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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 <glib.h>
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <pty.h>
#include <unistd.h>
#include <sys/wait.h>
#include <fcntl.h>
#include <assert.h>
#include <sys/ioctl.h>
#include <termio.h>
#include <sgtty.h>
#include "image.h"
#include "dirax.h"
#include "utils.h"
#include "sfac.h"
#include "peaks.h"
typedef enum {
DIRAX_INPUT_NONE,
DIRAX_INPUT_LINE,
DIRAX_INPUT_PROMPT
} DirAxInputType;
static void dirax_parseline(const char *line, struct image *image)
{
int i, rf;
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);
if ( strstr(line, "reflections from file") ) {
ERROR("DirAx can't understand this data.");
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->indexed_cell = 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, d;
sscanf(line, "%f %f %f %f %f %f", &d, &d, &d, &ax, &ay, &az);
cell_set_cartesian_a(image->indexed_cell,
ax*1e-10, ay*1e-10, az*1e-10);
image->dirax_read_cell++;
return;
} else if ( image->dirax_read_cell == 2 ) {
/* First row of unit cell values */
float bx, by, bz, d;
sscanf(line, "%f %f %f %f %f %f", &d, &d, &d, &bx, &by, &bz);
cell_set_cartesian_b(image->indexed_cell,
bx*1e-10, by*1e-10, bz*1e-10);
image->dirax_read_cell++;
return;
} else if ( image->dirax_read_cell == 3 ) {
/* First row of unit cell values */
float cx, cy, cz, d;
sscanf(line, "%f %f %f %f %f %f", &d, &d, &d, &cx, &cy, &cz);
cell_set_cartesian_c(image->indexed_cell,
cx*1e-10, cy*1e-10, cz*1e-10);
image->dirax_read_cell = 0;
return;
}
image->dirax_read_cell = 0;
}
static void dirax_sendline(const char *line, struct image *image)
{
char *copy;
int i;
write(image->dirax_pty, line, strlen(line));
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);
}
static void dirax_send_next(struct image *image)
{
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 :
/* Skip DirAx's 'acl' prompt */
dirax_sendline("\n", image);
break;
case 9 :
dirax_sendline("cell\n", image);
break;
default:
image->dirax_step = 0;
g_main_loop_quit(image->dirax_ml);
return;
}
image->dirax_step++;
}
static gboolean dirax_readable(GIOChannel *dirax, GIOCondition condition,
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) ) {
ERROR("Lost connection to DirAx (rval=%i)\n", rval);
waitpid(image->dirax_pid, NULL, 0);
g_io_channel_shutdown(image->dirax, FALSE, NULL);
image->dirax = NULL;
return FALSE;
}
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 ) {
if ( (strncmp(image->dirax_rbuffer+i,
"Dirax> ", 7) == 0)
|| (strncmp(image->dirax_rbuffer+i,
"PROMPT:", 7) == 0)
|| (strncmp(image->dirax_rbuffer+i,
"acl/auto:", 8) == 0) ) {
block_ready = 1;
type = DIRAX_INPUT_PROMPT;
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;
default :
/* Obviously, this never happens :) */
ERROR("Unrecognised DirAx input mode! "
"I don't know how to understand DirAx\n");
waitpid(image->dirax_pid, NULL, 0);
g_io_channel_shutdown(image->dirax, FALSE, NULL);
image->dirax = NULL;
return FALSE;
}
/* 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 TRUE;
}
void run_dirax(struct image *image)
{
unsigned int opts;
int saved_stderr;
int status;
saved_stderr = dup(STDERR_FILENO);
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);
/* Reconnect stderr */
dup2(saved_stderr, STDERR_FILENO);
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->dirax = g_io_channel_unix_new(image->dirax_pty);
g_io_add_watch(image->dirax, G_IO_IN | G_IO_HUP,
(GIOFunc)dirax_readable, image);
image->dirax_ml = g_main_loop_new(NULL, FALSE);
g_main_loop_run(image->dirax_ml);
close(image->dirax_pty);
wait(&status);
return;
}
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