diff options
| -rw-r--r-- | libcrystfel/src/cell-utils.c | 4 | ||||
| -rw-r--r-- | libcrystfel/src/cell-utils.h | 9 | ||||
| -rw-r--r-- | src/cell_tool.c | 47 |
3 files changed, 19 insertions, 41 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c index 7b1984bb..852887a6 100644 --- a/libcrystfel/src/cell-utils.c +++ b/libcrystfel/src/cell-utils.c @@ -1703,8 +1703,8 @@ static double moduli_check(double ax, double ay, double az, } -static int cells_are_similar(UnitCell *cell1, UnitCell *cell2, - const double ltl, const double atl) +int cells_are_similar(UnitCell *cell1, UnitCell *cell2, + const double ltl, const double atl) { double asx1, asy1, asz1, bsx1, bsy1, bsz1, csx1, csy1, csz1; double asx2, asy2, asz2, bsx2, bsy2, bsz2, csx2, csy2, csz2; diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h index 5e2b2825..cc721634 100644 --- a/libcrystfel/src/cell-utils.h +++ b/libcrystfel/src/cell-utils.h @@ -3,13 +3,13 @@ * * Unit Cell utility functions * - * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Lorenzo Galli * * Authors: - * 2009-2013,2014,2017 Thomas White <taw@physics.org> - * 2012 Lorenzo Galli + * 2009-2018 Thomas White <taw@physics.org> + * 2012 Lorenzo Galli * * This file is part of CrystFEL. * @@ -53,6 +53,9 @@ extern UnitCell *transform_cell_gsl(UnitCell *in, gsl_matrix *m); extern void cell_print(UnitCell *cell); +extern int cells_are_similar(UnitCell *cell1, UnitCell *cell2, + const double ltl, const double atl); + extern UnitCell *match_cell(UnitCell *cell, UnitCell *tempcell, int verbose, const float *ltl, int reduce); diff --git a/src/cell_tool.c b/src/cell_tool.c index 1403b394..4a719391 100644 --- a/src/cell_tool.c +++ b/src/cell_tool.c @@ -62,37 +62,12 @@ static void show_help(const char *s) " --compare-cell <file> Compare unit cell with cell from <file>.\n" "\n" " -y <pointgroup> Real point group of the structure.\n" -" --tolerance=<tol> Set the tolerances for cell reduction.\n" -" Default: 5,5,5,1.5.\n" +" --tolerance=<tol> Set the tolerances for cell comparison.\n" +" Default: 5,1.5 (axis percentage, angle deg).\n" ); } -static int cells_are_similar(UnitCell *cell1, UnitCell *cell2, float *tols) -{ - double a1, b1, c1, al1, be1, ga1; - double a2, b2, c2, al2, be2, ga2; - UnitCellTransformation *tfn1, *tfn2; - UnitCell *pcell1, *pcell2; - - /* Compare primitive cells, not centered */ - pcell1 = uncenter_cell(cell1, &tfn1); - pcell2 = uncenter_cell(cell2, &tfn2); - - cell_get_parameters(pcell1, &a1, &b1, &c1, &al1, &be1, &ga1); - cell_get_parameters(pcell2, &a2, &b2, &c2, &al2, &be2, &ga2); - - cell_free(pcell1); - cell_free(pcell2); - - if ( !within_tolerance(a1, a2, tols[0]) ) return 0; - if ( !within_tolerance(b1, b2, tols[1]) ) return 0; - if ( !within_tolerance(c1, c2, tols[2]) ) return 0; - if ( !within_tolerance(al1, al2, tols[3]) ) return 0; - if ( !within_tolerance(be1, be2, tols[3]) ) return 0; - if ( !within_tolerance(ga1, ga2, tols[3]) ) return 0; - - return 1; } @@ -205,7 +180,7 @@ static int all_rings(UnitCell *cell, SymOpList *sym) } -static int find_ambi(UnitCell *cell, SymOpList *sym, float *tols) +static int find_ambi(UnitCell *cell, SymOpList *sym, double ltl, double atl) { SymOpList *amb; SymOpList *ops; @@ -252,7 +227,7 @@ static int find_ambi(UnitCell *cell, SymOpList *sym, float *tols) tfn = tfn_from_intmat(m); nc = cell_transform(cell, tfn); - if ( cells_are_similar(cell, nc, tols) ) { + if ( cells_are_similar(cell, nc, ltl, atl) ) { if ( !intmat_is_identity(m) ) add_symop(ops, m); STATUS("-----------------------------------------------" "-------------------------------------------\n"); @@ -336,7 +311,8 @@ int main(int argc, char *argv[]) char *cell_file = NULL; UnitCell *cell; char *toler = NULL; - float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */ + double ltl = 5.0/100.0; + double atl = deg2rad(1.5); char *sym_str = NULL; SymOpList *sym = NULL; int mode = CT_NOTHING; @@ -414,13 +390,12 @@ int main(int argc, char *argv[]) free(cell_file); if ( toler != NULL ) { - int ttt; - ttt = sscanf(toler, "%f,%f,%f,%f", - &tols[0], &tols[1], &tols[2], &tols[3] ); - if ( ttt != 4 ) { - ERROR("Invalid parameters for '--tolerance'\n"); + if ( sscanf(toler, "%f,%f", <l, &atl) != 2 ) { + ERROR("Invalid parameters for --tolerance\n"); return 1; } + ltl /= 100.0; /* Percent to fraction */ + atl = deg2rad(atl); free(toler); } @@ -443,7 +418,7 @@ int main(int argc, char *argv[]) return 1; } - if ( mode == CT_FINDAMBI ) return find_ambi(cell, sym, tols); + if ( mode == CT_FINDAMBI ) return find_ambi(cell, sym, ltl, atl); if ( mode == CT_UNCENTER ) return uncenter(cell, out_file); if ( mode == CT_RINGS ) return all_rings(cell, sym); |