Move a load more stuff into libcrystfel

1 files changed, 463 insertions, 0 deletions

diff --git a/libcrystfel/src/diffraction.c b/libcrystfel/src/diffraction.c
new file mode 100644
index 00000000..9532a6ce
--- /dev/null
+++ b/libcrystfel/src/diffraction.c
@@ -0,0 +1,463 @@
+/*
+ * diffraction.c
+ *
+ * Calculate diffraction patterns by Fourier methods
+ *
+ * (c) 2006-2011 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#include <stdlib.h>
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include <complex.h>
+#include <assert.h>
+#include <fenv.h>
+
+#include "image.h"
+#include "utils.h"
+#include "cell.h"
+#include "diffraction.h"
+#include "beam-parameters.h"
+#include "symmetry.h"
+
+
+#define SAMPLING (4)
+#define BWSAMPLING (10)
+#define DIVSAMPLING (1)
+#define SINC_LUT_ELEMENTS (4096)
+
+
+static double *get_sinc_lut(int n)
+{
+	int i;
+	double *lut;
+
+	lut = malloc(SINC_LUT_ELEMENTS*sizeof(double));
+	lut[0] = n;
+	if ( n == 1 ) {
+		for ( i=1; i<SINC_LUT_ELEMENTS; i++ ) {
+			lut[i] = 1.0;
+		}
+	} else {
+		for ( i=1; i<SINC_LUT_ELEMENTS; i++ ) {
+			double x, val;
+			x = (double)i/SINC_LUT_ELEMENTS;
+			val = fabs(sin(M_PI*n*x)/sin(M_PI*x));
+			lut[i] = val;
+		}
+	}
+
+	return lut;
+}
+
+
+static double interpolate_lut(double *lut, double val)
+{
+	double i, pos, f;
+	unsigned int low, high;
+
+	pos = SINC_LUT_ELEMENTS * modf(fabs(val), &i);
+	low = (int)pos;  /* Discard fractional part */
+	high = low + 1;
+	f = modf(pos, &i);  /* Fraction */
+	if ( high == SINC_LUT_ELEMENTS ) high = 0;
+
+	return (1.0-f)*lut[low] + f*lut[high];
+}
+
+
+static double lattice_factor(struct rvec q, double ax, double ay, double az,
+                                            double bx, double by, double bz,
+                                            double cx, double cy, double cz,
+                                            double *lut_a, double *lut_b,
+                                            double *lut_c)
+{
+	struct rvec Udotq;
+	double f1, f2, f3;
+
+	Udotq.u = ax*q.u + ay*q.v + az*q.w;
+	Udotq.v = bx*q.u + by*q.v + bz*q.w;
+	Udotq.w = cx*q.u + cy*q.v + cz*q.w;
+
+	f1 = interpolate_lut(lut_a, Udotq.u);
+	f2 = interpolate_lut(lut_b, Udotq.v);
+	f3 = interpolate_lut(lut_c, Udotq.w);
+
+	return f1 * f2 * f3;
+}
+
+
+static double sym_lookup_intensity(const double *intensities,
+                                   const unsigned char *flags,
+                                   const SymOpList *sym,
+                                   signed int h, signed int k, signed int l)
+{
+	int i;
+	double ret = 0.0;
+
+	for ( i=0; i<num_equivs(sym, NULL); i++ ) {
+
+		signed int he;
+		signed int ke;
+		signed int le;
+		double f, val;
+
+		get_equiv(sym, NULL, i, h, k, l, &he, &ke, &le);
+
+		f = (double)lookup_flag(flags, he, ke, le);
+		val = lookup_intensity(intensities, he, ke, le);
+
+		ret += f*val;
+
+	}
+
+	return ret;
+}
+
+
+static double sym_lookup_phase(const double *phases,
+                               const unsigned char *flags, const SymOpList *sym,
+                               signed int h, signed int k, signed int l)
+{
+	int i;
+	double ret = 0.0;
+
+	for ( i=0; i<num_equivs(sym, NULL); i++ ) {
+
+		signed int he;
+		signed int ke;
+		signed int le;
+		double f, val;
+
+		get_equiv(sym, NULL, i, h, k, l, &he, &ke, &le);
+
+		f = (double)lookup_flag(flags, he, ke, le);
+		val = lookup_phase(phases, he, ke, le);
+
+		ret += f*val;
+
+	}
+
+	return ret;
+}
+
+
+static double interpolate_linear(const double *ref, const unsigned char *flags,
+                                 const SymOpList *sym, float hd,
+                                 signed int k, signed int l)
+{
+	signed int h;
+	double val1, val2;
+	float f;
+
+	h = (signed int)hd;
+	if ( hd < 0.0 ) h -= 1;
+	f = hd - (float)h;
+	assert(f >= 0.0);
+
+	val1 = sym_lookup_intensity(ref, flags, sym, h, k, l);
+	val2 = sym_lookup_intensity(ref, flags, sym, h+1, k, l);
+
+	val1 = val1;
+	val2 = val2;
+
+	return (1.0-f)*val1 + f*val2;
+}
+
+
+static double interpolate_bilinear(const double *ref,
+                                   const unsigned char *flags,
+                                   const SymOpList *sym,
+                                   float hd, float kd, signed int l)
+{
+	signed int k;
+	double val1, val2;
+	float f;
+
+	k = (signed int)kd;
+	if ( kd < 0.0 ) k -= 1;
+	f = kd - (float)k;
+	assert(f >= 0.0);
+
+	val1 = interpolate_linear(ref, flags, sym, hd, k, l);
+	val2 = interpolate_linear(ref, flags, sym, hd, k+1, l);
+
+	return (1.0-f)*val1 + f*val2;
+}
+
+
+static double interpolate_intensity(const double *ref,
+                                    const unsigned char *flags,
+                                    const SymOpList *sym,
+                                    float hd, float kd, float ld)
+{
+	signed int l;
+	double val1, val2;
+	float f;
+
+	l = (signed int)ld;
+	if ( ld < 0.0 ) l -= 1;
+	f = ld - (float)l;
+	assert(f >= 0.0);
+
+	val1 = interpolate_bilinear(ref, flags, sym, hd, kd, l);
+	val2 = interpolate_bilinear(ref, flags, sym, hd, kd, l+1);
+
+	return (1.0-f)*val1 + f*val2;
+}
+
+
+static double complex interpolate_phased_linear(const double *ref,
+                                                const double *phases,
+                                                const unsigned char *flags,
+                                                const SymOpList *sym,
+                                                float hd,
+                                                signed int k, signed int l)
+{
+	signed int h;
+	double val1, val2;
+	float f;
+	double ph1, ph2;
+	double re1, re2, im1, im2;
+	double re, im;
+
+	h = (signed int)hd;
+	if ( hd < 0.0 ) h -= 1;
+	f = hd - (float)h;
+	assert(f >= 0.0);
+
+	val1 = sym_lookup_intensity(ref, flags, sym, h, k, l);
+	val2 = sym_lookup_intensity(ref, flags, sym, h+1, k, l);
+	ph1 = sym_lookup_phase(phases, flags, sym, h, k, l);
+	ph2 = sym_lookup_phase(phases, flags, sym, h+1, k, l);
+
+	val1 = val1;
+	val2 = val2;
+
+	/* Calculate real and imaginary parts */
+	re1 = val1 * cos(ph1);
+	im1 = val1 * sin(ph1);
+	re2 = val2 * cos(ph2);
+	im2 = val2 * sin(ph2);
+
+	re = (1.0-f)*re1 + f*re2;
+	im = (1.0-f)*im1 + f*im2;
+
+	return re + im*I;
+}
+
+
+static double complex interpolate_phased_bilinear(const double *ref,
+                                                  const double *phases,
+                                                  const unsigned char *flags,
+                                                  const SymOpList *sym,
+                                                  float hd, float kd,
+                                                  signed int l)
+{
+	signed int k;
+	double complex val1, val2;
+	float f;
+
+	k = (signed int)kd;
+	if ( kd < 0.0 ) k -= 1;
+	f = kd - (float)k;
+	assert(f >= 0.0);
+
+	val1 = interpolate_phased_linear(ref, phases, flags, sym, hd, k, l);
+	val2 = interpolate_phased_linear(ref, phases, flags, sym, hd, k+1, l);
+
+	return (1.0-f)*val1 + f*val2;
+}
+
+
+static double interpolate_phased_intensity(const double *ref,
+                                           const double *phases,
+                                           const unsigned char *flags,
+                                           const SymOpList *sym,
+                                           float hd, float kd, float ld)
+{
+	signed int l;
+	double complex val1, val2;
+	float f;
+
+	l = (signed int)ld;
+	if ( ld < 0.0 ) l -= 1;
+	f = ld - (float)l;
+	assert(f >= 0.0);
+
+	val1 = interpolate_phased_bilinear(ref, phases, flags, sym,
+	                                   hd, kd, l);
+	val2 = interpolate_phased_bilinear(ref, phases, flags, sym,
+	                                   hd, kd, l+1);
+
+	return cabs((1.0-f)*val1 + f*val2);
+}
+
+
+/* Look up the structure factor for the nearest Bragg condition */
+static double molecule_factor(const double *intensities, const double *phases,
+                              const unsigned char *flags, struct rvec q,
+                              double ax, double ay, double az,
+                              double bx, double by, double bz,
+                              double cx, double cy, double cz,
+                              GradientMethod m, const SymOpList *sym)
+{
+	float hd, kd, ld;
+	signed int h, k, l;
+	double r;
+
+	hd = q.u * ax + q.v * ay + q.w * az;
+	kd = q.u * bx + q.v * by + q.w * bz;
+	ld = q.u * cx + q.v * cy + q.w * cz;
+
+	/* No flags -> flat intensity distribution */
+	if ( flags == NULL ) return 1.0e5;
+
+	switch ( m ) {
+	case GRADIENT_MOSAIC :
+		fesetround(1);  /* Round to nearest */
+		h = (signed int)rint(hd);
+		k = (signed int)rint(kd);
+		l = (signed int)rint(ld);
+		if ( abs(h) > INDMAX ) r = 0.0;
+		else if ( abs(k) > INDMAX ) r = 0.0;
+		else if ( abs(l) > INDMAX ) r = 0.0;
+		else r = sym_lookup_intensity(intensities, flags, sym, h, k, l);
+		break;
+	case GRADIENT_INTERPOLATE :
+		r = interpolate_intensity(intensities, flags, sym, hd, kd, ld);
+		break;
+	case GRADIENT_PHASED :
+		r = interpolate_phased_intensity(intensities, phases, flags,
+		                                 sym, hd, kd, ld);
+		break;
+	default:
+		ERROR("This gradient method not implemented yet.\n");
+		exit(1);
+	}
+
+	return r;
+}
+
+
+void get_diffraction(struct image *image, int na, int nb, int nc,
+                     const double *intensities, const double *phases,
+                     const unsigned char *flags, UnitCell *cell,
+                     GradientMethod m, const SymOpList *sym)
+{
+	unsigned int fs, ss;
+	double ax, ay, az;
+	double bx, by, bz;
+	double cx, cy, cz;
+	float klow, khigh, bwstep;
+	double *lut_a;
+	double *lut_b;
+	double *lut_c;
+	double divxlow, divylow, divxstep, divystep;
+
+	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+
+	/* Allocate (and zero) the "diffraction array" */
+	image->data = calloc(image->width * image->height, sizeof(float));
+
+	/* Needed later for Lorentz calculation */
+	image->twotheta = malloc(image->width * image->height * sizeof(double));
+
+	klow = 1.0/(image->lambda*(1.0 + image->beam->bandwidth/2.0));
+	khigh = 1.0/(image->lambda*(1.0 - image->beam->bandwidth/2.0));
+	bwstep = (khigh-klow) / BWSAMPLING;
+
+	divxlow = -image->beam->divergence/2.0;
+	divylow = -image->beam->divergence/2.0;
+	divxstep = image->beam->divergence / DIVSAMPLING;
+	divystep = image->beam->divergence / DIVSAMPLING;
+
+	lut_a = get_sinc_lut(na);
+	lut_b = get_sinc_lut(nb);
+	lut_c = get_sinc_lut(nc);
+
+	for ( fs=0; fs<image->width; fs++ ) {
+	for ( ss=0; ss<image->height; ss++ ) {
+
+		int fs_step, ss_step, kstep;
+		int divxval, divyval;
+		int idx = fs + image->width*ss;
+
+		for ( fs_step=0; fs_step<SAMPLING; fs_step++ ) {
+		for ( ss_step=0; ss_step<SAMPLING; ss_step++ ) {
+		for ( kstep=0; kstep<BWSAMPLING; kstep++ ) {
+		for ( divxval=0; divxval<DIVSAMPLING; divxval++ ) {
+		for ( divyval=0; divyval<DIVSAMPLING; divyval++ ) {
+
+			double k;
+			double intensity;
+			double f_lattice, I_lattice;
+			double I_molecule;
+			struct rvec q, qn;
+			double twotheta;
+			const double dfs = (double)fs
+			                    + ((double)fs_step / SAMPLING);
+			const double dss = (double)ss
+			                    + ((double)ss_step / SAMPLING);
+
+			double xdiv = divxlow + divxstep*(double)divxval;
+			double ydiv = divylow + divystep*(double)divyval;
+
+			/* Calculate k this time round */
+			k = klow + (double)kstep * bwstep;
+
+			qn = get_q(image, dfs, dss, &twotheta, k);
+
+			/* x divergence */
+			q.u =  qn.u*cos(xdiv) +qn.w*sin(xdiv);
+			q.v =  qn.v;
+			q.w = -qn.u*sin(xdiv) +qn.w*cos(xdiv);
+
+			qn = q;
+
+			/* y divergence */
+			q.v =  qn.v*cos(ydiv) +qn.w*sin(ydiv);
+			q.w = -qn.v*sin(ydiv) +qn.w*cos(ydiv);
+
+			f_lattice = lattice_factor(q, ax, ay, az,
+			                              bx, by, bz,
+			                              cx, cy, cz,
+			                              lut_a, lut_b, lut_c);
+
+			I_molecule = molecule_factor(intensities,
+			                             phases, flags, q,
+			                             ax,ay,az,bx,by,bz,cx,cy,cz,
+			                             m, sym);
+
+			I_lattice = pow(f_lattice, 2.0);
+			intensity = I_lattice * I_molecule;
+
+			image->data[idx] += intensity;
+
+			if ( fs_step + ss_step + kstep == 0 ) {
+				image->twotheta[idx] = twotheta;
+			}
+
+		}
+		}
+		}
+		}
+		}
+
+		image->data[idx] /= (SAMPLING*SAMPLING*BWSAMPLING
+		                     *DIVSAMPLING*DIVSAMPLING);
+
+
+	}
+	progress_bar(fs, image->width-1, "Calculating diffraction");
+	}
+
+	free(lut_a);
+	free(lut_b);
+	free(lut_c);
+}