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-rw-r--r--libcrystfel/Makefile.am4
-rw-r--r--libcrystfel/src/index.c2
-rw-r--r--libcrystfel/src/index.h2
-rw-r--r--libcrystfel/src/xds.c269
-rw-r--r--libcrystfel/src/xds.h2
5 files changed, 74 insertions, 205 deletions
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 2a02a20b..4da30aa9 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -8,7 +8,7 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
src/symmetry.c src/stream.c src/peaks.c \
src/reflist-utils.c src/filters.c \
src/render.c src/index.c src/dirax.c src/mosflm.c \
- src/cell-utils.c src/integer_matrix.c
+ src/cell-utils.c src/integer_matrix.c src/xds.c
if HAVE_FFTW
libcrystfel_la_SOURCES += src/reax.c
@@ -24,7 +24,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
src/render.h src/index.h src/image.h \
src/filters.h src/dirax.h src/mosflm.h \
src/index-priv.h src/reax.h src/cell-utils.h \
- src/integer_matrix.h
+ src/integer_matrix.h src/xds.h
INCLUDES = "-I$(top_srcdir)/data"
AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -Wall
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 49f5636b..c8a6b08f 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -309,7 +309,7 @@ IndexingMethod *build_indexer_list(const char *str, int *need_cell)
} else if ( strcmp(methods[i], "mosflm") == 0) {
list[i] = INDEXING_MOSFLM;
} else if ( strcmp(methods[i], "xds") == 0) {
- list[i] = INDEXING_xds;
+ list[i] = INDEXING_XDS;
} else if ( strcmp(methods[i], "reax") == 0) {
list[i] = INDEXING_REAX;
*need_cell = 1;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 406ad317..b2d7553d 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -48,7 +48,7 @@ typedef enum {
INDEXING_NONE,
INDEXING_DIRAX,
INDEXING_MOSFLM,
- INDEXING_xds,
+ INDEXING_XDS,
INDEXING_REAX,
} IndexingMethod;
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index d7968d6e..96c4aca3 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -1,13 +1,14 @@
/*
* xds.c
*
- * Invoke xds crystal autoindexing
+ * Invoke xds for crystal autoindexing
*
* Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2013 Thomas White <taw@physics.org>
+ * 2013 Cornelius Gati <cornelius.gati@cfel.de>
*
* This file is part of CrystFEL.
*
@@ -70,90 +71,6 @@ struct xds_data {
};
-
-static int read_matrix(struct image *image, char *filename)
-{
- FILE *fh;
- int d1;
- float d2;
- float ubi11, ubi12, ubi13;
- float ubi21, ubi22, ubi23;
- float ubi31, ubi32, ubi33;
- char line[1024];
- int r;
-
- fh = fopen(filename, "r");
- if ( fh == NULL ) {
- ERROR("Can't open '%s'\n", filename);
- return 1;
- }
-
- /* Read and discard first line */
- if ( fgets(line, 1024, fh) == NULL ) {
- ERROR("Failed to read GFF file.\n");
- return 1;
- }
-
- /* One line per grain */
- if ( fgets(line, 1024, fh) == NULL ) {
- ERROR("Failed to read GFF file.\n");
- return 1;
- }
-
- STATUS("'%s'\n", line);
-
- r = sscanf(line,
- "%i %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f",
- &d1, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2,
- &ubi11, &ubi12, &ubi13, &ubi21, &ubi22, &ubi23, &ubi31, &ubi32, &ubi33);
-
- if ( r != 24 ) {
- ERROR("Only %i parameters in GFF file\n", r);
- return 1;
- }
-
- fclose(fh);
-
- image->candidate_cells[0] = cell_new();
-
-// cell_set_cartesian(image->candidate_cells[0],
-// ubi11/1e10, ubi12/1e10, ubi13/1e10,
-// ubi21/1e10, ubi22/1e10, ubi23/1e10,
-// ubi31/1e10, ubi32/1e10, ubi33/1e10);
-
- cell_set_cartesian(image->candidate_cells[0],
- ubi12/1e10, ubi13/1e10, ubi11/1e10,
- ubi22/1e10, ubi23/1e10, ubi21/1e10,
- ubi32/1e10, ubi33/1e10, ubi31/1e10);
-
-
- image->ncells = 1;
- cell_print(image->candidate_cells[0]);
-
- return 0;
-}
-
-
-static int xds_readable(struct image *image,
- struct xds_data *xds)
-{
- int rval;
-
- rval = read(xds->pty,
- xds->rbuffer, xds->rbuflen);
-
- if ( rval == -1 ) {
- ERROR("Read failed: %s\n", strerror(errno));
- return 1;
- }
-
- xds->rbuffer[rval] = '\0';
-
- printf("xds: '%s'\n", xds->rbuffer);
-
- return 0;
-}
-
static void write_spot(struct image *image, const char *filename)
{
FILE *fh;
@@ -167,19 +84,10 @@ static void write_spot(struct image *image, const char *filename)
return;
}
- /* Number of pixels in x, number of pixels in y, pixel size (mm),
- * YSCALE, OMEGA */
- fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, 0.0, 1.0, 0.0);
-
- /* INVERTX, ISWUNG */
- fprintf(fh, "%10d %10d\n", 0, 1);
-
- /* XBEAM, YBEAM */
- fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0);
-
n = image_feature_count(image->features);
- for ( i=0; i<n; i++ ) {
-
+ for ( i=0; i<n; i++ )
+
+ {
struct imagefeature *f;
struct panel *p;
double xs, ys, rx, ry, x, y;
@@ -195,127 +103,88 @@ static void write_spot(struct image *image, const char *filename)
rx = (xs + p->cnx) / p->res;
ry = (ys + p->cny) / p->res;
- x = -rx*fclen/p->clen;
+ x = rx*fclen/p->clen;
y = ry*fclen/p->clen; /* Peak positions in m */
- fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
- x*1e3, y*1e3, 0.0, 0.0, 1000.0, 10.0);
+ fprintf(fh, "%10.2f %10.2f %10.2f %10.0f",
+ x*1e3, y*1e3, 0.0, 0.0);
}
-
- fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
- -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
fclose(fh);
}
-//void run_xds(struct image *image, UnitCell *cell)
+static char *write_INP(struct image *image)
{
- unsigned int opts;
- int status;
- int rval;
- struct xds_data *xds;
- char *ini_filename;
- char gff_filename[1024];
-
- write_gve(image, cell);
- ini_filename = write_ini(image);
-
- if ( ini_filename == NULL ) {
- ERROR("Failed to write ini file for xds.\n");
- return;
- }
-
- xds = malloc(sizeof(struct xds_data));
- if ( xds == NULL ) {
- ERROR("Couldn't allocate memory for xds data.\n");
- return;
- }
-
- snprintf(gff_filename, 1023, "xfel-%i.gff", image->id);
- remove(gff_filename);
-
- xds->pid = forkpty(&xds->pty, NULL, NULL, NULL);
- if ( xds->pid == -1 ) {
- ERROR("Failed to fork for xds: %s\n", strerror(errno));
- return;
- }
- if ( xds->pid == 0 ) {
-
- /* Child process: invoke xds */
- struct termios t;
+ FILE *fh;
+ char *filename;
+ //double tt;
- /* Turn echo off */
- tcgetattr(STDIN_FILENO, &t);
- t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
- tcsetattr(STDIN_FILENO, TCSANOW, &t);
+ filename = malloc(1024);
+ if ( filename == NULL ) return NULL;
- STATUS("Running xds.0.90 '%s'\n", ini_filename);
- execlp("xds.0.90", "", ini_filename, (char *)NULL);
- ERROR("Failed to invoke xds.\n");
- _exit(0);
+ snprintf(filename, 1023, filename, image->id);
+ fh = fopen(filename, "w");
+ if ( !fh ) {
+ ERROR("Couldn't open temporary file '%s'\n", filename);
+ free(filename);
+ return NULL;
}
- free(ini_filename);
-
- 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);
-
- do {
- fd_set fds;
- struct timeval tv;
- int sval;
+ //get_q_for_panel(image->det->furthest_out_panel,
+ // image->det->furthest_out_fs,
+ // image->det->furthest_out_ss,
+ // &tt, 1.0/image->lambda);
+
+ fprintf(fh, "JOB= IDXREF\n");
+ fprintf(fh, "ORGX= 1540.64\n");
+ fprintf(fh, "ORGY= 1543.78\n");
+ fprintf(fh, "DETECTOR_DISTANCE= 50.000\n");
+ fprintf(fh, "OSCILLATION_RANGE= 0.100\n");
+ fprintf(fh, "X-RAY_WAVELENGTH= 1.77000\n");
+ fprintf(fh, "NAME_TEMPLATE_OF_DATA_FRAMES=/home/dikay/insu/data_exp1/ins_ssad_1_???.img \n");
+ fprintf(fh, "DATA_RANGE=1 1\n");
+ fprintf(fh, "SPOT_RANGE=1 1\n");
+ fprintf(fh, "SPACE_GROUP_NUMBER=0\n");
+ fprintf(fh, "UNIT_CELL_CONSTANTS= 70 80 90 90 90 90\n");
+ fprintf(fh, "NX= 3072\n");
+ fprintf(fh, "NY= 3072\n");
+ fprintf(fh, "QX= .073242\n");
+ fprintf(fh, "QY= .073242\n");
+ fprintf(fh, "DIRECTION_OF_DETECTOR_X-AXIS=1 0 0\n");
+ fprintf(fh, "DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0\n");
+ fprintf(fh, "INCIDENT_BEAM_DIRECTION=0 0 1\n");
+ fprintf(fh, "ROTATION_AXIS=1 0 0\n");
+ fprintf(fh, "DETECTOR= CCDCHESS\n");
+ fprintf(fh, "MINIMUM_VALID_PIXEL_VALUE= 1\n");
+ fprintf(fh, "OVERLOAD= 65500\n");
- FD_ZERO(&fds);
- FD_SET(xds->pty, &fds);
-
- tv.tv_sec = 20000;
- 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");
- break;
-
- default:
- ERROR("select() failed: %s\n", strerror(err));
- rval = 1;
-
- }
-
- } else if ( sval != 0 ) {
- rval = xds_readable(image, xds);
- } else {
- ERROR("No response from xds..\n");
- rval = 1;
- }
+ fclose(fh);
- } while ( !rval );
+ return filename;
- close(xds->pty);
- free(xds->rbuffer);
- waitpid(xds->pid, &status, 0);
+void run_xds(struct image *image, UnitCell *cell)
+{
+ //unsigned int opts;
+ //int status;
+ //int rval;
+ struct xds_data *xds;
+ char *INP_filename;
+ //char gff_filename[1024];
- if ( status != 0 ) {
- ERROR("xds doesn't seem to be working properly.\n");
- }
+ write_INP(image);
+ INP_filename = write_INP(image);
- if ( read_matrix(image, gff_filename) != 0 ) {
- ERROR("Failed to read matrix\n");
+ if ( INP_filename == NULL ) {
+ ERROR("Failed to write XDS.INP file for XDS.\n");
+ return;
}
- free(xds);
-}
+ xds = malloc(sizeof(struct xds_data));
+ if ( xds == NULL ) {
+ ERROR("Couldn't allocate memory for xds data.\n");
+ return;
+ }}
+ //free(xds);
+//}
diff --git a/libcrystfel/src/xds.h b/libcrystfel/src/xds.h
index 3521ebc5..edf83b0b 100644
--- a/libcrystfel/src/xds.h
+++ b/libcrystfel/src/xds.h
@@ -1,5 +1,5 @@
/*
- * grainspotter.h
+ * xds.h
*
* Invoke xds for crystal autoindexing
*
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-30 11:49:01 +0000