Add process_hkl program (replaces integr_sim)

1 files changed, 0 insertions, 232 deletions

diff --git a/src/integr_sim.c b/src/integr_sim.c
deleted file mode 100644
index 08788277..00000000
--- a/src/integr_sim.c
+++ /dev/null
@@ -1,232 +0,0 @@
-/*
- * integr_sim.c
- *
- * Test integration of intensities
- *
- * (c) 2006-2009 Thomas White <thomas.white@desy.de>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdarg.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <unistd.h>
-
-#include "cell.h"
-#include "image.h"
-#include "utils.h"
-#include "statistics.h"
-#include "sfac.h"
-
-
-static void main_show_help(const char *s)
-{
-	printf("Syntax: %s\n\n", s);
-	printf("Test relrod integration\n\n");
-	printf("  -h              Display this help message\n");
-}
-
-
-static void write_RvsQ(const char *name, double *ref, double *trueref,
-                       unsigned int *counts, double scale, UnitCell *cell)
-{
-	FILE *fh;
-	double smax, sbracket;
-	signed int h, k, l;
-
-	fh = fopen(name, "w");
-
-	smax = 0.0;
-	for ( h=-INDMAX; h<INDMAX; h++ ) {
-	for ( k=-INDMAX; k<INDMAX; k++ ) {
-	for ( l=-INDMAX; l<INDMAX; l++ ) {
-		double s = resolution(cell, h, k, l);
-		if ( (lookup_count(counts, h, k, l) > 0) && (s > smax) ) {
-			smax = s;
-		}
-	}
-	}
-	}
-
-	for ( sbracket=0.0; sbracket<smax; sbracket+=smax/10.0 ) {
-
-		double top = 0.0;
-		double bot = 0.0;
-		int n = 0;
-
-		for ( h=-INDMAX; h<INDMAX; h++ ) {
-		for ( k=-INDMAX; k<INDMAX; k++ ) {
-		for ( l=-INDMAX; l<INDMAX; l++ ) {
-
-			double s;
-			int c;
-			c = lookup_count(counts, h, k, l);
-			s = resolution(cell, h, k, l);
-			if ((s>=sbracket) && (s<sbracket+smax/10.0) && (c>0)) {
-
-				double obs, calc, obsi;
-
-				obs = lookup_intensity(ref, h, k, l);
-				calc = lookup_intensity(trueref, h, k, l);
-
-				obsi = obs / (double)c;
-				top += fabs(obsi/scale - calc);
-				bot += obsi/scale;
-				n++;
-			}
-
-		}
-		}
-		}
-
-		fprintf(fh, "%8.5f %8.5f %i\n", sbracket+smax/20.0, top/bot, n);
-
-	}
-	fclose(fh);
-}
-
-
-int main(int argc, char *argv[])
-{
-	int c;
-	int i;
-	struct image image;
-	double *ref, *trueref;
-	unsigned int *counts;
-	size_t ref_size;
-	signed int h, k, l;
-	double R, scale;
-	FILE *fh;
-
-	while ((c = getopt(argc, argv, "h")) != -1) {
-
-		switch ( c ) {
-
-			case 'h' : {
-				main_show_help(argv[0]);
-				return 0;
-			}
-
-		}
-
-	}
-
-	/* Define image parameters */
-	image.width = 1024;
-	image.height = 1024;
-	image.fmode = FORMULATION_CLEN;
-	image.x_centre = 512.5;
-	image.y_centre = 512.5;
-	image.camera_len = 0.05;  /* 5 cm (front CCD can move from 5cm-20cm) */
-	image.resolution = 13333.3; /* 75 micron pixel size */
-	image.xray_energy = eV_to_J(2.0e3); /* 2 keV energy */
-	image.lambda = ph_en_to_lambda(image.xray_energy);  /* Wavelength */
-	image.molecule = load_molecule();
-
-	/* Prepare array for integrated intensities */
-	ref = new_list_intensity();
-
-	/* Array for sample counts */
-	counts = new_list_count();
-
-	/* Calculate true intensities */
-	get_reflections_cached(image.molecule, image.xray_energy);
-	/* Complex structure factors now in image.molecule->reflections */
-
-	for ( i=1; i<=10e3; i++ ) {
-
-		#if 0
-		image.orientation = random_quaternion();
-
-		/* Calculate reflections using large smax
-		 * (rather than the actual value) */
-		//get_reflections(&image, cell, 1.0e9);
-
-		nrefl = image_feature_count(image.rflist);
-		for ( j=0; j<nrefl; j++ ) {
-
-			struct imagefeature *f;
-			double t, s, intensity, F;
-
-			f = image_get_feature(image.rflist, j);
-
-			t = 100.0e-9;  /* Thickness 100 nm */
-			s = f->s;      /* Get excitation error */
-			F = structure_factor(f->h, f->k, f->l);
-
-			/* Calculate intensity from this reflection */
-			intensity = pow( F * SINC(M_PI*t*s), 2.0);
-
-			if ( intensity < 0.1 ) continue;
-
-			if ( (f->h == 2) && (f->k == 2) && (f->l == 2) ) {
-				fprintf(fh1, "%f %f\n", s, intensity);
-			}
-
-			if ( (f->h == 15) && (f->k == 15) && (f->l == 15) ) {
-				fprintf(fh2, "%f %f\n", s, intensity);
-			}
-
-			integrate_reflection(ref, f->h, f->k, f->l, intensity);
-			add_count(counts, f->h, f->k, f->l, 1);
-		}
-		#endif
-
-		if ( i % 1000 == 0 ) {
-
-			int j;
-			double mean_counts;
-			int ctot = 0;
-			int nmeas = 0;
-			double ff;
-			char name[64];
-
-			for ( j=0; j<ref_size; j++ ) {
-				ctot += counts[j];
-				if ( counts[j] > 0 ) nmeas++;
-			}
-			mean_counts = (double)ctot/nmeas;
-
-			ff = lookup_intensity(ref, 2, 2, 2)
-			                        / lookup_count(counts, 2, 2, 2);
-
-			R = stat_r2(ref, trueref, counts, ref_size, &scale);
-			printf("%8i: R=%5.2f%% (sf=%7.4f)"
-			       " mean meas/refl=%5.2f,"
-			       " %i reflections measured. %f\n",
-			       i, R*100.0, scale, mean_counts, nmeas,
-			       ff);
-
-			/* Record graph of R against q for this N */
-			snprintf(name, 63, "R_vs_q-%i.dat", i);
-			write_RvsQ(name, ref, trueref, counts,
-			           scale, image.molecule->cell);
-
-		}
-
-	}
-
-	fh = fopen("reflections.dat", "w");
-	for ( h=-INDMAX; h<INDMAX; h++ ) {
-	for ( k=-INDMAX; k<INDMAX; k++ ) {
-	for ( l=-INDMAX; l<INDMAX; l++ ) {
-		int N;
-		N = lookup_count(counts, h, k, l);
-		if ( N == 0 ) continue;
-		double F = lookup_intensity(ref, h, k, l) / N;
-		fprintf(fh, "%3i %3i %3i %f\n", h, k, l, F);
-	}
-	}
-	}
-	fclose(fh);
-
-	return 0;
-}