diff options
Diffstat (limited to 'src/dirax.c')
| -rw-r--r-- | src/dirax.c | 529 |
1 files changed, 0 insertions, 529 deletions
diff --git a/src/dirax.c b/src/dirax.c deleted file mode 100644 index bb1cb808..00000000 --- a/src/dirax.c +++ /dev/null @@ -1,529 +0,0 @@ -/* - * dirax.c - * - * Invoke the DirAx auto-indexing program - * - * (c) 2006-2010 Thomas White <taw@physics.org> - * - * Part of CrystFEL - crystallography with a FEL - * - */ - - -#ifdef HAVE_CONFIG_H -#include <config.h> -#endif - - -#include <stdlib.h> -#include <stdio.h> -#include <math.h> -#include <string.h> -#include <unistd.h> -#include <sys/wait.h> -#include <fcntl.h> -#include <assert.h> -#include <sys/ioctl.h> -#include <errno.h> - -#if HAVE_FORKPTY_LINUX -#include <pty.h> -#elif HAVE_FORKPTY_BSD -#include <util.h> -#endif - - -#include "image.h" -#include "dirax.h" -#include "utils.h" -#include "peaks.h" - - -#define DIRAX_VERBOSE 0 - -#define MAX_DIRAX_CELL_CANDIDATES (5) - - -typedef enum { - DIRAX_INPUT_NONE, - DIRAX_INPUT_LINE, - DIRAX_INPUT_PROMPT, - DIRAX_INPUT_ACL -} DirAxInputType; - - -struct dirax_data { - - /* DirAx auto-indexing low-level stuff */ - int pty; - pid_t pid; - char *rbuffer; - int rbufpos; - int rbuflen; - - /* DirAx auto-indexing high-level stuff */ - int step; - int finished_ok; - int read_cell; - int best_acl; - int best_acl_nh; - int acls_tried[MAX_CELL_CANDIDATES]; - int n_acls_tried; - -}; - - -static void dirax_parseline(const char *line, struct image *image, - struct dirax_data *dirax) -{ - int rf, i, di, acl, acl_nh; - float d; - - #if DIRAX_VERBOSE - char *copy; - - copy = strdup(line); - for ( i=0; i<strlen(copy); i++ ) { - if ( copy[i] == '\r' ) copy[i]='r'; - if ( copy[i] == '\n' ) copy[i]='\0'; - } - STATUS("DirAx: %s\n", copy); - free(copy); - #endif - - if ( strstr(line, "reflections from file") ) { - ERROR("DirAx can't understand this data.\n"); - return; - } - - /* Is this the first line of a unit cell specification? */ - rf = 0; i = 0; - while ( (i<strlen(line)) && ((line[i] == 'R') - || (line[i] == 'D') || (line[i] == ' ')) ) { - if ( line[i] == 'R' ) rf = 1; - if ( (line[i] == 'D') && rf ) { - dirax->read_cell = 1; - image->candidate_cells[image->ncells] = cell_new(); - return; - } - i++; - } - - /* Parse unit cell vectors as appropriate */ - if ( dirax->read_cell == 1 ) { - /* First row of unit cell values */ - float ax, ay, az; - int r; - r = sscanf(line, "%f %f %f %f %f %f", - &d, &d, &d, &ax, &ay, &az); - if ( r != 6 ) { - ERROR("Couldn't understand cell line:\n"); - ERROR("'%s'\n", line); - dirax->read_cell = 0; - cell_free(image->candidate_cells[image->ncells]); - return; - } - cell_set_cartesian_a(image->candidate_cells[image->ncells], - 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; - r = sscanf(line, "%f %f %f %f %f %f", - &d, &d, &d, &bx, &by, &bz); - if ( r != 6 ) { - ERROR("Couldn't understand cell line:\n"); - ERROR("'%s'\n", line); - dirax->read_cell = 0; - cell_free(image->candidate_cells[image->ncells]); - return; - } - cell_set_cartesian_b(image->candidate_cells[image->ncells], - 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; - r = sscanf(line, "%f %f %f %f %f %f", - &d, &d, &d, &cx, &cy, &cz); - if ( r != 6 ) { - ERROR("Couldn't understand cell line:\n"); - ERROR("'%s'\n", line); - dirax->read_cell = 0; - cell_free(image->candidate_cells[image->ncells]); - return; - } - cell_set_cartesian_c(image->candidate_cells[image->ncells++], - cx*1e-10, cy*1e-10, cz*1e-10); - dirax->read_cell = 0; - return; - } - - dirax->read_cell = 0; - - if ( sscanf(line, "%i %i %f %f %f %f %f %f %i", &acl, &acl_nh, - &d, &d, &d, &d, &d, &d, &di) == 9 ) { - if ( acl_nh > dirax->best_acl_nh ) { - - int i, found = 0; - - for ( i=0; i<dirax->n_acls_tried; i++ ) { - if ( dirax->acls_tried[i] == acl ) found = 1; - } - - if ( !found ) { - dirax->best_acl_nh = acl_nh; - dirax->best_acl = acl; - } - - } - } -} - - -static void dirax_sendline(const char *line, struct dirax_data *dirax) -{ - #if DIRAX_VERBOSE - char *copy; - int i; - - copy = strdup(line); - for ( i=0; i<strlen(copy); i++ ) { - if ( copy[i] == '\r' ) copy[i]='\0'; - if ( copy[i] == '\n' ) copy[i]='\0'; - } - STATUS("To DirAx: '%s'\n", copy); - free(copy); - #endif - - write(dirax->pty, line, strlen(line)); -} - - -static void dirax_send_next(struct image *image, struct dirax_data *dirax) -{ - char tmp[32]; - - switch ( dirax->step ) { - - case 1 : - dirax_sendline("\\echo off\n", dirax); - break; - - case 2 : - snprintf(tmp, 31, "read xfel-%i.drx\n", image->id); - dirax_sendline(tmp, dirax); - break; - - case 3 : - dirax_sendline("dmax 1000\n", dirax); - break; - - case 4 : - dirax_sendline("indexfit 2\n", dirax); - break; - - case 5 : - dirax_sendline("levelfit 1000\n", dirax); - break; - - case 6 : - dirax_sendline("go\n", dirax); - dirax->finished_ok = 1; - break; - - case 7 : - dirax_sendline("acl\n", dirax); - break; - - case 8 : - if ( dirax->best_acl_nh == 0 ) { - /* At this point, DirAx is presenting its ACL prompt - * and waiting for a single number. Use an extra - * newline to choose automatic ACL selection before - * exiting. */ - dirax_sendline("\nexit\n", dirax); - break; - } - snprintf(tmp, 31, "%i\n", dirax->best_acl); - dirax->acls_tried[dirax->n_acls_tried++] = dirax->best_acl; - dirax_sendline(tmp, dirax); - break; - - case 9 : - dirax_sendline("cell\n", dirax); - break; - - case 10 : - if ( dirax->n_acls_tried == MAX_DIRAX_CELL_CANDIDATES ) { - dirax_sendline("exit\n", dirax); - } else { - /* Go back round for another cell */ - dirax->best_acl_nh = 0; - dirax->step = 7; - dirax_sendline("acl\n", dirax); - } - break; - - default: - dirax_sendline("exit\n", dirax); - return; - - } - - dirax->step++; -} - - -static int dirax_readable(struct image *image, struct dirax_data *dirax) -{ - int rval; - int no_string = 0; - - rval = read(dirax->pty, dirax->rbuffer+dirax->rbufpos, - dirax->rbuflen-dirax->rbufpos); - - if ( (rval == -1) || (rval == 0) ) return 1; - - dirax->rbufpos += rval; - assert(dirax->rbufpos <= dirax->rbuflen); - - while ( (!no_string) && (dirax->rbufpos > 0) ) { - - int i; - int block_ready = 0; - DirAxInputType type = DIRAX_INPUT_NONE; - - /* See if there's a full line in the buffer yet */ - for ( i=0; i<dirax->rbufpos-1; i++ ) { - /* Means the last value looked at is rbufpos-2 */ - - /* Is there a prompt in the buffer? */ - if ( (i+7 <= dirax->rbufpos) - && (!strncmp(dirax->rbuffer+i, "Dirax> ", 7)) ) { - block_ready = 1; - type = DIRAX_INPUT_PROMPT; - break; - } - - /* How about an ACL prompt? */ - if ( (i+10 <= dirax->rbufpos) - && (!strncmp(dirax->rbuffer+i, "acl/auto [", 10)) ) { - block_ready = 1; - type = DIRAX_INPUT_ACL; - break; - } - - if ( (dirax->rbuffer[i] == '\r') - && (dirax->rbuffer[i+1] == '\n') ) { - block_ready = 1; - type = DIRAX_INPUT_LINE; - break; - } - - } - - if ( block_ready ) { - - unsigned int new_rbuflen; - unsigned int endbit_length; - char *block_buffer = NULL; - - switch ( type ) { - - case DIRAX_INPUT_LINE : - - block_buffer = malloc(i+1); - memcpy(block_buffer, dirax->rbuffer, i); - block_buffer[i] = '\0'; - - if ( block_buffer[0] == '\r' ) { - memmove(block_buffer, block_buffer+1, i); - } - - dirax_parseline(block_buffer, image, dirax); - free(block_buffer); - endbit_length = i+2; - break; - - case DIRAX_INPUT_PROMPT : - - dirax_send_next(image, dirax); - endbit_length = i+7; - break; - - case DIRAX_INPUT_ACL : - - dirax_send_next(image,dirax ); - endbit_length = i+10; - break; - - default : - - /* Obviously, this never happens :) */ - ERROR("Unrecognised DirAx input mode! " - "I don't know how to understand DirAx\n"); - return 1; - - } - - /* Now the block's been parsed, it should be - * forgotten about */ - memmove(dirax->rbuffer, - dirax->rbuffer + endbit_length, - dirax->rbuflen - endbit_length); - - /* Subtract the number of bytes removed */ - dirax->rbufpos = dirax->rbufpos - - endbit_length; - new_rbuflen = dirax->rbuflen - endbit_length; - if ( new_rbuflen == 0 ) new_rbuflen = 256; - dirax->rbuffer = realloc(dirax->rbuffer, - new_rbuflen); - dirax->rbuflen = new_rbuflen; - - } else { - - if ( dirax->rbufpos==dirax->rbuflen ) { - - /* More buffer space is needed */ - dirax->rbuffer = realloc( - dirax->rbuffer, - dirax->rbuflen + 256); - dirax->rbuflen = dirax->rbuflen - + 256; - /* The new space gets used at the next - * read, shortly... */ - - } - no_string = 1; - - } - - } - - return 0; -} - - -static void write_drx(struct image *image) -{ - FILE *fh; - int i; - char filename[1024]; - - snprintf(filename, 1023, "xfel-%i.drx", image->id); - - fh = fopen(filename, "w"); - if ( !fh ) { - ERROR("Couldn't open temporary file '%s'\n", filename); - return; - } - fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */ - - for ( i=0; i<image_feature_count(image->features); i++ ) { - - struct imagefeature *f; - - f = image_get_feature(image->features, i); - if ( f == NULL ) continue; - - fprintf(fh, "%10f %10f %10f %8f\n", - f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0); - - } - fclose(fh); -} - - -void run_dirax(struct image *image) -{ - unsigned int opts; - int status; - int rval; - struct dirax_data *dirax; - - write_drx(image); - - dirax = malloc(sizeof(struct dirax_data)); - if ( dirax == NULL ) { - ERROR("Couldn't allocate memory for DirAx data.\n"); - return; - } - - dirax->pid = forkpty(&dirax->pty, NULL, NULL, NULL); - if ( dirax->pid == -1 ) { - ERROR("Failed to fork for DirAx\n"); - return; - } - if ( dirax->pid == 0 ) { - - /* Child process: invoke DirAx */ - struct termios t; - - /* Turn echo off */ - tcgetattr(STDIN_FILENO, &t); - t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); - tcsetattr(STDIN_FILENO, TCSANOW, &t); - - execlp("dirax", "", (char *)NULL); - ERROR("Failed to invoke DirAx.\n"); - _exit(0); - - } - - dirax->rbuffer = malloc(256); - dirax->rbuflen = 256; - dirax->rbufpos = 0; - - /* Set non-blocking */ - opts = fcntl(dirax->pty, F_GETFL); - fcntl(dirax->pty, F_SETFL, opts | O_NONBLOCK); - - dirax->step = 1; /* This starts the "initialisation" procedure */ - dirax->finished_ok = 0; - dirax->read_cell = 0; - dirax->n_acls_tried = 0; - dirax->best_acl_nh = 0; - - do { - - fd_set fds; - struct timeval tv; - int sval; - - FD_ZERO(&fds); - FD_SET(dirax->pty, &fds); - - tv.tv_sec = 10; - tv.tv_usec = 0; - - sval = select(dirax->pty+1, &fds, NULL, NULL, &tv); - - if ( sval == -1 ) { - int err = errno; - ERROR("select() failed: %s\n", strerror(err)); - rval = 1; - } else if ( sval != 0 ) { - rval = dirax_readable(image, dirax); - } else { - ERROR("No response from DirAx..\n"); - rval = 1; - } - - } while ( !rval ); - - close(dirax->pty); - free(dirax->rbuffer); - waitpid(dirax->pid, &status, 0); - - if ( dirax->finished_ok == 0 ) { - ERROR("DirAx doesn't seem to be working properly.\n"); - } - - free(dirax); -} |