Remove 'estimate_background'

We should be estimating proper SNRs with sigma(I) estimates

1 files changed, 0 insertions, 231 deletions

diff --git a/src/estimate_background.c b/src/estimate_background.c
deleted file mode 100644
index 1f956377..00000000
--- a/src/estimate_background.c
+++ /dev/null
@@ -1,231 +0,0 @@
-/*
- * estimate-background.c
- *
- * Like 'process_hkl', but for signal/noise ratios
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * 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 <getopt.h>
-
-#include "utils.h"
-#include "statistics.h"
-#include "sfac.h"
-#include "reflections.h"
-#include "symmetry.h"
-#include "stream.h"
-
-
-/* Number of bins for plot of resolution shells */
-#define NBINS (10)
-
-
-
-static void show_help(const char *s)
-{
-	printf("Syntax: %s [options]\n\n", s);
-	printf(
-"Estimate peak SNR from FEL Bragg intensities.\n"
-"\n"
-"  -h, --help                Display this help message.\n"
-"  -i, --input=<filename>    Specify input filename (\"-\" for stdin).\n"
-);
-}
-
-
-
-int main(int argc, char *argv[])
-{
-	int c;
-	char *filename = NULL;
-	FILE *fh;
-	int rval;
-	double total_vol, vol_per_shell;
-	double rmin, rmax;
-	double rmins[NBINS];
-	double rmaxs[NBINS];
-	double snrs[NBINS];
-	unsigned int counts[NBINS];
-	UnitCell *real_cell;
-	double overall_snr;
-	unsigned int overall_counts;
-	int i;
-
-	/* Long options */
-	const struct option longopts[] = {
-		{"help",               0, NULL,               'h'},
-		{"input",              1, NULL,               'i'},
-		{0, 0, NULL, 0}
-	};
-
-	/* Short options */
-	while ((c = getopt_long(argc, argv, "hi:",
-	                        longopts, NULL)) != -1) {
-
-		switch (c) {
-		case 'h' :
-			show_help(argv[0]);
-			return 0;
-
-		case 'i' :
-			filename = strdup(optarg);
-			break;
-
-		case 0 :
-			break;
-
-		default :
-			return 1;
-		}
-
-	}
-
-	if ( filename == NULL ) {
-		ERROR("Please specify filename using the -i option\n");
-		return 1;
-	}
-
-	/* Open the data stream */
-	if ( strcmp(filename, "-") == 0 ) {
-		fh = stdin;
-	} else {
-		fh = fopen(filename, "r");
-	}
-	free(filename);
-	if ( fh == NULL ) {
-		ERROR("Failed to open input file\n");
-		return 1;
-	}
-
-	/* FIXME: Fixed resolution shells */
-	rmin = 0.120e9;
-	rmax = 1.172e9;
-
-	for ( i=0; i<NBINS; i++ ) {
-		counts[i] = 0;
-		snrs[i] = 0.0;
-	}
-
-	total_vol = pow(rmax, 3.0) - pow(rmin, 3.0);
-	vol_per_shell = total_vol / NBINS;
-	rmins[0] = rmin;
-	for ( i=1; i<NBINS; i++ ) {
-
-		double r;
-
-		r = vol_per_shell + pow(rmins[i-1], 3.0);
-		r = pow(r, 1.0/3.0);
-
-		/* Shells of constant volume */
-		rmaxs[i-1] = r;
-		rmins[i] = r;
-
-		/* Shells of constant thickness */
-		//rmins[i] = rmins[i-1] + (rmax-rmin)/NBINS;
-		//rmaxs[i-1] = rmins[i-1] + (rmax-rmin)/NBINS;
-
-		STATUS("Shell %i: %f to %f\n", i-1,
-		       rmins[i-1]/1e9, rmaxs[i-1]/1e9);
-
-	}
-	rmaxs[NBINS-1] = rmax;
-	STATUS("Shell %i: %f to %f\n", NBINS-1,
-	       rmins[NBINS-1]/1e9, rmaxs[NBINS-1]/1e9);
-
-	real_cell = load_cell_from_pdb("../../1JB0.pdb");
-
-	do {
-
-		char *rval2;
-		UnitCell *cell;
-		char *filename;
-		char line[1024];
-		int done = 0;
-		double ph_ev;
-
-		rval = find_chunk(fh, &cell, &filename, &ph_ev);
-		if ( rval != 0 ) break;
-
-		do {
-
-			signed int h, k, l;
-			float intensity, x, y, max, bg;
-			int r, j;
-			double d, snr;
-			int bin;
-
-			rval2 = fgets(line, 1024, fh);
-
-			if ( strncmp(line, "Peak statistics:", 16) == 0 ) {
-				done = 1;
-			}
-
-			r = sscanf(line, "%i %i %i %f (at %f,%f) max=%f bg=%f",
-			           &h, &k, &l, &intensity, &x, &y, &max, &bg);
-
-			if ( r != 8 ) {
-				continue;
-			}
-
-			d = resolution(real_cell, h, k, l) * 2.0;
-			//STATUS("'%s'", line);
-			//STATUS("-> %i %i %i %f\n", h, k, l, d/1e9);
-
-			bin = -1;
-			for ( j=0; j<NBINS; j++ ) {
-				if ( (d>rmins[j]) && (d<=rmaxs[j]) ) {
-					bin = j;
-					break;
-				}
-			}
-			if ( bin == -1 ) {
-				ERROR("Warnung! %i %i %i %f\n", h, k, l, d/1e9);
-				continue;
-			}
-
-			snr = max/bg;
-			snrs[bin] += snr;
-			counts[bin]++;
-
-		} while ( !done );
-
-	} while ( !rval );
-
-	/* Print out results */
-	overall_snr = 0.0;
-	overall_counts = 0;
-	for ( i=0; i<NBINS; i++ ) {
-
-		double snr, cen;
-
-		cen = rmins[i] + (rmaxs[i] - rmins[i])/2.0;
-		snr = snrs[i] / (double)counts[i];
-		printf("%f %f (%f / %i)\n", cen*1.0e-9, snr, snrs[i], counts[i]);
-		if ( i>0 ) {
-			overall_snr += snrs[i];
-			overall_counts += counts[i];
-		}
-
-	}
-
-	printf("Overall: %f (%f / %i)\n", overall_snr/(double)overall_counts,
-	                                  overall_snr, overall_counts);
-
-
-	fclose(fh);
-
-	return 0;
-}