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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>
#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 "sfac.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;
static void dirax_parseline(const char *line, struct image *image)
{
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 ) {
image->dirax_read_cell = 1;
image->candidate_cells[image->ncells] = cell_new();
return;
}
i++;
}
/* Parse unit cell vectors as appropriate */
if ( image->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");
image->dirax_read_cell = 0;
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);
image->dirax_read_cell++;
return;
} else if ( image->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");
image->dirax_read_cell = 0;
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);
image->dirax_read_cell++;
return;
} else if ( image->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");
image->dirax_read_cell = 0;
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);
image->dirax_read_cell = 0;
return;
}
image->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 > image->best_acl_nh ) {
int i, found = 0;
for ( i=0; i<image->n_acls_tried; i++ ) {
if ( image->acls_tried[i] == acl ) found = 1;
}
if ( !found ) {
image->best_acl_nh = acl_nh;
image->best_acl = acl;
}
}
}
}
static void dirax_sendline(const char *line, struct image *image)
{
#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(image->dirax_pty, line, strlen(line));
}
static void dirax_send_next(struct image *image)
{
char tmp[32];
switch ( image->dirax_step ) {
case 1 :
dirax_sendline("\\echo off\n", image);
break;
case 2 :
dirax_sendline("read xfel.drx\n", image);
break;
case 3 :
dirax_sendline("dmax 1000\n", image);
break;
case 4 :
dirax_sendline("indexfit 2\n", image);
break;
case 5 :
dirax_sendline("levelfit 1000\n", image);
break;
case 6 :
dirax_sendline("go\n", image);
break;
case 7 :
dirax_sendline("acl\n", image);
break;
case 8 :
if ( image->best_acl_nh == 0 ) {
STATUS("No more cells to try.\n");
/* 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", image);
break;
}
snprintf(tmp, 31, "%i\n", image->best_acl);
image->acls_tried[image->n_acls_tried++] = image->best_acl;
dirax_sendline(tmp, image);
break;
case 9 :
dirax_sendline("cell\n", image);
break;
case 10 :
if ( image->n_acls_tried == MAX_DIRAX_CELL_CANDIDATES ) {
dirax_sendline("exit\n", image);
} else {
/* Go back round for another cell */
image->best_acl_nh = 0;
image->dirax_step = 7;
dirax_sendline("acl\n", image);
}
break;
default:
dirax_sendline("exit\n", image);
return;
}
image->dirax_step++;
}
static int dirax_readable(struct image *image)
{
int rval;
int no_string = 0;
rval = read(image->dirax_pty, image->dirax_rbuffer+image->dirax_rbufpos,
image->dirax_rbuflen-image->dirax_rbufpos);
if ( (rval == -1) || (rval == 0) ) return 1;
image->dirax_rbufpos += rval;
assert(image->dirax_rbufpos <= image->dirax_rbuflen);
while ( (!no_string) && (image->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<image->dirax_rbufpos-1; i++ ) {
/* Means the last value looked at is rbufpos-2 */
/* Is there a prompt in the buffer? */
if ( (i+7 <= image->dirax_rbufpos)
&& (!strncmp(image->dirax_rbuffer+i, "Dirax> ", 7)) ) {
block_ready = 1;
type = DIRAX_INPUT_PROMPT;
break;
}
/* How about an ACL prompt? */
if ( (i+10 <= image->dirax_rbufpos)
&& (!strncmp(image->dirax_rbuffer+i, "acl/auto [", 10)) ) {
block_ready = 1;
type = DIRAX_INPUT_ACL;
break;
}
if ( (image->dirax_rbuffer[i] == '\r')
&& (image->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, image->dirax_rbuffer, i);
block_buffer[i] = '\0';
if ( block_buffer[0] == '\r' ) {
memmove(block_buffer, block_buffer+1, i);
}
dirax_parseline(block_buffer, image);
free(block_buffer);
endbit_length = i+2;
break;
case DIRAX_INPUT_PROMPT :
dirax_send_next(image);
endbit_length = i+7;
break;
case DIRAX_INPUT_ACL :
dirax_send_next(image);
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(image->dirax_rbuffer,
image->dirax_rbuffer + endbit_length,
image->dirax_rbuflen - endbit_length);
/* Subtract the number of bytes removed */
image->dirax_rbufpos = image->dirax_rbufpos
- endbit_length;
new_rbuflen = image->dirax_rbuflen - endbit_length;
if ( new_rbuflen == 0 ) new_rbuflen = 256;
image->dirax_rbuffer = realloc(image->dirax_rbuffer,
new_rbuflen);
image->dirax_rbuflen = new_rbuflen;
} else {
if ( image->dirax_rbufpos==image->dirax_rbuflen ) {
/* More buffer space is needed */
image->dirax_rbuffer = realloc(
image->dirax_rbuffer,
image->dirax_rbuflen + 256);
image->dirax_rbuflen = image->dirax_rbuflen
+ 256;
/* The new space gets used at the next
* read, shortly... */
}
no_string = 1;
}
}
return 0;
}
void run_dirax(struct image *image)
{
unsigned int opts;
int status;
int rval;
image->dirax_pid = forkpty(&image->dirax_pty, NULL, NULL, NULL);
if ( image->dirax_pid == -1 ) {
ERROR("Failed to fork for DirAx\n");
return;
}
if ( image->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);
}
image->dirax_rbuffer = malloc(256);
image->dirax_rbuflen = 256;
image->dirax_rbufpos = 0;
/* Set non-blocking */
opts = fcntl(image->dirax_pty, F_GETFL);
fcntl(image->dirax_pty, F_SETFL, opts | O_NONBLOCK);
image->dirax_step = 1; /* This starts the "initialisation" procedure */
image->dirax_read_cell = 0;
image->n_acls_tried = 0;
image->best_acl_nh = 0;
do {
fd_set fds;
struct timeval tv;
int sval;
FD_ZERO(&fds);
FD_SET(image->dirax_pty, &fds);
tv.tv_sec = 10;
tv.tv_usec = 0;
sval = select(image->dirax_pty+1, &fds, NULL, NULL, &tv);
if ( sval == -1 ) {
ERROR("select() failed.\n");
rval = 1;
} else if ( sval != 0 ) {
rval = dirax_readable(image);
} else {
ERROR("No response from DirAx..\n");
rval = 1;
}
} while ( !rval );
close(image->dirax_pty);
free(image->dirax_rbuffer);
wait(&status);
return;
}
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