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-rw-r--r--libcrystfel/Makefile.am4
-rw-r--r--libcrystfel/src/index.c18
-rw-r--r--libcrystfel/src/index.h2
-rw-r--r--libcrystfel/src/xds.c503
-rw-r--r--libcrystfel/src/xds.h43
5 files changed, 567 insertions, 3 deletions
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index ae315594..5f5ff7fa 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -9,7 +9,7 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.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/crystal.c \
- src/grainspotter.c
+ src/grainspotter.c src/xds.c
if HAVE_FFTW
libcrystfel_la_SOURCES += src/reax.c
@@ -26,7 +26,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.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/crystal.h \
- src/grainspotter.h
+ src/grainspotter.h src/xds.h
AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -Wall
AM_CPPFLAGS += -I$(top_srcdir)/lib @LIBCRYSTFEL_CFLAGS@
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index eee2e814..20e7cf24 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -11,6 +11,7 @@
* 2010-2013 Thomas White <taw@physics.org>
* 2010-2011 Richard Kirian <rkirian@asu.edu>
* 2012 Lorenzo Galli
+ * 2013 Cornelius Gati <cornelius.gati@cfel.de>
*
* This file is part of CrystFEL.
*
@@ -44,6 +45,7 @@
#include "peaks.h"
#include "dirax.h"
#include "mosflm.h"
+#include "xds.h"
#include "detector.h"
#include "index.h"
#include "index-priv.h"
@@ -84,6 +86,11 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
iprivs[n] = mosflm_prepare(&indm[n], cell, filename,
det, beam, ltl);
break;
+
+ case INDEXING_XDS :
+ iprivs[n] = indexing_private(indm[n]);
+ break;
+
case INDEXING_REAX :
iprivs[n] = reax_prepare(&indm[n], cell, filename,
det, beam, ltl);
@@ -153,6 +160,10 @@ void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs)
mosflm_cleanup(privs[n]);
break;
+ case INDEXING_XDS :
+ free(priv[n]);
+ break;
+
case INDEXING_REAX :
reax_cleanup(privs[n]);
break;
@@ -213,6 +224,10 @@ static int try_indexer(struct image *image, IndexingMethod indm,
return run_mosflm(image, ipriv);
break;
+ case INDEXING_XDS :
+ run_XDS(image, cell);
+ break;
+
case INDEXING_REAX :
return reax_index(image, ipriv);
break;
@@ -385,6 +400,9 @@ IndexingMethod *build_indexer_list(const char *str)
} else if ( strcmp(methods[i], "grainspotter") == 0) {
list[++nmeth] = INDEXING_DEFAULTS_GRAINSPOTTER;
+ } else if ( strcmp(methods[i], "xds") == 0) {
+ list[i] = INDEXING_XDS;
+
} else if ( strcmp(methods[i], "reax") == 0) {
list[++nmeth] = INDEXING_DEFAULTS_REAX;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 3c91486b..d550468b 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -69,7 +69,6 @@
**/
typedef enum {
-
INDEXING_NONE = 0,
/* The core indexing methods themselves */
@@ -77,6 +76,7 @@ typedef enum {
INDEXING_MOSFLM = 2,
INDEXING_REAX = 3,
INDEXING_GRAINSPOTTER = 4,
+ INDEXING_XDS = 5,
/* Bits at the top of the IndexingMethod are flags which modify the
* behaviour of the indexer. */
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
new file mode 100644
index 00000000..838b71b7
--- /dev/null
+++ b/libcrystfel/src/xds.c
@@ -0,0 +1,503 @@
+/*
+ * xds.c
+ *
+ * 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.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#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>
+#include <errno.h>
+
+#if HAVE_FORKPTY_LINUX
+#include <pty.h>
+#elif HAVE_FORKPTY_BSD
+#include <util.h>
+#endif
+
+
+#include "image.h"
+#include "utils.h"
+#include "peaks.h"
+#include "cell.h"
+#include "cell-utils.h"
+
+
+#define xds_VERBOSE 0
+
+
+struct xds_data {
+
+ /* Low-level stuff */
+ int pty;
+ pid_t pid;
+ char *rbuffer;
+ int rbufpos;
+ int rbuflen;
+
+ /* High-level stuff */
+ char newmatfile[128];
+ char spotfile[128];
+ int step;
+ int finished_ok;
+ UnitCell *target_cell;
+};
+
+static void xds_parseline(const char *line, struct image *image,
+ struct xds_data *xds)
+{
+
+ 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);
+}
+
+
+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 read_newmat(const char *filename, struct image *image)
+{
+ FILE * fh;
+ float axstar, aystar, azstar, bxstar, bystar, bzstar, cxstar, cystar, czstar;
+ char asx[11], asy[11], asz[11];
+ char bsx[11], bsy[11], bsz[11];
+ char csx[11], csy[11], csz[11];
+ char *rval, line[1024];
+ int r;
+
+ fh = fopen("IDXREF.LP", "r");
+ if ( fh == NULL ) {
+ ERROR("Couldn't open 'IDXREF.LP'\n");
+ return 1;
+ }
+
+ do {
+ rval = fgets(line, 1023, fh);
+
+ } while (strcmp(line, " # COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH\n") != 0 );
+
+ /*free line after chunk*/
+ rval = fgets(line, 1023, fh);
+ rval = fgets(line, 1023, fh);
+
+ memcpy(asx, line+7, 10); asx[10] = '\0';
+ memcpy(asy, line+17, 10); asy[10] = '\0';
+ memcpy(asz, line+27, 10); asz[10] = '\0';
+
+ rval = fgets(line, 1023, fh);
+
+ memcpy(bsx, line+7, 10); bsx[10] = '\0';
+ memcpy(bsy, line+17, 10); bsy[10] = '\0';
+ memcpy(bsz, line+27, 10); bsz[10] = '\0';
+
+ rval = fgets(line, 1023, fh);
+
+ memcpy(csx, line+7, 10); csx[10] = '\0';
+ memcpy(csy, line+17, 10); csy[10] = '\0';
+ memcpy(csz, line+27, 10); csz[10] = '\0';
+
+ r = sscanf(asx, "%f", &cxstar);
+ r += sscanf(asy, "%f", &cystar);
+ r += sscanf(asz, "%f", &czstar);
+ r += sscanf(bsx, "%f", &bxstar);
+ r += sscanf(bsy, "%f", &bystar);
+ r += sscanf(bsz, "%f", &bzstar);
+ r += sscanf(csx, "%f", &axstar);
+ r += sscanf(csy, "%f", &aystar);
+ r += sscanf(csz, "%f", &azstar);
+
+ if ( r != 9 ) {
+ STATUS("Fewer than 9 parameters found in NEWMAT file.\n");
+ return 1;}
+
+ fclose(fh);
+
+ //printf("asx='%s'\n", asx);
+ //printf("asy='%s'\n", asy);
+ //printf("asz='%s'\n", asz);
+ //printf("cxstar='%f'\n", cxstar);
+ //printf("cystar='%f'\n", cystar);
+ //printf("czstar='%f'\n", czstar);
+ //printf("bsx='%s'\n", bsx);
+ //printf("bsy='%s'\n", bsy);
+ //printf("bsz='%s'\n", bsz);
+ //printf("axstar='%f'\n", axstar);
+ //printf("aystar='%f'\n", aystar);
+ //printf("azstar='%f'\n", azstar);
+ //printf("csx='%s'\n", csx);
+ //printf("csy='%s'\n", csy);
+ //printf("csz='%s'\n", csz);
+ //printf("bxstar='%f'\n", bxstar);
+ //printf("bystar='%f'\n", bystar);
+ //printf("bzstar='%f'\n", bzstar);
+
+ image->candidate_cells[0] = cell_new();
+
+ cell_set_reciprocal(image->candidate_cells[0],
+ axstar*10e9, aystar*10e9, azstar*10e9,
+ bxstar*10e9, bystar*10e9, bzstar*10e9,
+ -cxstar*10e9, -cystar*10e9, -czstar*10e9);
+ image->ncells = 1;
+
+ cell_print(image->candidate_cells[0]);
+
+ return 0;
+}
+
+
+static void write_spot(struct image *image, const char *filename)
+{
+ FILE *fh;
+ int i;
+ double fclen = 99.0e-3; /* fake camera length in m */
+ int n;
+
+ fh = fopen("SPOT.XDS", "w");
+ if ( !fh ) {
+ ERROR("Couldn't open temporary file '%s'\n", "SPOT.XDS");
+ return;
+ }
+
+ n = image_feature_count(image->features);
+ for ( i=0; i<n; i++ )
+
+ {
+ struct imagefeature *f;
+ struct panel *p;
+ double xs, ys, rx, ry, x, y;
+
+ f = image_get_feature(image->features, i);
+ if ( f == NULL ) continue;
+
+ p = find_panel(image->det, f->fs, f->ss);
+ if ( p == NULL ) continue;
+
+ xs = (f->fs-p->min_fs)*p->fsx + (f->ss-p->min_ss)*p->ssx;
+ ys = (f->fs-p->min_fs)*p->fsy + (f->ss-p->min_ss)*p->ssy;
+ rx = ((xs + p->cnx) / p->res);
+ ry = ((ys + p->cny) / p->res);
+
+ //printf("xs=%f ys=%f ----> rx=%f ry=%f\n", xs, ys, rx, ry);
+
+ x = rx*fclen/p->clen;
+ y = ry*fclen/p->clen; /* Peak positions in m */
+
+ //printf("x=%f y=%f\n", x, y);
+
+ x = (rx / 70e-6) + 1500;
+ y = (ry / 70e-6) + 1500;
+
+ if (f->intensity <= 0) continue;
+
+ fprintf(fh, "%10.2f %10.2f %10.2f %10.0f.\n",
+ x, y, 0.5, f->intensity);
+
+ }
+ fclose(fh);
+}
+
+
+static char *write_inp(struct image *image)
+{
+ FILE *fh;
+ char *filename;
+
+ filename = malloc(1024);
+ if ( filename == NULL ) return NULL;
+
+ snprintf(filename, 1023, "XDS.INP");
+
+ fh = fopen(filename, "w");
+ if ( !fh ) {
+ ERROR("Couldn't open temporary file '%s'\n", filename);
+ free(filename);
+ return NULL;
+ }
+
+ fprintf(fh, "JOB= IDXREF\n");
+ fprintf(fh, "ORGX= 1500\n");
+ fprintf(fh, "ORGY= 1500\n");
+ fprintf(fh, "DETECTOR_DISTANCE= 99.00\n"); //IMPORTANT
+ fprintf(fh, "OSCILLATION_RANGE= 0.300\n");
+ fprintf(fh, "X-RAY_WAVELENGTH= 1.32\n"); // IMPORTANT
+ 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= 94\n"); //CatB 94
+ fprintf(fh, "UNIT_CELL_CONSTANTS= 126.2 126.2 54.2 90 90 90\n"); //CatB 125.4 125.4 54.56 90 90 90
+ //fprintf(fh, "SPACE_GROUP_NUMBER=194\n"); //PS1 194
+ //fprintf(fh, "UNIT_CELL_CONSTANTS=281 281 165.2 90 90 120\n"); //PS1 281 281 165.2 90 90 120
+ //fprintf(fh, "SPACE_GROUP_NUMBER= 0\n"); //LYS 96
+ //fprintf(fh, "UNIT_CELL_CONSTANTS= 0 0 0 0 0 0\n"); //LYS 77.32 77.32 38.16 90 90 90
+ fprintf(fh, "NX= 3000\n");
+ fprintf(fh, "NY= 3000\n");
+ fprintf(fh, "QX= 0.07\n");
+ fprintf(fh, "QY= 0.07\n");
+ 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");
+ fprintf(fh, "INCIDENT_BEAM_DIRECTION=0 0 1\n");
+ fprintf(fh, "ROTATION_AXIS=0 1 0\n");
+ fprintf(fh, "DETECTOR= CSPAD\n");
+ fprintf(fh, "MINIMUM_VALID_PIXEL_VALUE= 1\n");
+ fprintf(fh, "OVERLOAD= 200000000\n");
+ fprintf(fh, "INDEX_ERROR= 0.4\n");
+ //fprintf(fh, "INDEX_QUALITY= 0.5\n");
+ //fprintf(fh, "REFINE(IDXREF)= ALL\n");
+ //fprintf(fh, "MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 1\n");
+ //fprintf(fh, "MAXIMUM_ERROR_OF_SPOT_POSITION= 20.0\n");
+
+ fclose(fh);
+
+ return filename;
+}
+
+void run_xds(struct image *image, UnitCell *cell)
+{
+
+ unsigned int opts;
+ int status;
+ int rval;
+ int n;
+ struct xds_data *xds;
+ char *inp_filename;
+
+ xds = malloc(sizeof(struct xds_data));
+ if ( xds == NULL ) {
+ ERROR("Couldn't allocate memory for xds data.\n");
+ return;
+ }
+
+ xds->target_cell = cell;
+
+ write_inp(image);
+ inp_filename = write_inp(image);
+
+ if ( inp_filename == NULL ) {
+ ERROR("Failed to write XDS.INP file for XDS.\n");
+ return;
+ }
+
+ n= image_feature_count(image->features);
+ if (n < 25) return;
+
+ snprintf(xds->spotfile, 127, "SPOT.XDS");
+
+ write_spot(image, xds->spotfile);
+
+ xds->pid = forkpty(&xds->pty, NULL, NULL, NULL);
+
+ if ( xds->pid == -1 ) {
+ ERROR("Failed to fork for XDS\n");
+ free(xds);
+ return;
+ }
+ if ( xds->pid == 0 ) {
+
+ /* Child process: invoke XDS */
+ struct termios t;
+
+ /* Turn echo off */
+ tcgetattr(STDIN_FILENO, &t);
+ t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
+ tcsetattr(STDIN_FILENO, TCSANOW, &t);
+
+ execlp("xds", "", (char *)NULL);
+ ERROR("Failed to invoke XDS.\n");
+ _exit(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");
+ 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;
+ }
+
+ } while ( !rval );
+
+ close(xds->pty);
+ free(xds->rbuffer);
+ waitpid(xds->pid, &status, 0);
+
+ //FIXME//
+ //if ( xds->finished_ok == 1 ) {
+ // ERROR("XDS doesn't seem to be working properly.\n");
+ //} else {
+ /* Read the XDS NEWMAT file and get cell if found */
+ read_newmat(xds->newmatfile, image);
+
+ //}
+
+ free(xds);
+}
diff --git a/libcrystfel/src/xds.h b/libcrystfel/src/xds.h
new file mode 100644
index 00000000..edf83b0b
--- /dev/null
+++ b/libcrystfel/src/xds.h
@@ -0,0 +1,43 @@
+/*
+ * xds.h
+ *
+ * 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.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef xds_H
+#define xds_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "cell.h"
+
+
+extern void run_xds(struct image *image, UnitCell *cell);
+
+
+#endif /* XDS_H */
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