From b6f9a2f6b7efe10b7d2746e907210d9248ffe9fe Mon Sep 17 00:00:00 2001 From: Thomas White Date: Tue, 19 Feb 2013 14:35:00 +0100 Subject: Tidy up etc --- libcrystfel/src/xds.c | 144 ++++++++++++++++++++++++-------------------------- 1 file changed, 68 insertions(+), 76 deletions(-) (limited to 'libcrystfel') diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c index 4034a8e4..84cf828a 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'; @@ -377,64 +382,6 @@ static void write_spot(struct image *image, const char *filename) } -static char *write_inp(struct image *image, struct xds_private *xp) -{ - FILE *fh; - char *filename; - const char *spacegroup_for_lattice; - double a, b, c, al, be, ga; - - 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= %.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"); - //symm = spacegroup_for_lattice(xds->xp->template); - fprintf(fh, "SPACE_GROUP_NUMBER= %s\n", spacegroup_for_lattice); - cell_get_parameters(xp->cell, &a, &b, &c, &al, &be, &ga); - fprintf(fh, "UNIT_CELL_CONSTANTS= %.6f %.6f %.6f %.6f %.6f %.6f P\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"); - 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; -} - /* 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) @@ -453,21 +400,20 @@ static const char *spacegroup_for_lattice(UnitCell *cell) break; case L_MONOCLINIC : - if ( centering != 'P' ) + if ( centering != 'P' ) { g = "3"; - } else - { + } else { g = "5"; } break; case L_ORTHORHOMBIC : if ( centering != 'P' ) { - g = "16";} - else if ( centering != 'C' ) { - g = "20";} - else if ( centering != 'F' ) { + g = "16"; + } else if ( centering != 'C' ) { + g = "20"; + } else if ( centering != 'F' ) { g = "22"; } else { g = "23"; @@ -477,9 +423,7 @@ static const char *spacegroup_for_lattice(UnitCell *cell) case L_TETRAGONAL : if ( centering != 'P' ) { g = "75"; - } - else - { + } else { g = "79"; } break; @@ -489,7 +433,7 @@ static const char *spacegroup_for_lattice(UnitCell *cell) g = "143"; } else { g = "146"; - } + } break; case L_HEXAGONAL : @@ -499,19 +443,70 @@ static const char *spacegroup_for_lattice(UnitCell *cell) case L_CUBIC : if ( centering != 'P' ) { g = "195"; - } - else if ( centering != 'F' ) { + } else if ( centering != 'F' ) { g = "196"; } else { g = "197"; } break; - } + } assert(g != NULL); return g; } + +static int write_inp(struct image *image, struct xds_private *xp) +{ + FILE *fh; + double a, b, c, al, be, ga; + + fh = fopen("XDS.INP", "w"); + if ( !fh ) { + ERROR("Couldn't open XDS.INP\n"); + return 1; + } + + 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= %.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= %s\n", + spacegroup_for_lattice(xp->cell)); + cell_get_parameters(xp->cell, &a, &b, &c, &al, &be, &ga); + fprintf(fh, "UNIT_CELL_CONSTANTS= %.6f %.6f %.6f %.6f %.6f %.6f P\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"); + 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 0; +} + + int run_xds(struct image *image, IndexingPrivate *priv) { unsigned int opts; @@ -519,7 +514,6 @@ 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)); @@ -530,9 +524,7 @@ int run_xds(struct image *image, IndexingPrivate *priv) xds->target_cell = xp->cell; - write_inp(image, xp); - - if ( inp_filename == NULL ) { + if ( write_inp(image, xp) ) { ERROR("Failed to write XDS.INP file for XDS.\n"); return 0; } -- cgit v1.2.3