facetron: Work on geometry

1 files changed, 128 insertions, 60 deletions

diff --git a/src/geometry.c b/src/geometry.c
index cca2d050..2b94e7ba 100644
--- a/src/geometry.c
+++ b/src/geometry.c
@@ -15,18 +15,93 @@
 
 
 #include <stdlib.h>
+#include <gsl/gsl_poly.h>
+#include <assert.h>
 
 #include "utils.h"
 #include "cell.h"
 #include "image.h"
 #include "peaks.h"
+#include "beam-parameters.h"
 
 
-#define MAX_CPEAKS (1024)
+#define MAX_CPEAKS (256 * 256)
+
+
+static signed int locate_peak(double x, double y, double z, double lambda,
+                              struct detector *det, double *xdap, double *ydap)
+{
+	int p;
+	signed int found = -1;
+	const double den = 1.0/lambda + z;
+
+	for ( p=0; p<det->n_panels; p++ ) {
+
+		double xd, yd, cl;
+		double xda, yda;
+
+		/* Camera length for this panel */
+		cl = det->panels[p].clen;
+
+		/* Coordinates of peak relative to central beam, in m */
+		xd = cl * x / den;
+		yd = cl * y / den;
+
+		/* Convert to pixels */
+		xd *= det->panels[p].res;
+		yd *= det->panels[p].res;
+
+		/* Add the coordinates of the central beam */
+		xda = xd + det->panels[p].cx;
+		yda = yd + det->panels[p].cy;
+
+		/* Now, is this on this panel? */
+		if ( xda < det->panels[p].min_x ) continue;
+		if ( xda > det->panels[p].max_x ) continue;
+		if ( yda < det->panels[p].min_y ) continue;
+		if ( yda > det->panels[p].max_y ) continue;
+
+		/* If peak appears on multiple panels, reject it */
+		if ( found != -1 ) return -1;
+
+		/* Woohoo! */
+		found = p;
+		*xdap = xda;
+		*ydap = yda;
+
+	}
+
+	return found;
+}
+
+
+static double excitation_error(double xl, double yl, double zl,
+                               double ds_sq, double lambda)
+{
+	double tt;
+	double a, b, c;
+	double r1, r2;
+	int n;
+
+	tt = angle_between(0.0, 0.0, 1.0,  xl, yl, zl+1.0/lambda);
+
+	a = 1.0;
+	b = - cos(tt) * 2.0/lambda;
+	c = pow(lambda, -2.0) - ds_sq;
+
+	/* FIXME: I don't trust GSL's quadratic solver */
+	n = gsl_poly_solve_quadratic(a, b, c, &r1, &r2);
+	assert(n == 2);
+
+	r1 -= 1.0/lambda;
+	r2 -= 1.0/lambda;
+
+	if ( r1 > r2 ) return r2;
+	return r1;
+}
 
 
 struct cpeak *find_intersections(struct image *image, UnitCell *cell,
-                                 double divergence, double bandwidth,
                                  int *n, int output)
 {
 	double asx, asy, asz;
@@ -37,6 +112,11 @@ struct cpeak *find_intersections(struct image *image, UnitCell *cell,
 	int hmax, kmax, lmax;
 	double mres;
 	signed int h, k, l;
+	double bandwidth = image->bw;
+	double divergence = image->div;
+	double lambda = image->lambda;
+	const double profile_cutoff = 0.05e9;  /* 0.1 nm^-1 */
+	double llow, lhigh;    /* Wavelength */
 
 	cpeaks = malloc(sizeof(struct cpeak)*MAX_CPEAKS);
 	if ( cpeaks == NULL ) {
@@ -48,103 +128,91 @@ struct cpeak *find_intersections(struct image *image, UnitCell *cell,
 	                          &bsx, &bsy, &bsz,
 	                          &csx, &csy, &csz);
 
+	/* FIXME: Account for left-handed indexing */
+	asz = -asz;  bsz = -bsz;  csz = -csz;
+
 	mres = 1.0 / 8.0e-10;  /* 8 Angstroms */
 	hmax = mres / modulus(asx, asy, asz);
 	kmax = mres / modulus(bsx, bsy, bsz);
 	lmax = mres / modulus(csx, csy, csz);
 
+	/* "low" gives the largest Ewald sphere,
+	 * "high" gives the smallest Ewald sphere. */
+	llow = lambda - lambda*bandwidth/2.0;
+	lhigh = lambda + lambda*bandwidth/2.0;
+
 	for ( h=-hmax; h<hmax; h++ ) {
 	for ( k=-kmax; k<kmax; k++ ) {
 	for ( l=-lmax; l<lmax; l++ ) {
 
 		double xl, yl, zl;
-		double ds_sq, dps_sq;
-		double delta, divfact;
-		double llow, lhigh;
-		double xd, yd, cl;
+		double ds, ds_sq;
+		double rlow, rhigh;    /* "Excitation error" */
+		signed int plow, phigh;
+		double xdalow, xdahigh;
+		double ydalow, ydahigh;
 		double xda, yda;
-		int p;
-		int found = 0;
 
+		/* Ignore central beam */
 		if ( (h==0) && (k==0) && (l==0) ) continue;
 
-		llow = image->lambda - image->lambda*bandwidth/2.0;
-		lhigh = image->lambda + image->lambda*bandwidth/2.0;
-
 		/* Get the coordinates of the reciprocal lattice point */
 		zl = h*asz + k*bsz + l*csz;
-		if ( zl < 0.0 ) continue;  /* Do this check very early */
+		if ( zl > 0.0 ) continue;  /* Throw out if it's "in front" */
 		xl = h*asx + k*bsx + l*csx;
 		yl = h*asy + k*bsy + l*csy;
 
+		/* Calculate reciprocal lattice point modulus (and square) */
 		ds_sq = modulus_squared(xl, yl, zl);  /* d*^2 */
-		delta = divergence/image->lambda;
-		dps_sq = ds_sq + pow(delta, 2.0);  /* d'*^2 */
-
-		/* In range? */
-		divfact = 2.0 * delta * sqrt(xl*xl + yl*yl);
-		if ( ds_sq - 2.0*zl/llow > 0.0 ) continue;
-		if ( ds_sq - 2.0*zl/lhigh < 0.0 ) continue;
-
-		/* Work out which panel this peak would fall on */
-		for ( p=0; p<image->det->n_panels; p++ ) {
-
-			/* Camera length for this panel */
-			cl = image->det->panels[p].clen;
-
-			/* Coordinates of peak relative to central beam, in m */
-			xd = cl*xl / (ds_sq/(2.0*zl) - zl);
-			yd = cl*yl / (ds_sq/(2.0*zl) - zl);
-
-			/* Convert to pixels */
-			xd *= image->det->panels[p].res;
-			yd *= image->det->panels[p].res;
-
-			/* Add the coordinates of the central beam */
-			xda = xd + image->det->panels[p].cx;
-			yda = yd + image->det->panels[p].cy;
-
-			/* Now, is this on this panel? */
-			if ( xda < image->det->panels[p].min_x ) continue;
-			if ( xda > image->det->panels[p].max_x ) continue;
-			if ( yda < image->det->panels[p].min_y ) continue;
-			if ( yda > image->det->panels[p].max_y ) continue;
-
-			/* Woohoo! */
-			found = 1;
-			break;
-
+		ds = sqrt(ds_sq);
+		if ( ds > mres ) continue;  /* Outside resolution range */
+
+		/* Calculate excitation errors */
+		rlow = excitation_error(xl, yl, zl, ds_sq, llow);
+		rhigh = excitation_error(xl, yl, zl, ds_sq, lhigh);
+
+		if ( (fabs(rlow) > profile_cutoff)
+		  && (fabs(rhigh) > profile_cutoff) ) {
+			/* Reflection is not close to Bragg at either of
+			 * the two extremes of wavelength, so skip it. */
+			continue;
 		}
 
-		if ( !found ) continue;
-
+		/* Locate peak on detector, and check it doesn't span panels */
+		plow = locate_peak(xl, yl, zl, llow, image->det,
+		                   &xdalow, &ydalow);
+		if ( plow == -1 ) continue;
+		phigh = locate_peak(xl, yl, zl, lhigh, image->det,
+		                    &xdahigh, &ydahigh);
+		if ( phigh == -1 ) continue;
+		if ( plow != phigh ) continue;
+
+		xda = xdahigh;
+		yda = ydahigh;
 		cpeaks[np].h = h;
 		cpeaks[np].k = k;
 		cpeaks[np].l = l;
-		cpeaks[np].x = xda;
-		cpeaks[np].y = yda;
+		cpeaks[np].x = xdahigh;
+		cpeaks[np].y = ydahigh;
 		np++;
 
 		if ( output ) {
-			printf("%i %i %i 0.0 (at %f,%f)\n", h, k, l, xda, yda);
+			printf("%3i %3i %3i %6f (at %5.2f,%5.2f) %9e %9e\n",
+			       h, k, l, 0.0, xda, yda, rlow, rhigh);
 		}
 
+		if ( np == MAX_CPEAKS ) goto out;
+
 	}
 	}
 	}
 
+out:
 	*n = np;
 	return cpeaks;
 }
 
 
-/* Return the partiality of this reflection in this image */
-double partiality(struct image *image, signed int h, signed int k, signed int l)
-{
-	return 1.0;
-}
-
-
 double integrate_all(struct image *image, struct cpeak *cpeaks, int n)
 {
 	double itot = 0.0;