Update XDS for new indexing subsystem

4 files changed, 211 insertions, 103 deletions

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 20e7cf24..0ab467a6 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -88,7 +88,8 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
 			break;
 
 			case INDEXING_XDS :
-                        iprivs[n] = indexing_private(indm[n]);
+                        iprivs[n] = xds_prepare(&indm[n], cell, filename,
+			                        det, beam, ltl);
 			break;
 
 			case INDEXING_REAX :
@@ -161,7 +162,7 @@ void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs)
 			break;
 
                         case INDEXING_XDS :
-			free(priv[n]);
+			xds_cleanup(privs[n]);
 			break;
 
 			case INDEXING_REAX :
@@ -225,7 +226,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		break;
 
 		case INDEXING_XDS :
-		run_XDS(image, cell);
+		return run_xds(image, ipriv);
 		break;
 
 		case INDEXING_REAX :
@@ -348,6 +349,10 @@ char *indexer_str(IndexingMethod indm)
 		strcpy(str, "grainspotter");
 		break;
 
+		case INDEXING_XDS :
+		strcpy(str, "xds");
+		break;
+
 		default :
 		ERROR("Unrecognised indexing method %i\n",
 		      indm & INDEXING_METHOD_MASK);
@@ -401,7 +406,7 @@ IndexingMethod *build_indexer_list(const char *str)
 			list[++nmeth] = INDEXING_DEFAULTS_GRAINSPOTTER;
 
                 } else if ( strcmp(methods[i], "xds") == 0) {
-			list[i] = INDEXING_XDS;
+			list[++nmeth] = INDEXING_DEFAULTS_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 d550468b..94b0d457 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -58,6 +58,9 @@
                                      | INDEXING_USE_LATTICE_TYPE               \
                                      | INDEXING_CHECK_PEAKS)
 
+#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE        \
+                                     | INDEXING_CHECK_PEAKS)
+
 /**
  * IndexingMethod:
  * @INDEXING_NONE: No indexing to be performed
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 838b71b7..786e2ae0 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -5,6 +5,7 @@
  *
  * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
  *                  a research centre of the Helmholtz Association.
+ * Copyright © 2013 Cornelius Gati
  *
  * Authors:
  *   2010-2013 Thomas White <taw@physics.org>
@@ -60,6 +61,15 @@
 #define xds_VERBOSE 0
 
 
+/* Global private data, prepared once */
+struct xds_private
+{
+	IndexingMethod indm;
+	float *ltl;
+	UnitCell *cell;
+};
+
+
 struct xds_data {
 
 	/* Low-level stuff */
@@ -179,97 +189,139 @@ static int xds_readable(struct image *image, struct xds_data *xds)
 }
 
 
+static int check_cell(struct xds_private *xp, struct image *image,
+                      UnitCell *cell)
+{
+	UnitCell *out;
+	Crystal *cr;
+
+	if ( xp->indm & INDEXING_CHECK_CELL_COMBINATIONS ) {
+
+		out = match_cell(cell, xp->cell, 0, xp->ltl, 1);
+		if ( out == NULL ) return 0;
+
+	} else if ( xp->indm & INDEXING_CHECK_CELL_AXES ) {
+
+		out = match_cell(cell, xp->cell, 0, xp->ltl, 0);
+		if ( out == NULL ) return 0;
+
+	} else {
+		out = cell_new_from_cell(cell);
+	}
+
+	cr = crystal_new();
+	if ( cr == NULL ) {
+		ERROR("Failed to allocate crystal.\n");
+		return 0;
+	}
+
+	crystal_set_cell(cr, out);
+
+	if ( xp->indm & INDEXING_CHECK_PEAKS ) {
+		if ( !peak_sanity_check(image, &cr, 1) ) {
+			cell_free(out);
+			crystal_free(cr);
+			return 0;
+		}
+	}
 
+	image_add_crystal(image, cr);
 
+	return 1;
+}
 
 
-static int read_newmat(const char *filename, struct image *image)
+static int read_cell(const char *filename, struct image *image,
+                     struct xds_private *xp)
 {
 	FILE * fh;
-	float axstar, aystar, azstar, bxstar, bystar, bzstar, cxstar, cystar, czstar;
-	char asx[11], asy[11], asz[11];	
+	float axstar, aystar, azstar;
+	float bxstar, bystar, bzstar;
+	float 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;
-	
+	UnitCell *cell;
+
 	fh = fopen("IDXREF.LP", "r");
 	if ( fh == NULL ) {
 		ERROR("Couldn't open 'IDXREF.LP'\n");
-		return 1;
+		return 0;
 	}
 
 	do {
 		rval = fgets(line, 1023, fh);
 
-	} while (strcmp(line, "   #  COORDINATES OF REC. BASIS VECTOR    LENGTH   1/LENGTH\n") != 0 );
+	} while ( strcmp(line, "   #  COORDINATES OF REC. BASIS VECTOR"
+	                       "    LENGTH   1/LENGTH\n") != 0 );
 
-	/*free line after chunk*/
+	/* 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(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], 
+
+	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 0;
+	}
+
+	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);
+
+	cell = cell_new();
+	cell_set_reciprocal(cell,
 	                    axstar*10e9, aystar*10e9, azstar*10e9,
 	                    bxstar*10e9, bystar*10e9, bzstar*10e9,
 	                   -cxstar*10e9, -cystar*10e9, -czstar*10e9);
-	image->ncells = 1;
+	r = check_cell(xp, image, cell);
+	cell_free(cell);
 
-	cell_print(image->candidate_cells[0]);
-
-	return 0;
+	return r;
 }
 
 
@@ -279,7 +331,7 @@ static void write_spot(struct image *image, const char *filename)
 	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");
@@ -287,8 +339,8 @@ static void write_spot(struct image *image, const char *filename)
 	}
 
 	n = image_feature_count(image->features);
-	for ( i=0; i<n; i++ ) 
-        
+	for ( i=0; i<n; i++ )
+
         {
 		struct imagefeature *f;
 		struct panel *p;
@@ -304,9 +356,9 @@ static void write_spot(struct image *image, const char *filename)
 		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); 
-		
+
+		//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 */
 
@@ -316,7 +368,7 @@ static void write_spot(struct image *image, const char *filename)
 		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);
 
@@ -329,7 +381,7 @@ static char *write_inp(struct image *image)
 {
 	FILE *fh;
 	char *filename;
-	
+
 	filename = malloc(1024);
 	if ( filename == NULL ) return NULL;
 
@@ -351,7 +403,7 @@ static char *write_inp(struct image *image)
 	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, "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
@@ -372,7 +424,7 @@ static char *write_inp(struct image *image)
 	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, "MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 1\n");
 	//fprintf(fh, "MAXIMUM_ERROR_OF_SPOT_POSITION= 20.0\n");
 
 	fclose(fh);
@@ -380,35 +432,36 @@ static char *write_inp(struct image *image)
 	return filename;
 }
 
-void run_xds(struct image *image, UnitCell *cell)
+
+int run_xds(struct image *image, IndexingPrivate *priv)
 {
-	
-	unsigned int 	opts;	
-	int 		status;
-	int 		rval;
-	int		n;
-	struct 		xds_data *xds;
-	char 		*inp_filename;
-	
+	unsigned int opts;
+	int status;
+	int rval;
+	int n;
+	struct xds_data *xds;
+	char *inp_filename;
+	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;
+		return 0;
 	}
 
-	xds->target_cell = cell;
+	xds->target_cell = xp->cell;
 
 	write_inp(image);
 	inp_filename = write_inp(image);
 
 	if ( inp_filename == NULL ) {
 		ERROR("Failed to write XDS.INP file for XDS.\n");
-		return;
+		return 0;
 	}
-	
+
 	n= image_feature_count(image->features);
-	if (n < 25) return;
-	
+	if (n < 25) return 0;
+
 	snprintf(xds->spotfile, 127, "SPOT.XDS");
 
 	write_spot(image, xds->spotfile);
@@ -418,7 +471,7 @@ void run_xds(struct image *image, UnitCell *cell)
 	if ( xds->pid == -1 ) {
 		ERROR("Failed to fork for XDS\n");
 		free(xds);
-		return;
+		return 0;
 	}
 	if ( xds->pid == 0 ) {
 
@@ -429,7 +482,7 @@ void run_xds(struct image *image, UnitCell *cell)
 		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);
@@ -474,6 +527,7 @@ void run_xds(struct image *image, UnitCell *cell)
 				default:
 				ERROR("select() failed: %s\n", strerror(err));
 				rval = 1;
+				break;
 
 			}
 
@@ -489,15 +543,54 @@ void run_xds(struct image *image, UnitCell *cell)
 	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);
-	
+	rval = read_cell(xds->newmatfile, image, xp);
+
 	//}
 
 	free(xds);
+
+	return rval;
+}
+
+
+IndexingPrivate *xds_prepare(IndexingMethod *indm, UnitCell *cell,
+                             const char *filename,
+                             struct detector *det,
+                             struct beam_params *beam, float *ltl)
+{
+	struct xds_private *xp;
+
+	if ( cell == NULL ) {
+		ERROR("XDS needs a unit cell.\n");
+		return NULL;
+	}
+
+	xp = calloc(1, sizeof(*xp));
+	if ( xp == NULL ) return NULL;
+
+	/* Flags that XDS knows about */
+	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
+	          | INDEXING_CHECK_CELL_AXES | INDEXING_USE_LATTICE_TYPE
+	          | INDEXING_CHECK_PEAKS;
+
+	xp->ltl = ltl;
+	xp->cell = cell;
+	xp->indm = *indm;
+
+	return (IndexingPrivate *)xp;
+}
+
+
+void xds_cleanup(IndexingPrivate *pp)
+{
+	struct xds_private *xp;
+
+	xp = (struct xds_private *)pp;
+	free(xp);
 }
diff --git a/libcrystfel/src/xds.h b/libcrystfel/src/xds.h
index edf83b0b..7dd7c6a8 100644
--- a/libcrystfel/src/xds.h
+++ b/libcrystfel/src/xds.h
@@ -5,6 +5,7 @@
  *
  * Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
  *                  a research centre of the Helmholtz Association.
+ * Copyright © 2013 Cornelius Gati
  *
  * Authors:
  *   2010-2013 Thomas White <taw@physics.org>
@@ -27,17 +28,23 @@
  *
  */
 
-#ifndef xds_H
-#define xds_H
+#ifndef XDS_H
+#define XDS_H
 
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
 
 #include "cell.h"
+#include "index.h"
 
 
-extern void run_xds(struct image *image, UnitCell *cell);
+extern int run_xds(struct image *image, IndexingPrivate *ipriv);
 
+extern IndexingPrivate *xds_prepare(IndexingMethod *indm, UnitCell *cell,
+                                    const char *filename, struct detector *det,
+                                    struct beam_params *beam, float *ltl);
+
+extern void xds_cleanup(IndexingPrivate *pp);
 
 #endif	/* XDS_H */