예제 #1
0
int main(int argc, char *argv[])
{
	struct image image;
	const double incr_frac = 1.0/1000000.0;
	double incr_val;
	double ax, ay, az;
	double bx, by, bz;
	double cx, cy, cz;
	UnitCell *cell;
	Crystal *cr;
	struct quaternion orientation;
	int i;
	int fail = 0;
	int quiet = 0;
	int plot = 0;
	int c;
	gsl_rng *rng;

	const struct option longopts[] = {
		{"quiet",       0, &quiet,        1},
		{"plot",        0, &plot,         1},
		{0, 0, NULL, 0}
	};

	while ((c = getopt_long(argc, argv, "", longopts, NULL)) != -1) {
		switch (c) {

			case 0 :
			break;

			case '?' :
			break;

			default :
			ERROR("Unhandled option '%c'\n", c);
			break;

		}

	}

	image.width = 1024;
	image.height = 1024;
	image.det = simple_geometry(&image);
	image.det->panels[0].res = 13333.3;
	image.det->panels[0].clen = 80e-3;
	image.det->panels[0].coffset = 0.0;

	image.lambda = ph_en_to_lambda(eV_to_J(8000.0));
	image.div = 1e-3;
	image.bw = 0.01;
	image.filename = malloc(256);

	cr = crystal_new();
	if ( cr == NULL ) {
		ERROR("Failed to allocate crystal.\n");
		return 1;
	}
	crystal_set_mosaicity(cr, 0.0);
	crystal_set_profile_radius(cr, 0.005e9);
	crystal_set_image(cr, &image);

	cell = cell_new_from_parameters(10.0e-9, 10.0e-9, 10.0e-9,
	                                deg2rad(90.0),
	                                deg2rad(90.0),
	                                deg2rad(90.0));

	rng = gsl_rng_alloc(gsl_rng_mt19937);

	for ( i=0; i<2; i++ ) {

		UnitCell *rot;
		double val;
		PartialityModel pmodel;

		if ( i == 0 ) {
			pmodel = PMODEL_SCSPHERE;
			STATUS("Testing SCSphere model:\n");
		} else if ( i == 1 ) {
			pmodel = PMODEL_SCGAUSSIAN;
			STATUS("Testing SCGaussian model.\n");
		} else {
			ERROR("WTF?\n");
			return 1;
		}

		orientation = random_quaternion(rng);
		rot = cell_rotate(cell, orientation);
		crystal_set_cell(cr, rot);

		cell_get_reciprocal(rot,
			            &ax, &ay, &az, &bx, &by,
			            &bz, &cx, &cy, &cz);

		incr_val = incr_frac * image.div;
		val =  test_gradients(cr, incr_val, REF_DIV, "div", "div",
		                      pmodel, quiet, plot);
		if ( val < 0.99 ) fail = 1;

		incr_val = incr_frac * crystal_get_profile_radius(cr);
		val = test_gradients(cr, incr_val, REF_R, "R", "R", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;

		incr_val = incr_frac * ax;
		val = test_gradients(cr, incr_val, REF_ASX, "ax*", "x", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;
		incr_val = incr_frac * bx;
		val = test_gradients(cr, incr_val, REF_BSX, "bx*", "x", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;
		incr_val = incr_frac * cx;
		val = test_gradients(cr, incr_val, REF_CSX, "cx*", "x", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;

		incr_val = incr_frac * ay;
		val = test_gradients(cr, incr_val, REF_ASY, "ay*", "y", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;
		incr_val = incr_frac * by;
		val = test_gradients(cr, incr_val, REF_BSY, "by*", "y", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;
		incr_val = incr_frac * cy;
		val = test_gradients(cr, incr_val, REF_CSY, "cy*", "y", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;

		incr_val = incr_frac * az;
		val = test_gradients(cr, incr_val, REF_ASZ, "az*", "z", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;
		incr_val = incr_frac * bz;
		val = test_gradients(cr, incr_val, REF_BSZ, "bz*", "z", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;
		incr_val = incr_frac * cz;
		val = test_gradients(cr, incr_val, REF_CSZ, "cz*", "z", pmodel,
		                     quiet, plot);
		if ( val < 0.99 ) fail = 1;

	}

	gsl_rng_free(rng);

	return fail;
}
예제 #2
0
static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
{
	char line[1024];
	char *rval = NULL;
	struct rvec as, bs, cs;
	int have_as = 0;
	int have_bs = 0;
	int have_cs = 0;
	int have_latt = 0;
	int have_cen = 0;
	int have_ua = 0;
	char centering = 'P';
	char unique_axis = '*';
	LatticeType lattice_type = L_TRICLINIC;
	Crystal *cr;
	int n;
	Crystal **crystals_new;

	cr = crystal_new();
	if ( cr == NULL ) {
		ERROR("Failed to allocate crystal!\n");
		return;
	}

	do {

		float u, v, w, lim, rad;
		char c;

		rval = fgets(line, 1023, st->fh);

		/* Trouble? */
		if ( rval == NULL ) break;

		chomp(line);
		if ( (srf & STREAM_READ_UNITCELL)
		  && (sscanf(line, "astar = %f %f %f", &u, &v, &w) == 3) )
		{
			as.u = u*1e9;  as.v = v*1e9;  as.w = w*1e9;
			have_as = 1;
		}

		if ( (srf & STREAM_READ_UNITCELL)
		  && (sscanf(line, "bstar = %f %f %f", &u, &v, &w) == 3) )
		{
			bs.u = u*1e9;  bs.v = v*1e9;  bs.w = w*1e9;
			have_bs = 1;
		}

		if ( (srf & STREAM_READ_UNITCELL)
		  && (sscanf(line, "cstar = %f %f %f", &u, &v, &w) == 3) )
		{
			cs.u = u*1e9;  cs.v = v*1e9;  cs.w = w*1e9;
			have_cs = 1;
		}

		if ( (srf & STREAM_READ_UNITCELL)
		  && (sscanf(line, "centering = %c", &c) == 1) )
		{
			if ( !have_cen ) {
				centering = c;
				have_cen = 1;
			} else {
				ERROR("Duplicate centering ignored.\n");
			}
		}

		if ( (srf & STREAM_READ_UNITCELL)
		  && (sscanf(line, "unique_axis = %c", &c) == 1) )
		{
			if ( !have_ua ) {
				unique_axis = c;
				have_ua = 1;
			} else {
				ERROR("Duplicate unique axis ignored.\n");
			}
		}

		if ( (srf & STREAM_READ_UNITCELL)
		  && (strncmp(line, "lattice_type = ", 15) == 0) )
		{
			if ( !have_latt ) {
				lattice_type = lattice_from_str(line+15);
				have_latt = 1;
			} else {
				ERROR("Duplicate lattice type ignored.\n");
			}
		}

		if ( strncmp(line, "num_saturated_reflections = ", 28) == 0 ) {
			int n = atoi(line+28);
			crystal_set_num_saturated_reflections(cr, n);
		}

		if ( sscanf(line, "diffraction_resolution_limit = %f nm^-1",
		            &lim) == 1 ) {
			crystal_set_resolution_limit(cr, lim*1e9);
		}

		if ( sscanf(line, "profile_radius = %f nm^-1", &rad) == 1 ) {
			crystal_set_profile_radius(cr, rad*1e9);
		}

		if ( (strcmp(line, REFLECTION_START_MARKER) == 0)
		  && (srf & STREAM_READ_REFLECTIONS) )
		{

			RefList *reflist;

			/* The reflection list format in the stream diverges
			 * after 2.2 */
			if ( AT_LEAST_VERSION(st, 2, 2) ) {
				reflist = read_stream_reflections(st->fh);
			} else {
				reflist = read_stream_reflections_2_1(st->fh);
			}
			if ( reflist == NULL ) {
				ERROR("Failed while reading reflections\n");
				break;
			}

			crystal_set_reflections(cr, reflist);

		}

		if ( strcmp(line, CRYSTAL_END_MARKER) == 0 ) break;

	} while ( 1 );

	if ( have_as && have_bs && have_cs ) {

		UnitCell *cell;

		cell = crystal_get_cell(cr);

		if ( cell != NULL ) {
			ERROR("Duplicate cell found in stream!\n");
			ERROR("I'll use the most recent one.\n");
			cell_free(cell);
		}

		cell = cell_new_from_reciprocal_axes(as, bs, cs);

		if ( have_cen && have_ua && have_latt ) {
			cell_set_centering(cell, centering);
			cell_set_unique_axis(cell, unique_axis);
			cell_set_lattice_type(cell, lattice_type);
		} /* else keep default triclinic P */

		crystal_set_cell(cr, cell);

		have_as = 0;  have_bs = 0;  have_cs = 0;
		have_latt = 0;  have_ua = 0;  have_cen = 0;

	}

	/* Unused at the moment */
	crystal_set_mosaicity(cr, 0.0);

	/* Add crystal to the list for this image */
	n = image->n_crystals+1;
	crystals_new = realloc(image->crystals, n*sizeof(Crystal *));

	if ( crystals_new == NULL ) {
		ERROR("Failed to expand crystal list!\n");
	} else {
		image->crystals = crystals_new;
		image->crystals[image->n_crystals++] = cr;
	}

}