Merge remote-tracking branch 'bitwiz/cornelius/xds' into tom/multicrystal

1 files changed, 95 insertions, 24 deletions

diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 9660b5bc..92619d65 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -253,25 +253,30 @@ static int read_cell(const char *filename, struct image *image,
 
 	do {
 		rval = fgets(line, 1023, fh);
+		if ( rval == NULL ) return 0;
 
 	} while ( strcmp(line, "   #  COORDINATES OF REC. BASIS VECTOR"
 	                       "    LENGTH   1/LENGTH\n") != 0 );
 
 	/* Free line after chunk */
 	rval = fgets(line, 1023, fh);
+	if ( rval == NULL ) return 0;
 	rval = fgets(line, 1023, fh);
+	if ( rval == NULL ) return 0;
 
 	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);
+	if ( rval == NULL ) return 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);
+	if ( rval == NULL ) return 0;
 
 	memcpy(csx, line+7, 10);    csx[10] = '\0';
 	memcpy(csy, line+17, 10);   csy[10] = '\0';
@@ -377,21 +382,88 @@ static void write_spot(struct image *image, const char *filename)
 }
 
 
-static char *write_inp(struct image *image)
+/* Turn what we know about the unit cell into something which we can give to
+ * XDS to make it give us only indexing results compatible with the cell. */
+static const char *spacegroup_for_lattice(UnitCell *cell)
 {
-	FILE *fh;
-	char *filename;
+	LatticeType latt;
+	char centering;
+	char *g = NULL;
+
+	latt = cell_get_lattice_type(cell);
+	centering = cell_get_centering(cell);
+
+	switch ( latt )
+	{
+		case L_TRICLINIC :
+		g = "1";
+		break;
+
+		case L_MONOCLINIC :
+		if ( centering == 'P' )	{
+			g = "3";
+		} else {
+			g = "5";
+		}
+		break;
+
+		case L_ORTHORHOMBIC :
+		if ( centering == 'P' ) {
+			g = "16";
+		} else if ( centering == 'C' ) {
+			g = "20";
+		} else if ( centering == 'F' ) {
+			g = "22";
+		} else {
+			g = "23";
+		}
+		break;
+
+		case L_TETRAGONAL :
+		if ( centering == 'P' ) {
+			g = "75";
+		} else {
+			g = "79";
+		}
+		break;
+
+		case L_RHOMBOHEDRAL :
+		if ( centering == 'P' ) {
+			g = "143";
+		} else {
+			g = "146";
+		}
+		break;
+
+		case L_HEXAGONAL :
+		g = "168";
+		break;
+
+		case L_CUBIC :
+		if ( centering == 'P' ) {
+			g = "195";
+		} else if ( centering == 'F' ) {
+			g = "196";
+		} else {
+			g = "197";
+		}
+		break;
+	}
+	assert(g != NULL);
+
+	return g;
+}
 
-	filename = malloc(1024);
-	if ( filename == NULL ) return NULL;
 
-	snprintf(filename, 1023, "XDS.INP");
+static int write_inp(struct image *image, struct xds_private *xp)
+{
+	FILE *fh;
+	double a, b, c, al, be, ga;
 
-	fh = fopen(filename, "w");
+	fh = fopen("XDS.INP", "w");
 	if ( !fh ) {
-		ERROR("Couldn't open temporary file '%s'\n", filename);
-		free(filename);
-		return NULL;
+		ERROR("Couldn't open XDS.INP\n");
+		return 0;
 	}
 
 	fprintf(fh, "JOB= IDXREF\n");
@@ -399,16 +471,17 @@ static char *write_inp(struct image *image)
 	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, "X-RAY_WAVELENGTH= %.6f\n", image->lambda*1e10);
+	fprintf(fh, "NAME_TEMPLATE_OF_DATA_FRAMES=/home/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, "SPACE_GROUP_NUMBER= %s\n",
+	        spacegroup_for_lattice(xp->cell));
+	cell_get_parameters(xp->cell, &a, &b, &c, &al, &be, &ga);
+	fprintf(fh, "UNIT_CELL_CONSTANTS= %.2f %.2f %.2f %.2f %.2f %.2f\n",
+                a*1e10, b*1e10, c*1e10,rad2deg(al), rad2deg(be), rad2deg(ga));
+	//fprintf(fh, "SPACE_GROUP_NUMBER= 0\n");
+	//fprintf(fh, "UNIT_CELL_CONSTANTS= 0 0 0 0 0 0\n");
 	fprintf(fh, "NX= 3000\n");
 	fprintf(fh, "NY= 3000\n");
 	fprintf(fh, "QX= 0.07\n");
@@ -429,7 +502,7 @@ static char *write_inp(struct image *image)
 
 	fclose(fh);
 
-	return filename;
+	return 0;
 }
 
 
@@ -440,7 +513,6 @@ int run_xds(struct image *image, IndexingPrivate *priv)
 	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));
@@ -451,10 +523,9 @@ int run_xds(struct image *image, IndexingPrivate *priv)
 
 	xds->target_cell = xp->cell;
 
-	write_inp(image);
-	inp_filename = write_inp(image);
-
-	if ( inp_filename == NULL ) {
+	write_inp(image, xp);
+	
+	if ( write_inp == NULL ) {
 		ERROR("Failed to write XDS.INP file for XDS.\n");
 		return 0;
 	}