aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel
diff options
context:
space:
mode:
Diffstat (limited to 'libcrystfel')
-rw-r--r--libcrystfel/src/xds.c247
1 files changed, 26 insertions, 221 deletions
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 4723761b..b28dc93a 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -54,7 +54,8 @@
#include "cell-utils.h"
-#define XDS_VERBOSE 0
+/* Fake pixel size and camera length, both in metres */
+#define FAKE_PIXEL_SIZE (70e-6)
#define FAKE_CLEN (0.1)
@@ -66,142 +67,7 @@ struct xds_private
};
-struct xds_data {
-
- /* Low-level stuff */
- int pty;
- pid_t pid;
- char *rbuffer;
- int rbufpos;
- int rbuflen;
-
- /* High-level stuff */
- int step;
- int finished_ok;
- UnitCell *target_cell;
-};
-
-static void xds_parseline(const char *line, struct image *image,
- struct xds_data *xds)
-{
-#if XDS_VERBOSE
- char *copy;
- int i;
-
- 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("XDS: %s\n", copy);
- free(copy);
-#endif
-}
-
-
-static int xds_readable(struct image *image, struct xds_data *xds)
-{
- int rval;
- int no_string = 0;
-
- rval = read(xds->pty, xds->rbuffer+xds->rbufpos,
- xds->rbuflen-xds->rbufpos);
- if ( (rval == -1) || (rval == 0) ) return 1;
-
- xds->rbufpos += rval;
- assert(xds->rbufpos <= xds->rbuflen);
-
- while ( (!no_string) && (xds->rbufpos > 0) ) {
-
- int i;
- int block_ready = 0;
-
- /* See if there's a full line in the buffer yet */
- for ( i=0; i<xds->rbufpos-1; i++ ) {
- /* Means the last value looked at is rbufpos-2 */
-
- if ( (xds->rbuffer[i] == '\r')
- && (xds->rbuffer[i+1] == '\n') ) {
- block_ready = 1;
- break;
- }
-
- }
-
- if ( block_ready ) {
-
- unsigned int new_rbuflen;
- unsigned int endbit_length;
- char *block_buffer = NULL;
-
- block_buffer = malloc(i+1);
- memcpy(block_buffer, xds->rbuffer, i);
- block_buffer[i] = '\0';
-
- if ( block_buffer[0] == '\r' ) {
- memmove(block_buffer, block_buffer+1, i);
- }
-
- xds_parseline(block_buffer, image, xds);
- free(block_buffer);
- endbit_length = i+2;
-
- /* Now the block's been parsed, it should be
- * forgotten about */
- memmove(xds->rbuffer,
- xds->rbuffer + endbit_length,
- xds->rbuflen - endbit_length);
-
- /* Subtract the number of bytes removed */
- xds->rbufpos = xds->rbufpos
- - endbit_length;
- new_rbuflen = xds->rbuflen - endbit_length;
- if ( new_rbuflen == 0 ) new_rbuflen = 256;
- xds->rbuffer = realloc(xds->rbuffer,
- new_rbuflen);
- xds->rbuflen = new_rbuflen;
-
- } else {
-
- if ( xds->rbufpos==xds->rbuflen ) {
-
- /* More buffer space is needed */
- xds->rbuffer = realloc(
- xds->rbuffer,
- xds->rbuflen + 256);
- xds->rbuflen = xds->rbuflen + 256;
- /* The new space gets used at the next
- * read, shortly... */
-
- }
- no_string = 1;
-
- }
-
- }
-
- return 0;
-}
-
-
-static int check_cell(struct xds_private *xp, struct image *image,
- UnitCell *cell)
-{
- Crystal *cr;
-
- cr = crystal_new();
- if ( cr == NULL ) {
- ERROR("Failed to allocate crystal.\n");
- return 0;
- }
- crystal_set_cell(cr, cell);
- image_add_crystal(image, cr);
-
- return 1;
-}
-
-
-static int read_cell(struct image *image, struct xds_private *xp)
+static int read_cell(struct image *image)
{
FILE * fh;
float axstar, aystar, azstar;
@@ -213,6 +79,7 @@ static int read_cell(struct image *image, struct xds_private *xp)
char *rval, line[1024];
int r;
UnitCell *cell;
+ Crystal *cr;
fh = fopen("IDXREF.LP", "r");
if ( fh == NULL ) return 0; /* Not indexable */
@@ -292,9 +159,16 @@ static int read_cell(struct image *image, struct xds_private *xp)
axstar*10e9, aystar*10e9, azstar*10e9,
bxstar*10e9, bystar*10e9, bzstar*10e9,
-cxstar*10e9, -cystar*10e9, -czstar*10e9);
- r = check_cell(xp, image, cell);
- return r;
+ cr = crystal_new();
+ if ( cr == NULL ) {
+ ERROR("Failed to allocate crystal.\n");
+ return 0;
+ }
+ crystal_set_cell(cr, cell);
+ image_add_crystal(image, cr);
+
+ return 1;
}
@@ -330,8 +204,8 @@ static void write_spot(struct image *image)
x = tan(ttx)*FAKE_CLEN;
y = tan(tty)*FAKE_CLEN;
- x = (x / 70e-6) + 1500;
- y = (y / 70e-6) + 1500;
+ x = (x / FAKE_PIXEL_SIZE) + 1500;
+ y = (y / FAKE_PIXEL_SIZE) + 1500;
fprintf(fh, "%10.2f %10.2f %10.2f %10.0f.\n",
x, y, 0.5, f->intensity);
@@ -458,8 +332,8 @@ static int write_inp(struct image *image, struct xds_private *xp)
fprintf(fh, "NX= 3000\n");
fprintf(fh, "NY= 3000\n");
- fprintf(fh, "QX= 0.07\n");
- fprintf(fh, "QY= 0.07\n");
+ fprintf(fh, "QX= %f\n", FAKE_PIXEL_SIZE*1e3); /* Pixel size in mm */
+ fprintf(fh, "QY= %f\n", FAKE_PIXEL_SIZE*1e3); /* Pixel size in mm */
fprintf(fh, "INDEX_ORIGIN=0 0 0\n");
fprintf(fh, "DIRECTION_OF_DETECTOR_X-AXIS=1 0 0\n");
fprintf(fh, "DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0\n");
@@ -482,46 +356,33 @@ static int write_inp(struct image *image, struct xds_private *xp)
int run_xds(struct image *image, void *priv)
{
- unsigned int opts;
int status;
int rval;
int n;
- struct xds_data *xds;
+ pid_t pid;
+ int pty;
struct xds_private *xp = (struct xds_private *)priv;
- xds = malloc(sizeof(struct xds_data));
- if ( xds == NULL ) {
- ERROR("Couldn't allocate memory for xds data.\n");
- return 0;
- }
-
- xds->target_cell = xp->cell;
-
if ( write_inp(image, xp) ) {
ERROR("Failed to write XDS.INP file for XDS.\n");
- free(xds);
return 0;
}
n = image_feature_count(image->features);
- if ( n < 25 ) {
- free(xds);
- return 0;
- }
+ if ( n < 25 ) return 0;
write_spot(image);
/* Delete any old indexing result which may exist */
remove("IDXREF.LP");
- xds->pid = forkpty(&xds->pty, NULL, NULL, NULL);
+ pid = forkpty(&pty, NULL, NULL, NULL);
- if ( xds->pid == -1 ) {
+ if ( pid == -1 ) {
ERROR("Failed to fork for XDS\n");
- free(xds);
return 0;
}
- if ( xds->pid == 0 ) {
+ if ( pid == 0 ) {
/* Child process: invoke XDS */
struct termios t;
@@ -536,66 +397,10 @@ int run_xds(struct image *image, void *priv)
_exit(0);
}
+ waitpid(pid, &status, 0);
- xds->rbuffer = malloc(256);
- xds->rbuflen = 256;
- xds->rbufpos = 0;
-
- /* Set non-blocking */
- opts = fcntl(xds->pty, F_GETFL);
- fcntl(xds->pty, F_SETFL, opts | O_NONBLOCK);
-
- //xds->step = 1; /* This starts the "initialisation" procedure */
- xds->finished_ok = 0;
-
- do {
-
- fd_set fds;
- struct timeval tv;
- int sval;
-
- FD_ZERO(&fds);
- FD_SET(xds->pty, &fds);
-
- tv.tv_sec = 30;
- tv.tv_usec = 0;
-
- sval = select(xds->pty+1, &fds, NULL, NULL, &tv);
-
- if ( sval == -1 ) {
-
- const int err = errno;
-
- switch ( err ) {
-
- case EINTR:
- STATUS("Restarting select()\n");
- rval = 0;
- break;
-
- default:
- ERROR("select() failed: %s\n", strerror(err));
- rval = 1;
- break;
-
- }
-
- } else if ( sval != 0 ) {
- rval = xds_readable(image, xds);
- } else {
- ERROR("No response from XDS..\n");
- rval = 1;
- }
-
- } while ( !rval );
-
- close(xds->pty);
- free(xds->rbuffer);
- waitpid(xds->pid, &status, 0);
-
- rval = read_cell(image, xp);
-
- free(xds);
+ close(pty);
+ rval = read_cell(image);
return rval;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 13:09:22 +0000