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-rw-r--r--libcrystfel/src/dirax.c529
1 files changed, 529 insertions, 0 deletions
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
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+++ b/libcrystfel/src/dirax.c
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+/*
+ * 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);
+}
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