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-rw-r--r--.gitignore1
-rw-r--r--src/Makefile.am5
-rw-r--r--src/Makefile.in26
-rw-r--r--src/estimate_background.c230
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;
+}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-24 00:37:24 +0000