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-rw-r--r--src/dirax.c455
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+/*
+ * dirax.c
+ *
+ * Invoke the DirAx auto-indexing program
+ *
+ * (c) 2006-2009 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"
+
+
+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;
+ if ( image->cell ) {
+ free(image->cell);
+ }
+ image->cell = cell_new();
+ return;
+ }
+ i++;
+ }
+
+ /* Parse unit cell vectors as appropriate */
+ if ( image->dirax_read_cell == 1 ) {
+ /* First row of unit cell values */
+ float x1, x2, x3;
+ sscanf(line, "%f %f %f", &x1, &x2, &x3);
+ cell_set_cartesian_x(image->cell, x1*1e10, x2*1e10, x3*1e10);
+ image->dirax_read_cell++;
+ return;
+ } else if ( image->dirax_read_cell == 2 ) {
+ /* First row of unit cell values */
+ float y1, y2, y3;
+ sscanf(line, "%f %f %f", &y1, &y2, &y3);
+ cell_set_cartesian_y(image->cell, y1*1e10, y2*1e10, y3*1e10);
+ image->dirax_read_cell++;
+ return;
+ } else if ( image->dirax_read_cell == 3 ) {
+ /* First row of unit cell values */
+ float z1, z2, z3;
+ sscanf(line, "%f %f %f", &z1, &z2, &z3);
+ cell_set_cartesian_z(image->cell, z1*1e10, z2*1e10, z3*1e10);
+ STATUS("Read a reciprocal unit cell from DirAx\n");
+ /* FIXME: Do something */
+ 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);
+ image->dirax_step++;
+ break;
+ }
+
+ case 2 : {
+ dirax_sendline("read xfel.drx\n", image);
+ image->dirax_step++;
+ break;
+ }
+
+ case 3 : {
+ dirax_sendline("dmax 10\n", image);
+ image->dirax_step++;
+ break;
+ }
+
+ case 4 : {
+ dirax_sendline("indexfit 2\n", image);
+ image->dirax_step++;
+ break;
+ }
+
+ case 5 : {
+ dirax_sendline("levelfit 200\n", image);
+ image->dirax_step++;
+ break;
+ }
+
+ case 6 : {
+ dirax_sendline("go\n", image);
+ image->dirax_step++;
+ break;
+ }
+
+ case 7 : {
+ dirax_sendline("cell\n", image);
+ image->dirax_step++;
+ break;
+ }
+
+ default: {
+ image->dirax_step = 0;
+ STATUS("DirAx is idle\n");
+ }
+
+ }
+}
+
+
+static gboolean dirax_readable(GIOChannel *dirax, GIOCondition condition,
+ struct image *image)
+{
+ int rval;
+
+ 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\n");
+ waitpid(image->dirax_pid, NULL, 0);
+ g_io_channel_shutdown(image->dirax, FALSE, NULL);
+ image->dirax = NULL;
+ return FALSE;
+
+ } else {
+
+ int no_string = 0;
+
+ 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) ) {
+ 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;
+
+ switch ( type ) {
+
+ case DIRAX_INPUT_LINE : {
+
+ char *block_buffer = NULL;
+
+ 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 : {
+ ERROR(
+ " Unrecognised input mode (this never happens!)\n");
+ abort();
+ }
+
+ }
+
+ /* 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;
+}
+
+
+static int map_position(struct image *image, double x, double y,
+ double *rx, double *ry, double *rz)
+{
+ /* "Input" space */
+ double d;
+
+ /* Angular description of reflection */
+ double theta, psi, k;
+
+ x -= image->x_centre;
+ y -= image->y_centre;
+ k = 1.0 / image->lambda;
+
+ if ( image->fmode == FORMULATION_CLEN ) {
+
+ /* Convert pixels to metres */
+ x /= image->resolution;
+ y /= image->resolution;
+ x = x * k / image->camera_len;
+ y = y * k / image->camera_len;
+ x /= image->resolution;
+ y /= image->resolution; /* Convert pixels to metres */
+ d = sqrt((x*x) + (y*y));
+ theta = atan2(d, image->camera_len);
+
+ } else if (image->fmode == FORMULATION_PIXELSIZE ) {
+
+ /* Convert pixels to metres^-1 */
+ x = x * image->pixel_size;
+ y = y * image->pixel_size;
+ x *= image->pixel_size;
+ y *= image->pixel_size; /* Convert pixels to metres^-1 */
+ d = sqrt((x*x) + (y*y));
+ theta = atan2(d, k);
+
+ } else {
+ ERROR("Unrecognised formulation mode in mapping_scale.\n");
+ return -1;
+ }
+
+ psi = atan2(y, x);
+
+ *rx = k*sin(theta)*cos(psi);
+ *ry = k*sin(theta)*sin(psi);
+ *rz = k - k*cos(theta);
+
+ return 0;
+}
+
+
+void index_pattern(struct image *image)
+{
+ FILE *fh;
+ unsigned int opts;
+ int saved_stderr;
+ int x, y;
+ GMainLoop *ml;
+
+ fh = fopen("xfel.drx", "w");
+ if ( !fh ) {
+ ERROR("Couldn't open temporary file xfel.drx\n");
+ return;
+ }
+ fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */
+
+ for ( x=0; x<image->width; x++ ) {
+ for ( y=0; y<image->height; y++ ) {
+
+ int val;
+
+ val = image->data[y+image->height*(image->width-1-x)];
+
+ if ( val > 1000 ) {
+
+ double rx, ry, rz;
+
+ /* Map and record reflection */
+ map_position(image, x, y, &rx, &ry, &rz);
+ fprintf(fh, "%10f %10f %10f %8f\n",
+ rx/1e10, ry/1e10, rz/1e10, 1.0);
+ }
+
+ }
+ }
+
+ fclose(fh);
+
+ 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);
+
+ ml = g_main_loop_new(NULL, FALSE);
+ g_main_loop_run(ml);
+
+ return;
+}
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