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-rw-r--r--libcrystfel/src/cell-utils.c398
-rw-r--r--libcrystfel/src/cell-utils.h5
-rw-r--r--tests/cellcompare_check.c10
3 files changed, 5 insertions, 408 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index e59f1fa1..2af3f293 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -574,404 +574,6 @@ UnitCell *uncenter_cell(UnitCell *in, IntegerMatrix **pC, RationalMatrix **pCi)
}
-#define MAX_CAND (1024)
-
-static int right_handed_vec(struct rvec a, struct rvec b, struct rvec c)
-{
- struct rvec aCb;
- double aCb_dot_c;
-
- /* "a" cross "b" */
- aCb.u = a.v*b.w - a.w*b.v;
- aCb.v = - (a.u*b.w - a.w*b.u);
- aCb.w = a.u*b.v - a.v*b.u;
-
- /* "a cross b" dot "c" */
- aCb_dot_c = aCb.u*c.u + aCb.v*c.v + aCb.w*c.w;
-
- if ( aCb_dot_c > 0.0 ) return 1;
- return 0;
-}
-
-
-struct cvec {
- struct rvec vec;
- float na;
- float nb;
- float nc;
- float fom;
-};
-
-
-static int same_vector(struct cvec a, struct cvec b)
-{
- if ( a.na != b.na ) return 0;
- if ( a.nb != b.nb ) return 0;
- if ( a.nc != b.nc ) return 0;
- return 1;
-}
-
-
-/* Attempt to make 'cell' fit into 'template' somehow */
-UnitCell *match_cell(UnitCell *cell_in, UnitCell *template_in, int verbose,
- const float *tols, int reduce)
-{
- signed int n1l, n2l, n3l;
- double asx, asy, asz;
- double bsx, bsy, bsz;
- double csx, csy, csz;
- int i, j;
- double lengths[3];
- double angles[3];
- struct cvec *cand[3];
- UnitCell *new_cell = NULL;
- float best_fom = +999999999.9; /* Large number.. */
- int ncand[3] = {0,0,0};
- signed int ilow, ihigh;
- float angtol = deg2rad(tols[3]);
- UnitCell *cell;
- UnitCell *template;
- IntegerMatrix *centering;
- UnitCell *new_cell_trans;
-
- /* "Un-center" the template unit cell to make the comparison easier */
- template = uncenter_cell(template_in, &centering, NULL);
- if ( template == NULL ) return NULL;
-
- /* The candidate cell is also uncentered, because it might be centered
- * if it came from (e.g.) MOSFLM */
- cell = uncenter_cell(cell_in, NULL, NULL);
- if ( cell == NULL ) return NULL;
-
- if ( cell_get_reciprocal(template, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz) ) {
- ERROR("Couldn't get reciprocal cell for template.\n");
- cell_free(template);
- cell_free(cell);
- intmat_free(centering);
- return NULL;
- }
-
- lengths[0] = modulus(asx, asy, asz);
- lengths[1] = modulus(bsx, bsy, bsz);
- lengths[2] = modulus(csx, csy, csz);
-
- angles[0] = angle_between(bsx, bsy, bsz, csx, csy, csz);
- angles[1] = angle_between(asx, asy, asz, csx, csy, csz);
- angles[2] = angle_between(asx, asy, asz, bsx, bsy, bsz);
-
- cand[0] = malloc(MAX_CAND*sizeof(struct cvec));
- cand[1] = malloc(MAX_CAND*sizeof(struct cvec));
- cand[2] = malloc(MAX_CAND*sizeof(struct cvec));
-
- if ( cell_get_reciprocal(cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz) ) {
- ERROR("Couldn't get reciprocal cell.\n");
- cell_free(template);
- cell_free(cell);
- intmat_free(centering);
- return NULL;
- }
-
- if ( reduce ) {
- ilow = -2; ihigh = 4;
- } else {
- ilow = 0; ihigh = 1;
- }
-
- /* Negative values mean 1/n, positive means n, zero means zero */
- for ( n1l=ilow; n1l<=ihigh; n1l++ ) {
- for ( n2l=ilow; n2l<=ihigh; n2l++ ) {
- for ( n3l=ilow; n3l<=ihigh; n3l++ ) {
-
- float n1, n2, n3;
- signed int b1, b2, b3;
-
- n1 = (n1l>=0) ? (n1l) : (1.0/n1l);
- n2 = (n2l>=0) ? (n2l) : (1.0/n2l);
- n3 = (n3l>=0) ? (n3l) : (1.0/n3l);
-
- if ( !reduce ) {
- if ( n1l + n2l + n3l > 1 ) continue;
- }
-
- /* 'bit' values can be +1 or -1 */
- for ( b1=-1; b1<=1; b1+=2 ) {
- for ( b2=-1; b2<=1; b2+=2 ) {
- for ( b3=-1; b3<=1; b3+=2 ) {
-
- double tx, ty, tz;
- double tlen;
- int i;
-
- n1 *= b1; n2 *= b2; n3 *= b3;
-
- tx = n1*asx + n2*bsx + n3*csx;
- ty = n1*asy + n2*bsy + n3*csy;
- tz = n1*asz + n2*bsz + n3*csz;
- tlen = modulus(tx, ty, tz);
-
- /* Test modulus for agreement with moduli of template */
- for ( i=0; i<3; i++ ) {
-
- if ( !within_tolerance(lengths[i], tlen,
- tols[i]) )
- {
- continue;
- }
-
- if ( ncand[i] == MAX_CAND ) {
- ERROR("Too many cell candidates - ");
- ERROR("consider tightening the unit ");
- ERROR("cell tolerances.\n");
- } else {
-
- double fom;
-
- fom = fabs(lengths[i] - tlen);
-
- cand[i][ncand[i]].vec.u = tx;
- cand[i][ncand[i]].vec.v = ty;
- cand[i][ncand[i]].vec.w = tz;
- cand[i][ncand[i]].na = n1;
- cand[i][ncand[i]].nb = n2;
- cand[i][ncand[i]].nc = n3;
- cand[i][ncand[i]].fom = fom;
-
- ncand[i]++;
-
- }
- }
-
- }
- }
- }
-
- }
- }
- }
-
- if ( verbose ) {
- STATUS("Candidates: %i %i %i\n", ncand[0], ncand[1], ncand[2]);
- }
-
- for ( i=0; i<ncand[0]; i++ ) {
- for ( j=0; j<ncand[1]; j++ ) {
-
- double ang;
- int k;
- float fom1;
-
- if ( same_vector(cand[0][i], cand[1][j]) ) continue;
-
- /* Measure the angle between the ith candidate for axis 0
- * and the jth candidate for axis 1 */
- ang = angle_between(cand[0][i].vec.u, cand[0][i].vec.v,
- cand[0][i].vec.w, cand[1][j].vec.u,
- cand[1][j].vec.v, cand[1][j].vec.w);
-
- /* Angle between axes 0 and 1 should be angle 2 */
- if ( fabs(ang - angles[2]) > angtol ) continue;
-
- fom1 = fabs(ang - angles[2]);
-
- for ( k=0; k<ncand[2]; k++ ) {
-
- float fom2, fom3;
-
- if ( same_vector(cand[1][j], cand[2][k]) ) continue;
-
- /* Measure the angle between the current candidate for
- * axis 0 and the kth candidate for axis 2 */
- ang = angle_between(cand[0][i].vec.u, cand[0][i].vec.v,
- cand[0][i].vec.w, cand[2][k].vec.u,
- cand[2][k].vec.v, cand[2][k].vec.w);
-
- /* ... it should be angle 1 ... */
- if ( fabs(ang - angles[1]) > angtol ) continue;
-
- fom2 = fom1 + fabs(ang - angles[1]);
-
- /* Finally, the angle between the current candidate for
- * axis 1 and the kth candidate for axis 2 */
- ang = angle_between(cand[1][j].vec.u, cand[1][j].vec.v,
- cand[1][j].vec.w, cand[2][k].vec.u,
- cand[2][k].vec.v, cand[2][k].vec.w);
-
- /* ... it should be angle 0 ... */
- if ( fabs(ang - angles[0]) > angtol ) continue;
-
- /* Unit cell must be right-handed */
- if ( !right_handed_vec(cand[0][i].vec, cand[1][j].vec,
- cand[2][k].vec) ) continue;
-
- fom3 = fom2 + fabs(ang - angles[0]);
- fom3 += LWEIGHT * (cand[0][i].fom + cand[1][j].fom
- + cand[2][k].fom);
-
- if ( fom3 < best_fom ) {
- if ( new_cell != NULL ) free(new_cell);
- new_cell = cell_new_from_reciprocal_axes(
- cand[0][i].vec, cand[1][j].vec,
- cand[2][k].vec);
- best_fom = fom3;
- }
-
- }
-
- }
- }
-
- free(cand[0]);
- free(cand[1]);
- free(cand[2]);
-
- cell_free(cell);
-
- /* Reverse the de-centering transformation */
- if ( new_cell != NULL ) {
-
- new_cell_trans = cell_transform_intmat(new_cell, centering);
- cell_free(new_cell);
- cell_set_lattice_type(new_cell_trans,
- cell_get_lattice_type(template_in));
- cell_set_centering(new_cell_trans,
- cell_get_centering(template_in));
- cell_set_unique_axis(new_cell_trans,
- cell_get_unique_axis(template_in));
-
- cell_free(template);
- intmat_free(centering);
-
- return new_cell_trans;
-
- } else {
- cell_free(template);
- intmat_free(centering);
- return NULL;
- }
-}
-
-
-UnitCell *match_cell_ab(UnitCell *cell_in, UnitCell *template_in)
-{
- double ax, ay, az;
- double bx, by, bz;
- double cx, cy, cz;
- int i;
- double lengths[3];
- int used[3];
- struct rvec real_a, real_b, real_c;
- struct rvec params[3];
- double alen, blen;
- float ltl = 5.0; /* percent */
- int have_real_a;
- int have_real_b;
- int have_real_c;
- UnitCell *cell;
- UnitCell *template;
- IntegerMatrix *to_given_cell;
- UnitCell *new_cell;
- UnitCell *new_cell_trans;
-
- /* "Un-center" the template unit cell to make the comparison easier */
- template = uncenter_cell(template_in, &to_given_cell, NULL);
-
- /* The candidate cell is also uncentered, because it might be centered
- * if it came from (e.g.) MOSFLM */
- cell = uncenter_cell(cell_in, NULL, NULL);
-
- /* Get the lengths to match */
- if ( cell_get_cartesian(template, &ax, &ay, &az,
- &bx, &by, &bz,
- &cx, &cy, &cz) )
- {
- ERROR("Couldn't get cell for template.\n");
- return NULL;
- }
- alen = modulus(ax, ay, az);
- blen = modulus(bx, by, bz);
-
- /* Get the lengths from the cell and turn them into anonymous vectors */
- if ( cell_get_cartesian(cell, &ax, &ay, &az,
- &bx, &by, &bz,
- &cx, &cy, &cz) )
- {
- ERROR("Couldn't get cell.\n");
- return NULL;
- }
- lengths[0] = modulus(ax, ay, az);
- lengths[1] = modulus(bx, by, bz);
- lengths[2] = modulus(cx, cy, cz);
- used[0] = 0; used[1] = 0; used[2] = 0;
- params[0].u = ax; params[0].v = ay; params[0].w = az;
- params[1].u = bx; params[1].v = by; params[1].w = bz;
- params[2].u = cx; params[2].v = cy; params[2].w = cz;
-
- real_a.u = 0.0; real_a.v = 0.0; real_a.w = 0.0;
- real_b.u = 0.0; real_b.v = 0.0; real_b.w = 0.0;
- real_c.u = 0.0; real_c.v = 0.0; real_c.w = 0.0;
-
- /* Check each vector against a and b */
- have_real_a = 0;
- have_real_b = 0;
- for ( i=0; i<3; i++ ) {
- if ( within_tolerance(lengths[i], alen, ltl)
- && !used[i] && !have_real_a )
- {
- used[i] = 1;
- memcpy(&real_a, &params[i], sizeof(struct rvec));
- have_real_a = 1;
- }
- if ( within_tolerance(lengths[i], blen, ltl)
- && !used[i] && !have_real_b )
- {
- used[i] = 1;
- memcpy(&real_b, &params[i], sizeof(struct rvec));
- have_real_b = 1;
- }
- }
-
- /* Have we matched both a and b? */
- if ( !(have_real_a && have_real_b) ) return NULL;
-
- /* "c" is "the other one" */
- have_real_c = 0;
- for ( i=0; i<3; i++ ) {
- if ( !used[i] ) {
- memcpy(&real_c, &params[i], sizeof(struct rvec));
- have_real_c = 1;
- }
- }
-
- if ( !have_real_c ) {
- ERROR("Huh? Couldn't find the third vector.\n");
- ERROR("Matches: %i %i %i\n", used[0], used[1], used[2]);
- return NULL;
- }
-
- /* Flip c if not right-handed */
- if ( !right_handed_vec(real_a, real_b, real_c) ) {
- real_c.u = -real_c.u;
- real_c.v = -real_c.v;
- real_c.w = -real_c.w;
- }
-
- new_cell = cell_new_from_direct_axes(real_a, real_b, real_c);
-
- /* Reverse the de-centering transformation */
- new_cell_trans = cell_transform_intmat_inverse(new_cell, to_given_cell);
- cell_free(new_cell);
- cell_set_lattice_type(new_cell, cell_get_lattice_type(template_in));
- cell_set_centering(new_cell, cell_get_centering(template_in));
- cell_set_unique_axis(new_cell, cell_get_unique_axis(template_in));
-
- return new_cell_trans;
-}
-
-
/* Return sin(theta)/lambda = 1/2d. Multiply by two if you want 1/d */
double resolution(UnitCell *cell, signed int h, signed int k, signed int l)
{
diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h
index bb1e5cd0..5b705247 100644
--- a/libcrystfel/src/cell-utils.h
+++ b/libcrystfel/src/cell-utils.h
@@ -59,11 +59,6 @@ extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi,
extern void cell_print(UnitCell *cell);
extern void cell_print_full(UnitCell *cell);
-extern UnitCell *match_cell(UnitCell *cell, UnitCell *tempcell, int verbose,
- const float *ltl, int reduce);
-
-extern UnitCell *match_cell_ab(UnitCell *cell, UnitCell *tempcell);
-
extern UnitCell *load_cell_from_pdb(const char *filename);
extern UnitCell *load_cell_from_file(const char *filename);
extern void write_cell(UnitCell *cell, FILE *fh);
diff --git a/tests/cellcompare_check.c b/tests/cellcompare_check.c
index 107702c4..7aa59fe4 100644
--- a/tests/cellcompare_check.c
+++ b/tests/cellcompare_check.c
@@ -217,7 +217,7 @@ static void yaro_test()
UnitCell *cell;
UnitCell *reference;
UnitCell *cmatch;
- float tols[] = {5, 5, 5, 1.5};
+ //float tols[] = {5, 5, 5, 1.5};
double dtols[] = {0.05, 0.05, 0.05, deg2rad(5.0), deg2rad(5.0), deg2rad(5.0)};
cell = cell_new_from_parameters(63.24e-10, 63.94e-10, 64.61e-10,
@@ -236,10 +236,10 @@ static void yaro_test()
cell_print(cell);
STATUS("The reference:\n");
cell_print(reference);
- cmatch = match_cell(cell, reference, 0, tols, 1);
- STATUS("The match:\n");
- cell_print(cmatch);
- cell_free(cmatch);
+ //cmatch = match_cell(cell, reference, 0, tols, 1);
+ //STATUS("The match:\n");
+ //cell_print(cmatch);
+ //cell_free(cmatch);
RationalMatrix *m = NULL;
cmatch = compare_reindexed_cell_parameters(cell, reference, dtols, &m);
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-28 03:54:35 +0000