Move a load more stuff into libcrystfel

1 files changed, 0 insertions, 463 deletions

diff --git a/src/diffraction.c b/src/diffraction.c
deleted file mode 100644
index 9532a6ce..00000000
--- a/src/diffraction.c
+++ /dev/null
@@ -1,463 +0,0 @@
-/*
- * 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);
-}