Merge branch 'cornelius/xds' into tom/multicrystal

Conflicts:
	libcrystfel/Makefile.am
	libcrystfel/src/index.c
	libcrystfel/src/index.h

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 */