix_set(mat, 2, 1, csy);
+ gsl_matrix_set(mat, 2, 2, csz);
+}
+
+static int generate_rotation_sym_ops(struct TakeTwoCell *ttCell)
+{
+ SymOpList *rawList = sym_ops_for_cell(ttCell->cell);
+
+ /* Now we must convert these into rotation matrices rather than hkl
+ * transformations (affects triclinic, monoclinic, rhombohedral and
+ * hexagonal space groups only) */
+
+ double asx, asy, asz;
+ double bsx, bsy, bsz;
+ double csx, csy, csz;
+
+ gsl_matrix *recip = gsl_matrix_alloc(3, 3);
+ gsl_matrix *cart = gsl_matrix_alloc(3, 3);
+ cell_get_reciprocal(ttCell->cell, &asx, &asy, &asz, &bsx, &bsy,
+ &bsz, &csx, &csy, &csz);
+
+ set_gsl_matrix(recip, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+
+ cell_get_cartesian(ttCell->cell, &asx, &asy, &asz, &bsx, &bsy,
+ &bsz, &csx, &csy, &csz);
+
+ set_gsl_matrix(cart, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+
+ int i, j, k;
+ int numOps = num_equivs(rawList, NULL);
+
+ ttCell->rotSymOps = malloc(numOps * sizeof(gsl_matrix *));
+ ttCell->numOps = numOps;
+
+ if (ttCell->rotSymOps == NULL) {
+ apologise();
+ return 0;
+ }
+
+ for (i = 0; i < numOps; i++)
+ {
+ gsl_matrix *symOp = gsl_matrix_alloc(3, 3);
+ IntegerMatrix *op = get_symop(rawList, NULL, i);
+
+ for (j = 0; j < 3; j++) {
+ for (k = 0; k < 3; k++) {
+ gsl_matrix_set(symOp, j, k, intmat_get(op, j, k));
+ }
+ }
+
+ gsl_matrix *first = gsl_matrix_calloc(3, 3);
+ gsl_matrix *second = gsl_matrix_calloc(3, 3);
+
+ /* Each equivalence is of the form:
+ cartesian * symOp * reciprocal.
+ First multiplication: symOp * reciprocal */
+
+ gsl_blas_dgemm(CblasNoTrans, CblasNoTrans,
+ 1.0, symOp, recip,
+ 0.0, first);
+
+ /* Second multiplication: cartesian * first */
+
+ gsl_blas_dgemm(CblasNoTrans, CblasNoTrans,
+ 1.0, cart, first,
+ 0.0, second);
+
+ ttCell->rotSymOps[i] = second;
+
+ gsl_matrix_free(symOp);
+ gsl_matrix_free(first);
+ }
+
+ gsl_matrix_free(cart);
+ gsl_matrix_free(recip);
+
+ free_symoplist(rawList);
+
+ return 1;
+}
+
+
+struct sortme
+{
+ struct rvec v;
+ double dist;
+};
+
+static int sort_func(const void *av, const void *bv)
+{
+ struct sortme *a = (struct sortme *)av;
+ struct sortme *b = (struct sortme *)bv;
+ return a->dist > b->dist;
+}
+
+
+static int match_obs_to_cell_vecs(struct rvec *cell_vecs, int cell_vec_count,
+ struct SpotVec *obs_vecs, int obs_vec_count,
+ int is_asymmetric)
+{
+ int i, j;
+
+ for ( i=0; i<obs_vec_count; i++ ) {
+
+ int count = 0;
+ struct sortme *for_sort = NULL;
+
+ for ( j=0; j<cell_vec_count; j++ ) {
+ /* get distance for unit cell vector */
+ double cell_length = rvec_length(cell_vecs[j]);
+ double obs_length = obs_vecs[i].distance;
+
+ /* check if this matches the observed length */
+ double dist_diff = fabs(cell_length - obs_length);
+
+ if ( dist_diff > RECIP_TOLERANCE ) continue;
+
+ /* we have a match, add to array! */
+
+ size_t new_size = (count+1)*sizeof(struct sortme);
+ for_sort = realloc(for_sort, new_size);
+
+ if ( for_sort == NULL ) return 0;
+
+ for_sort[count].v = cell_vecs[j];
+ for_sort[count].dist = dist_diff;
+ count++;
+
+ }
+
+ /* Pointers to relevant things */
+
+ struct rvec **match_array;
+ int *match_count;
+
+ if (!is_asymmetric) {
+ match_array = &(obs_vecs[i].matches);
+ match_count = &(obs_vecs[i].match_num);
+ } else {
+ match_array = &(obs_vecs[i].asym_matches);
+ match_count = &(obs_vecs[i].asym_match_num);
+ }
+
+ /* Sort in order to get most agreeable matches first */
+ qsort(for_sort, count, sizeof(struct sortme), sort_func);
+ *match_array = malloc(count*sizeof(struct rvec));
+ *match_count = count;
+ for ( j=0; j<count; j++ ) {
+ (*match_array)[j] = for_sort[j].v;
+
+ }
+ free(for_sort);
+ }
+
+ return 1;
+}
+
+static int compare_spot_vecs(const void *av, const void *bv)
+{
+ struct SpotVec *a = (struct SpotVec *)av;
+ struct SpotVec *b = (struct SpotVec *)bv;
+ return a->distance > b->distance;
+}
+
+static int gen_observed_vecs(struct rvec *rlps, int rlp_count,
+ struct SpotVec **obs_vecs, int *obs_vec_count)
+{
+ int i, j;
+ int count = 0;
+
+ /* maximum distance squared for comparisons */
+ double max_sq_length = pow(MAX_RECIP_DISTANCE, 2);
+
+ for ( i=0; i<rlp_count-1 && count < MAX_OBS_VECTORS; i++ ) {
+ for ( j=i+1; j<rlp_count; j++ ) {
+
+
+ /* calculate difference vector between rlps */
+ struct rvec diff = diff_vec(rlps[i], rlps[j]);
+
+ /* are these two far from each other? */
+ double sqlength = sq_length(diff);
+
+ if ( sqlength > max_sq_length ) continue;
+
+ count++;
+
+ struct SpotVec *temp_obs_vecs;
+ temp_obs_vecs = realloc(*obs_vecs,
+ count*sizeof(struct SpotVec));
+
+ if ( temp_obs_vecs == NULL ) {
+ return 0;
+ } else {
+ *obs_vecs = temp_obs_vecs;
+
+ /* initialise all SpotVec struct members */
+
+ struct SpotVec spot_vec;
+ spot_vec.obsvec = diff;
+ spot_vec.distance = sqrt(sqlength);
+ spot_vec.matches = NULL;
+ spot_vec.match_num = 0;
+ spot_vec.her_rlp = &rlps[i];
+ spot_vec.his_rlp = &rlps[j];
+
+ (*obs_vecs)[count - 1] = spot_vec;
+ }
+ }
+ }
+
+ /* Sort such that the shortest and least error-prone distances
+ are searched first.
+ */
+ qsort(*obs_vecs, count, sizeof(struct SpotVec), compare_spot_vecs);
+
+ *obs_vec_count = count;
+
+ return 1;
+}
+
+
+static int gen_theoretical_vecs(UnitCell *cell, struct rvec **cell_vecs,
+ struct rvec **asym_vecs, int *vec_count,
+ int *asym_vec_count)
+{
+ double a, b, c, alpha, beta, gamma;
+ int h_max, k_max, l_max;
+ double asx, asy, asz;
+ double bsx, bsy, bsz;
+ double csx, csy, csz;
+
+ cell_get_reciprocal(cell, &asx, &asy, &asz,
+ &bsx, &bsy, &bsz,
+ &csx, &csy, &csz);
+
+ SymOpList *rawList = sym_ops_for_cell(cell);
+
+ cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
+
+ /* find maximum Miller (h, k, l) indices for a given resolution */
+ h_max = MAX_RECIP_DISTANCE * a;
+ k_max = MAX_RECIP_DISTANCE * b;
+ l_max = MAX_RECIP_DISTANCE * c;
+
+ int h, k, l;
+ int _h, _k, _l;
+ int count = 0;
+ int asym_count = 0;
+
+ for ( h=-h_max; h<=+h_max; h++ ) {
+ for ( k=-k_max; k<=+k_max; k++ ) {
+ for ( l=-l_max; l<=+l_max; l++ ) {
+
+ struct rvec cell_vec;
+
+ /* Exclude systematic absences from centering concerns */
+ if ( forbidden_reflection(cell, h, k, l) ) continue;
+
+ int asymmetric = 0;
+ get_asymm(rawList, h, k, l, &_h, &_k, &_l);
+
+ if (h == _h && k == _k && l == _l) {
+ asymmetric = 1;
+ asym_count++;
+ }
+
+ cell_vec.u = h*asx + k*bsx + l*csx;
+ cell_vec.v = h*asy + k*bsy + l*csy;
+ cell_vec.w = h*asz + k*bsz + l*csz;
+
+ /* add this to our array - which may require expanding */
+ count++;
+
+ struct rvec *temp_cell_vecs;
+ temp_cell_vecs = realloc(*cell_vecs, count*sizeof(struct rvec));
+ struct rvec *temp_asym_vecs = NULL;
+
+ if (asymmetric) {
+ temp_asym_vecs = realloc(*asym_vecs,
+ count*sizeof(struct rvec));
+ }
+
+ if ( temp_cell_vecs == NULL ) {
+ return 0;
+ } else if (asymmetric && temp_asym_vecs == NULL) {
+ return 0;
+ } else {
+ *cell_vecs = temp_cell_vecs;
+ (*cell_vecs)[count - 1] = cell_vec;
+
+ if (!asymmetric) {
+ continue;
+ }
+
+ *asym_vecs = temp_asym_vecs;
+ (*asym_vecs)[asym_count - 1] = cell_vec;
+ }
+ }
+ }
+ }
+
+ *vec_count = count;
+ *asym_vec_count = asym_count;
+
+ free_symoplist(rawList);
+
+
+ return 1;
+}
+
+
+/* ------------------------------------------------------------------------
+ * cleanup functions - called from run_taketwo().
+ * ------------------------------------------------------------------------*/
+
+static void cleanup_taketwo_obs_vecs(struct SpotVec *obs_vecs,
+ int obs_vec_count)
+{
+ int i;
+ for ( i=0; i<obs_vec_count; i++ ) {
+ free(obs_vecs[i].matches);
+ free(obs_vecs[i].asym_matches);
+ }
+
+ free(obs_vecs);
+}
+
+static void cleanup_taketwo_cell(struct TakeTwoCell *ttCell)
+{
+ int i;
+ for ( i=0; i<ttCell->numOps; i++ ) {
+ gsl_matrix_free(ttCell->rotSymOps[i]);
+ }
+
+ free(ttCell->vec1Tmp);
+ free(ttCell->vec2Tmp);
+ free(ttCell->twiz1Tmp);
+ free(ttCell->twiz2Tmp);
+ free(ttCell->rotSymOps);
+}
+
+
+/* ------------------------------------------------------------------------
+ * external functions - top level functions (Level 1)
+ * ------------------------------------------------------------------------*/
+
+/**
+ * @cell: target unit cell
+ * @rlps: spot positions on detector back-projected into recripocal
+ * space depending on detector geometry etc.
+ * @rlp_count: number of rlps in rlps array.
+ * @rot: pointer to be given an assignment (hopefully) if indexing is
+ * successful.
+ **/
+static UnitCell *run_taketwo(UnitCell *cell, struct rvec *rlps, int rlp_count)
+{
+ int cell_vec_count = 0;
+ int asym_vec_count = 0;
+ struct rvec *cell_vecs = NULL;
+ struct rvec *asym_vecs = NULL;
+ UnitCell *result;
+ int obs_vec_count = 0;
+ struct SpotVec *obs_vecs = NULL;
+ int success = 0;
+ gsl_matrix *solution = NULL;
+
+ struct TakeTwoCell ttCell;
+ ttCell.cell = cell;
+ ttCell.rotSymOps = NULL;
+ ttCell.twiz1Tmp = gsl_matrix_calloc(3, 3);
+ ttCell.twiz2Tmp = gsl_matrix_calloc(3, 3);
+ ttCell.vec1Tmp = gsl_vector_calloc(3);
+ ttCell.vec2Tmp = gsl_vector_calloc(3);
+ ttCell.numOps = 0;
+
+ success = generate_rotation_sym_ops(&ttCell);
+
+ success = gen_theoretical_vecs(cell, &cell_vecs, &asym_vecs,
+ &cell_vec_count, &asym_vec_count);
+ if ( !success ) return NULL;
+
+ success = gen_observed_vecs(rlps, rlp_count, &obs_vecs, &obs_vec_count);
+ if ( !success ) return NULL;
+
+ ttCell.obs_vecs = &obs_vecs;
+ ttCell.obs_vec_count = obs_vec_count;
+
+ success = match_obs_to_cell_vecs(asym_vecs, asym_vec_count,
+ obs_vecs, obs_vec_count, 1);
+
+ success = match_obs_to_cell_vecs(cell_vecs, cell_vec_count,
+ obs_vecs, obs_vec_count, 0);
+
+ free(cell_vecs);
+ free(asym_vecs);
+
+ if ( !success ) return NULL;
+
+ find_seed(&solution, &ttCell);
+
+ if ( solution == NULL ) {
+ cleanup_taketwo_obs_vecs(obs_vecs, obs_vec_count);
+ return NULL;
+ }
+
+ result = transform_cell_gsl(cell, solution);
+ gsl_matrix_free(solution);
+ cleanup_taketwo_obs_vecs(obs_vecs, obs_vec_count);
+ cleanup_taketwo_cell(&ttCell);
+
+ return result;
+}
+
+
+/* CrystFEL interface hooks */
+
+int taketwo_index(struct image *image, void *priv)
+{
+ Crystal *cr;
+ UnitCell *cell;
+ struct rvec *rlps;
+ int n_rlps = 0;
+ int i;
+ struct taketwo_private *tp = (struct taketwo_private *)ipriv;
+
+ rlps = malloc((image_feature_count(image->features)+1)*sizeof(struct rvec));
+ for ( i=0; i<image_feature_count(image->features); i++ ) {
+ struct imagefeature *pk = image_get_feature(image->features, i);
+ if ( pk == NULL ) continue;
+ rlps[n_rlps].u = pk->rx;
+ rlps[n_rlps].v = pk->ry;
+ rlps[n_rlps].w = pk->rz;
+ n_rlps++;
+ }
+ rlps[n_rlps].u = 0.0;
+ rlps[n_rlps].v = 0.0;
+ rlps[n_rlps++].w = 0.0;
+
+ cell = run_taketwo(tp->cell, rlps, n_rlps);
+ free(rlps);
+ if ( cell == NULL ) return 0;
+
+ cr = crystal_new();
+ if ( cr == NULL ) {
+ ERROR("Failed to allocate crystal.\n");
+ return 0;
+ }
+
+ crystal_set_cell(cr, cell);
+
+ if ( tp->indm & INDEXING_CHECK_PEAKS ) {
+ if ( !peak_sanity_check(image, &cr, 1) ) {
+ cell_free(cell);
+ crystal_free(cr);
+ // STATUS("Rubbish!!\n");
+
+ return 0;
+ } else {
+ // STATUS("That's good!\n");
+ }
+ }
+
+ image_add_crystal(image, cr);
+
+ return 1;
+}
+
+
+void *taketwo_prepare(IndexingMethod *indm, UnitCell *cell,
+ struct detector *det, float *ltl)
+{
+ struct taketwo_private *tp;
+
+ /* Flags that TakeTwo knows about */
+ *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
+ | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS
+ | INDEXING_CONTROL_FLAGS;
+
+ if ( !( (*indm & INDEXING_USE_LATTICE_TYPE)
+ && (*indm & INDEXING_USE_CELL_PARAMETERS)) )
+ {
+ ERROR("TakeTwo indexing requires cell and lattice type "
+ "information.\n");
+ return NULL;
+ }
+
+ if ( cell == NULL ) {
+ ERROR("TakeTwo indexing requires a unit cell.\n");
+ return NULL;
+ }
+
+ STATUS("*******************************************************************\n");
+ STATUS("***** Welcome to TakeTwo *****\n");
+ STATUS("*******************************************************************\n");
+ STATUS(" If you use these indexing results, please keep a roof\n");
+ STATUS(" over the author's head by citing this paper.\n\n");
+
+ STATUS("o o o o o o o o o o o o\n");
+ STATUS(" o o o o o o o o o o o \n");
+ STATUS("o o\n");
+ STATUS(" o The citation is: o \n");
+ STATUS("o Ginn et al., Acta Cryst. (2016). D72, 956-965 o\n");
+ STATUS(" o Thank you! o \n");
+ STATUS("o o\n");
+ STATUS(" o o o o o o o o o o o \n");
+ STATUS("o o o o o o o o o o o o\n");
+
+
+ STATUS("\n");
+
+ tp = malloc(sizeof(struct taketwo_private));
+ if ( tp == NULL ) return NULL;
+
+ tp->ltl = ltl;
+ tp->cell = cell;
+ tp->indm = *indm;
+
+ return tp;
+}
+
+
+void taketwo_cleanup(IndexingPrivate *pp)
+{
+ struct taketwo_private *tp = (struct taketwo_private *)pp;
+ free(tp);
+}
+
diff --git a/libcrystfel/src/taketwo.h b/libcrystfel/src/taketwo.h
new file mode 100644
index 00000000..4c06e334
--- /dev/null
+++ b/libcrystfel/src/taketwo.h
@@ -0,0 +1,41 @@
+/*
+ * taketwo.h
+ *
+ * Rewrite of TakeTwo algorithm (Acta D72 (8) 956-965) for CrystFEL
+ *
+ * Copyright © 2016 Helen Ginn
+ * Copyright © 2016 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2016 Helen Ginn <helen@strubi.ox.ac.uk>
+ * 2016 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef TAKETWO_H
+#define TAKETWO_H
+
+#include "cell.h"
+
+extern void *taketwo_prepare(IndexingMethod *indm, UnitCell *cell,
+ struct detector *det, float *ltl);
+extern int taketwo_index(struct image *image, void *priv);
+extern void taketwo_cleanup(IndexingPrivate *pp);
+
+#endif /* TAKETWO_H */
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