Add estimate_background

4 files changed, 254 insertions, 8 deletions

diff --git a/.gitignore b/.gitignore
index 7bd9572d..df16c5d7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,4 +18,5 @@ src/calibrate_detector
 src/facetron
 src/cubeit
 src/reintegrate
+src/estimate_background
 *~
diff --git a/src/Makefile.am b/src/Makefile.am
index 2b5c11d0..fc9e3b07 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,6 +1,6 @@
 bin_PROGRAMS = pattern_sim process_hkl get_hkl indexamajig compare_hkl \
                powder_plot render_hkl calibrate_detector facetron cubeit \
-               reintegrate
+               reintegrate estimate_background
 
 if HAVE_GTK
 bin_PROGRAMS += hdfsee
@@ -70,4 +70,7 @@ reintegrate_SOURCES = reintegrate.c cell.c hdf5-file.c utils.c detector.c \
                       thread-pool.c
 reintegrate_LDADD = @LIBS@
 
+estimate_background_SOURCES = estimate_background.c stream.c utils.c cell.c
+estimate_background_LDADD = @LIBS@
+
 INCLUDES = "-I$(top_srcdir)/data"
diff --git a/src/Makefile.in b/src/Makefile.in
index 6c47670f..b4b8d63f 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -36,7 +36,8 @@ bin_PROGRAMS = pattern_sim$(EXEEXT) process_hkl$(EXEEXT) \
 	get_hkl$(EXEEXT) indexamajig$(EXEEXT) compare_hkl$(EXEEXT) \
 	powder_plot$(EXEEXT) render_hkl$(EXEEXT) \
 	calibrate_detector$(EXEEXT) facetron$(EXEEXT) cubeit$(EXEEXT) \
-	reintegrate$(EXEEXT) $(am__EXEEXT_1)
+	reintegrate$(EXEEXT) estimate_background$(EXEEXT) \
+	$(am__EXEEXT_1)
 @HAVE_GTK_TRUE@am__append_1 = hdfsee
 @HAVE_OPENCL_TRUE@am__append_2 = diffraction-gpu.c cl-utils.c
 @HAVE_OPENCL_TRUE@am__append_3 = diffraction-gpu.c cl-utils.c
@@ -70,6 +71,10 @@ am_cubeit_OBJECTS = cubeit.$(OBJEXT) cell.$(OBJEXT) \
 	symmetry.$(OBJEXT) stream.$(OBJEXT) thread-pool.$(OBJEXT)
 cubeit_OBJECTS = $(am_cubeit_OBJECTS)
 cubeit_DEPENDENCIES =
+am_estimate_background_OBJECTS = estimate_background.$(OBJEXT) \
+	stream.$(OBJEXT) utils.$(OBJEXT) cell.$(OBJEXT)
+estimate_background_OBJECTS = $(am_estimate_background_OBJECTS)
+estimate_background_DEPENDENCIES =
 am_facetron_OBJECTS = facetron.$(OBJEXT) cell.$(OBJEXT) \
 	hdf5-file.$(OBJEXT) utils.$(OBJEXT) detector.$(OBJEXT) \
 	peaks.$(OBJEXT) image.$(OBJEXT) geometry.$(OBJEXT) \
@@ -155,13 +160,14 @@ AM_V_GEN = $(am__v_GEN_$(V))
 am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
 am__v_GEN_0 = @echo "  GEN   " $@;
 SOURCES = $(calibrate_detector_SOURCES) $(compare_hkl_SOURCES) \
-	$(cubeit_SOURCES) $(facetron_SOURCES) $(get_hkl_SOURCES) \
-	$(hdfsee_SOURCES) $(indexamajig_SOURCES) \
-	$(pattern_sim_SOURCES) $(powder_plot_SOURCES) \
-	$(process_hkl_SOURCES) $(reintegrate_SOURCES) \
-	$(render_hkl_SOURCES)
+	$(cubeit_SOURCES) $(estimate_background_SOURCES) \
+	$(facetron_SOURCES) $(get_hkl_SOURCES) $(hdfsee_SOURCES) \
+	$(indexamajig_SOURCES) $(pattern_sim_SOURCES) \
+	$(powder_plot_SOURCES) $(process_hkl_SOURCES) \
+	$(reintegrate_SOURCES) $(render_hkl_SOURCES)
 DIST_SOURCES = $(calibrate_detector_SOURCES) $(compare_hkl_SOURCES) \
-	$(cubeit_SOURCES) $(facetron_SOURCES) $(get_hkl_SOURCES) \
+	$(cubeit_SOURCES) $(estimate_background_SOURCES) \
+	$(facetron_SOURCES) $(get_hkl_SOURCES) \
 	$(am__hdfsee_SOURCES_DIST) $(am__indexamajig_SOURCES_DIST) \
 	$(am__pattern_sim_SOURCES_DIST) $(powder_plot_SOURCES) \
 	$(process_hkl_SOURCES) $(reintegrate_SOURCES) \
@@ -311,6 +317,8 @@ reintegrate_SOURCES = reintegrate.c cell.c hdf5-file.c utils.c detector.c \
                       thread-pool.c
 
 reintegrate_LDADD = @LIBS@
+estimate_background_SOURCES = estimate_background.c stream.c utils.c cell.c
+estimate_background_LDADD = @LIBS@
 INCLUDES = "-I$(top_srcdir)/data"
 all: all-am
 
@@ -392,6 +400,9 @@ compare_hkl$(EXEEXT): $(compare_hkl_OBJECTS) $(compare_hkl_DEPENDENCIES)
 cubeit$(EXEEXT): $(cubeit_OBJECTS) $(cubeit_DEPENDENCIES) 
 	@rm -f cubeit$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(cubeit_OBJECTS) $(cubeit_LDADD) $(LIBS)
+estimate_background$(EXEEXT): $(estimate_background_OBJECTS) $(estimate_background_DEPENDENCIES) 
+	@rm -f estimate_background$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(estimate_background_OBJECTS) $(estimate_background_LDADD) $(LIBS)
 facetron$(EXEEXT): $(facetron_OBJECTS) $(facetron_DEPENDENCIES) 
 	@rm -f facetron$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(facetron_OBJECTS) $(facetron_LDADD) $(LIBS)
@@ -436,6 +447,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/diffraction.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dirax.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/displaywindow.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/estimate_background.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/facetron.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/filters.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/geometry.Po@am__quote@
diff --git a/src/estimate_background.c b/src/estimate_background.c
new file mode 100644
index 00000000..d12bc37e
--- /dev/null
+++ b/src/estimate_background.c
@@ -0,0 +1,230 @@
+/*
+ * 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:e:ro:p:y:g:f:a:r:",
+	                        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;
+
+		rval = find_chunk(fh, &cell, &filename);
+		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;
+}