From e132f0a215392b13bf289cad55f2fece6e193625 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Mon, 4 Feb 2013 17:42:40 +0100 Subject: Indexing stuff --- libcrystfel/src/dirax.c | 123 ++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 104 insertions(+), 19 deletions(-) (limited to 'libcrystfel/src/dirax.c') diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c index 160df719..0b2debda 100644 --- a/libcrystfel/src/dirax.c +++ b/libcrystfel/src/dirax.c @@ -53,6 +53,7 @@ #include "dirax.h" #include "utils.h" #include "peaks.h" +#include "cell-utils.h" #define DIRAX_VERBOSE 0 @@ -68,6 +69,13 @@ typedef enum { } DirAxInputType; +struct dirax_private { + IndexingMethod indm; + float *ltl; + UnitCell *template; +}; + + struct dirax_data { /* DirAx auto-indexing low-level stuff */ @@ -85,10 +93,56 @@ struct dirax_data { int best_acl_nh; int acls_tried[MAX_CELL_CANDIDATES]; int n_acls_tried; + UnitCell *cur_cell; + int done; + int success; + + struct dirax_private *dp; }; +static int check_cell(struct dirax_private *dp, struct image *image, + UnitCell *cell) +{ + UnitCell *out; + Crystal *cr; + + if ( dp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) { + + out = match_cell(cell, dp->template, 0, dp->ltl, 1); + if ( out == NULL ) return 0; + + } else if ( dp->indm & INDEXING_CHECK_CELL_AXES ) { + + out = match_cell(cell, dp->template, 0, dp->ltl, 0); + if ( out == NULL ) return 0; + + } else { + out = cell_new_from_cell(cell); + } + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to allocate crystal.\n"); + return 0; + } + + crystal_set_cell(cr, cell); + + if ( dp->indm & INDEXING_CHECK_PEAKS ) { + if ( !peak_sanity_check(image, &cr, 1) ) { + crystal_free(cr); /* Frees the cell as well */ + return 0; + } + } + + image_add_crystal(image, cr); + + return 1; +} + + static void dirax_parseline(const char *line, struct image *image, struct dirax_data *dirax) { @@ -119,7 +173,7 @@ static void dirax_parseline(const char *line, struct image *image, if ( line[i] == 'R' ) rf = 1; if ( (line[i] == 'D') && rf ) { dirax->read_cell = 1; - image->candidate_cells[image->ncells] = cell_new(); + dirax->cur_cell = cell_new(); return; } i++; @@ -127,6 +181,7 @@ static void dirax_parseline(const char *line, struct image *image, /* Parse unit cell vectors as appropriate */ if ( dirax->read_cell == 1 ) { + /* First row of unit cell values */ float ax, ay, az; int r; @@ -136,14 +191,16 @@ static void dirax_parseline(const char *line, struct image *image, ERROR("Couldn't understand cell line:\n"); ERROR("'%s'\n", line); dirax->read_cell = 0; - cell_free(image->candidate_cells[image->ncells]); + cell_free(dirax->cur_cell); return; } - cell_set_cartesian_a(image->candidate_cells[image->ncells], + cell_set_cartesian_a(dirax->cur_cell, ax*1e-10, ay*1e-10, az*1e-10); dirax->read_cell++; return; + } else if ( dirax->read_cell == 2 ) { + /* Second row of unit cell values */ float bx, by, bz; int r; @@ -153,14 +210,16 @@ static void dirax_parseline(const char *line, struct image *image, ERROR("Couldn't understand cell line:\n"); ERROR("'%s'\n", line); dirax->read_cell = 0; - cell_free(image->candidate_cells[image->ncells]); + cell_free(dirax->cur_cell); return; } - cell_set_cartesian_b(image->candidate_cells[image->ncells], + cell_set_cartesian_b(dirax->cur_cell, bx*1e-10, by*1e-10, bz*1e-10); dirax->read_cell++; return; + } else if ( dirax->read_cell == 3 ) { + /* Third row of unit cell values */ float cx, cy, cz; int r; @@ -170,13 +229,21 @@ static void dirax_parseline(const char *line, struct image *image, ERROR("Couldn't understand cell line:\n"); ERROR("'%s'\n", line); dirax->read_cell = 0; - cell_free(image->candidate_cells[image->ncells]); + cell_free(dirax->cur_cell); return; } - cell_set_cartesian_c(image->candidate_cells[image->ncells++], + cell_set_cartesian_c(dirax->cur_cell, cx*1e-10, cy*1e-10, cz*1e-10); dirax->read_cell = 0; + + /* Finished reading a cell. Time to check it... */ + if ( check_cell(dirax->dp, image, dirax->cur_cell) ) { + dirax->done = 1; + dirax->success = 1; + } + return; + } dirax->read_cell = 0; @@ -351,8 +418,7 @@ static int dirax_readable(struct image *image, struct dirax_data *dirax) switch ( type ) { - case DIRAX_INPUT_LINE : - + case DIRAX_INPUT_LINE : block_buffer = malloc(i+1); memcpy(block_buffer, dirax->rbuffer, i); block_buffer[i] = '\0'; @@ -366,20 +432,17 @@ static int dirax_readable(struct image *image, struct dirax_data *dirax) endbit_length = i+2; break; - case DIRAX_INPUT_PROMPT : - + case DIRAX_INPUT_PROMPT : dirax_send_next(image, dirax); endbit_length = i+7; break; - case DIRAX_INPUT_ACL : - + case DIRAX_INPUT_ACL : dirax_send_next(image,dirax ); endbit_length = i+10; break; - default : - + default : /* Obviously, this never happens :) */ ERROR("Unrecognised DirAx input mode! " "I don't know how to understand DirAx\n"); @@ -456,7 +519,7 @@ static void write_drx(struct image *image) } -void run_dirax(struct image *image) +int run_dirax(struct image *image, IndexingPrivate *ipriv) { unsigned int opts; int status; @@ -468,13 +531,13 @@ void run_dirax(struct image *image) dirax = malloc(sizeof(struct dirax_data)); if ( dirax == NULL ) { ERROR("Couldn't allocate memory for DirAx data.\n"); - return; + return 0; } dirax->pid = forkpty(&dirax->pty, NULL, NULL, NULL); if ( dirax->pid == -1 ) { ERROR("Failed to fork for DirAx: %s\n", strerror(errno)); - return; + return 0; } if ( dirax->pid == 0 ) { @@ -505,6 +568,9 @@ void run_dirax(struct image *image) dirax->read_cell = 0; dirax->n_acls_tried = 0; dirax->best_acl_nh = 0; + dirax->done = 0; + dirax->success = 0; + dirax->dp = (struct dirax_private *)ipriv; do { @@ -543,7 +609,7 @@ void run_dirax(struct image *image) rval = 1; } - } while ( !rval ); + } while ( !rval && !dirax->success ); close(dirax->pty); free(dirax->rbuffer); @@ -553,5 +619,24 @@ void run_dirax(struct image *image) ERROR("DirAx doesn't seem to be working properly.\n"); } + rval = dirax->success; free(dirax); + return rval; +} + + +IndexingPrivate *dirax_prepare(IndexingMethod indm, UnitCell *cell, + const char *filename, struct detector *det, + struct beam_params *beam, float *ltl) +{ + struct dirax_private *dp; + + dp = malloc(sizeof(struct dirax_private)); + if ( dp == NULL ) return NULL; + + dp->ltl = ltl; + dp->template = cell; + dp->indm = indm; + + return (IndexingPrivate *)dp; } -- cgit v1.2.3