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-rw-r--r--Makefile.am5
-rw-r--r--Makefile.in7
-rw-r--r--src/detector.c23
-rw-r--r--src/detector.h4
-rw-r--r--src/indexamajig.c1
-rw-r--r--src/powder_plot.c913
-rw-r--r--src/stream.c21
-rw-r--r--src/stream.h2
8 files changed, 924 insertions, 52 deletions
diff --git a/Makefile.am b/Makefile.am
index e1ff7441..00c9fd8b 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -94,7 +94,8 @@ src_check_hkl_SOURCES = src/check_hkl.c src/cell.c src/utils.c \
src_powder_plot_SOURCES = src/powder_plot.c src/cell.c src/utils.c src/image.c \
src/hdf5-file.c src/detector.c src/thread-pool.c \
- src/beam-parameters.c
+ src/reflist-utils.c src/beam-parameters.c src/stream.c \
+ src/reflist.c src/symmetry.c
src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflist-utils.c \
src/utils.c src/povray.c src/symmetry.c src/render.c \
@@ -118,6 +119,8 @@ src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
src/symmetry.c src/post-refinement.c \
src/hrs-scaling.c src/reflist.c
+src_stream_SOURCES = src/reflist-utils.c
+
if BUILD_CUBEIT
src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
src/detector.c src/render.c src/filters.c src/image.c \
diff --git a/Makefile.in b/Makefile.in
index 1efd5f8c..584d4ace 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -207,7 +207,9 @@ src_pattern_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am_src_powder_plot_OBJECTS = src/powder_plot.$(OBJEXT) \
src/cell.$(OBJEXT) src/utils.$(OBJEXT) src/image.$(OBJEXT) \
src/hdf5-file.$(OBJEXT) src/detector.$(OBJEXT) \
- src/thread-pool.$(OBJEXT) src/beam-parameters.$(OBJEXT)
+ src/thread-pool.$(OBJEXT) src/reflist-utils.$(OBJEXT) \
+ src/beam-parameters.$(OBJEXT) src/stream.$(OBJEXT) \
+ src/reflist.$(OBJEXT) src/symmetry.$(OBJEXT)
src_powder_plot_OBJECTS = $(am_src_powder_plot_OBJECTS)
src_powder_plot_LDADD = $(LDADD)
src_powder_plot_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
@@ -669,7 +671,8 @@ src_check_hkl_SOURCES = src/check_hkl.c src/cell.c src/utils.c \
src_powder_plot_SOURCES = src/powder_plot.c src/cell.c src/utils.c src/image.c \
src/hdf5-file.c src/detector.c src/thread-pool.c \
- src/beam-parameters.c
+ src/reflist-utils.c src/beam-parameters.c src/stream.c \
+ src/reflist.c src/symmetry.c
src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflist-utils.c \
src/utils.c src/povray.c src/symmetry.c src/render.c \
diff --git a/src/detector.c b/src/detector.c
index 5c1db570..e201c454 100644
--- a/src/detector.c
+++ b/src/detector.c
@@ -919,6 +919,29 @@ double largest_q(struct image *image)
return qmax;
}
+double smallest_q(struct image *image)
+{
+ int fs, ss;
+ double ttm = +INFINITY;
+ double qmin = +INFINITY;
+ for ( fs=0; fs<image->width; fs++ ) {
+ for ( ss=0; ss<image->height; ss++ ) {
+
+ struct rvec q;
+ double tt;
+
+ q = get_q(image, fs, ss, &tt, 1.0/image->lambda);
+
+ if ( tt < ttm ) {
+ qmin = modulus(q.u, q.v, q.w);
+ ttm = tt;
+ }
+
+ }
+ }
+
+ return qmin;
+}
void get_pixel_extents(struct detector *det,
double *min_x, double *min_y,
diff --git a/src/detector.h b/src/detector.h
index fce60ff6..7073a47a 100644
--- a/src/detector.h
+++ b/src/detector.h
@@ -118,9 +118,9 @@ extern int reverse_2d_mapping(double x, double y, double *pfs, double *pss,
extern double largest_q(struct image *image);
-extern int write_detector_geometry(const char *filename, struct detector *det);
-
+extern double smallest_q(struct image *image);
+extern int write_detector_geometry(const char *filename, struct detector *det);
#endif /* DETECTOR_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 569a41bd..4985ccbe 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -43,6 +43,7 @@
#include "reflist-utils.h"
+
/* Write statistics at APPROXIMATELY this interval */
#define STATS_EVERY_N_SECONDS (5)
diff --git a/src/powder_plot.c b/src/powder_plot.c
index c6d2f045..515c8c4e 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -3,7 +3,8 @@
*
* Plot powder patterns
*
- * (c) 2006-2010 Thomas White <taw@physics.org>
+ * (c) 2011 Andrew Aquila <andrew.aquila@cfel.de>
+ * (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
@@ -21,64 +22,611 @@
#include <unistd.h>
#include <getopt.h>
+#include "stream.h"
+#include "reflist.h"
#include "utils.h"
#include "image.h"
#include "detector.h"
#include "index.h"
#include "hdf5-file.h"
#include "beam-parameters.h"
+#include "reflist-utils.h"
+#include "symmetry.h"
+struct bin_stats {
+ unsigned int N;
+ double total;
+ double mean;
+ double std_dev;
+ double q_min;
+ double q_max;
+ double q_value;
+ double fract;
+};
+
+struct histogram_info {
+ double q_max;
+ double q_min;
+ double q_delta;
+ unsigned int histsize;
+ int spacing; //linear, q^2, & equal volume
+};
+
+enum {
+ PLOT_PEAKS,
+ PLOT_HKL,
+ PLOT_REFL,
+ PLOT_H5,
+ PLOT_D
+};
+
+enum {
+ FILE_STREAM,
+ FILE_HKL,
+ FILE_H5
+};
+
+enum {
+ LINEAR,
+ q2,
+ VOLUME
+};
+
+static int find_q_bin_index(double q, struct histogram_info *info,
+ struct bin_stats *hist)
+{
+ /* bisection search alg. find q_bin index of order Log(n) time */
+ int mid;
+ int min = 0;
+ int max = (*info).histsize-1;
+ if (q < hist[min].q_max) {return min;}
+ if (q > hist[max].q_min) {return max;}
+ do {
+ mid = (min + max) / 2;
+ if (q < hist[mid].q_min) {
+ max = mid;
+ } else if (q > hist[mid].q_max){
+ min = mid ;
+ } else {
+ return mid;
+ }
+ } while(max - min > 1);
+ return mid;
+}
+
+static int add_peak_to_histogram(double fs, double ss, double intensity,
+ struct image *image, struct histogram_info *info,
+ struct bin_stats *hist)
+{
+ /* used for h5 files, peak/feature list and stream positions*/
+ /* See Knuth TAOCP vol 2, 3rd ed, pg 232 for running variance*/
+ struct rvec r;
+ double q, delta;
+ int i;
+
+ r = get_q(image, fs, ss, NULL, 1.0/ (*image).lambda);
+ q = modulus(r.u, r.v, r.w);
+
+ /* ignore q value if outside of range */
+ if ((q<(*info).q_min) || (q>(*info).q_max)) {
+ return 1;
+ }
+ i = find_q_bin_index(q, info, hist);
+
+ delta = intensity - hist[i].mean;
+ hist[i].N++;
+ hist[i].total += intensity;
+ hist[i].mean = hist[i].mean + delta /hist[i].N;
+ hist[i].std_dev = hist[i].std_dev +
+ (delta *(intensity - hist[i].mean));
+ return 0;
+}
+
+static int add_d_to_histogram(double q, double intensity,
+ struct histogram_info *info, struct bin_stats *hist)
+{
+ /* used for d and hkl of stream files where redundancy = 1 */
+ double delta;
+ int i;
+
+ /* ignore q value if outside of range */
+ if ((q<(*info).q_min) || (q>(*info).q_max)) {
+ return 1;
+ }
+ i = find_q_bin_index(q, info, hist);
+
+ delta = intensity - hist[i].mean;
+ hist[i].N++;
+ hist[i].total += intensity;
+ hist[i].mean = hist[i].mean + delta /hist[i].N;
+ hist[i].std_dev = hist[i].std_dev +
+ (delta *(intensity - hist[i].mean));
+ return 0;
+}
+
+static int add_hkl_to_histogram(double q, double intensity,
+ int redundancy, int q_scaling, struct histogram_info *info,
+ struct bin_stats *hist)
+{
+ int i = 0;
+
+ /* ignore q value if outside of range */
+ if ((q<(*info).q_min) || (q>(*info).q_max)) {
+ return 1;
+ }
+
+ /* The accounting is the intensity of the reflection times the
+ The number of occurance of that reflection smeered out over the
+ surface area which is 4 Pi q^2 the 4 pi is left out as it is a
+ common consant and the total is in arbiturary units.
+ */
+ for (i=0; i<redundancy; i++) {
+ if (q_scaling) {
+ add_d_to_histogram(q, intensity/(q*q), info, hist);
+ } else {
+ add_d_to_histogram(q, intensity, info, hist);
+ }
+ }
+ return 0;
+}
+
+
+static int histogram_setup(struct histogram_info *info,
+ struct bin_stats *histdata)
+{
+ int i;
+ double x;
+ /* setup histogram*/
+ if ((*info).spacing == LINEAR) {x = 1.0;}
+ else if ((*info).spacing == q2) {x = 2.0;}
+ else {x = 3.0;}
+ for ( i=0; i<(*info).histsize; i++) {
+ histdata[i].N = 0;
+ histdata[i].total = 0.0;
+ histdata[i].mean = 0.0;
+ histdata[i].std_dev = 0.0;
+ histdata[i].fract = 0.0;
+ histdata[i].q_min = pow(( i *(*info).q_delta) +
+ pow((*info).q_min, x), 1.0/x);
+ histdata[i].q_max = pow(((i+1.0)*(*info).q_delta) +
+ pow((*info).q_min, x), 1.0/x);
+ histdata[i].q_value = pow(((i+0.5)*(*info).q_delta) +
+ pow((*info).q_min, x), 1.0/x);
+ }
+ return 0;
+}
+
+static int ring_fraction_calc(struct histogram_info *info,
+ struct bin_stats *hist, struct image *image)
+{
+ struct panel *p;
+ struct rvec r;
+ int i,fs,ss;
+ double q, q_fs, q_ss;
+ double pi = 3.14159265;
+
+ /* check if detector geometry is loaded */
+ if ( ((*image).det == NULL) || ((*image).lambda < 0.0)) {
+ return 1;
+ }
+
+ /* loop over all pixels */
+ for ( ss=0; ss<(*image).height; ss++ ) {
+ for ( fs=0; fs<(*image).width; fs++ ) {
+ r = get_q(image, fs, ss, NULL, 1.0/ (*image).lambda);
+ q = modulus(r.u, r.v, r.w);
+
+ /* if pixel is valid (not a bad pixel and not out of range) */
+ if ( (q>(*info).q_min) && (q<(*info).q_max) &&
+ (in_bad_region((*image).det,fs,ss) == 0) ) {
+
+ /* using the panel to determine the pixel size
+ takes care of edge pixels correctly */
+ p = find_panel((*image).det, fs, ss);
+ r = get_q_for_panel(p, (fs+1)-(double)p->min_fs,
+ ss-(double)p->min_ss,
+ NULL, 1.0/(*image).lambda);
+ q_fs = modulus(r.u, r.v, r.w);
+ r = get_q_for_panel(p, fs-(double)p->min_fs,
+ (ss+1) -(double)p->min_ss,
+ NULL, 1.0/(*image).lambda);
+ q_ss = modulus(r.u, r.v, r.w);
+ i = find_q_bin_index(q, info, hist);
+ hist[i].fract = hist[i].fract +
+ fabs((q_fs - q) * (q_ss - q)); //approx pixel size
+ }
+ }
+ }
+ /* divide measured area by ring area */
+ for ( i=0; i<(*info).histsize; i++) {
+ hist[i].fract = hist[i].fract /
+ (pi * (pow(hist[i].q_max,2.0) - pow(hist[i].q_min,2.0)));
+ }
+ return 0;
+}
+
+static unsigned int process_h5(struct image *image, struct histogram_info *info,
+ struct bin_stats *histdata, unsigned int processing_total)
+{
+ int fs, ss;
+ double intensity;
+ for ( ss=0; ss<(*image).height; ss++ ) {
+ for ( fs=0; fs<(*image).width; fs++ ) {
+ intensity = (*image).data[fs + (*image).width*ss];
+ progress_bar(fs + (*image).width*ss, processing_total,
+ "Processing");
+ if (in_bad_region((*image).det,fs,ss) == 0) {
+ add_peak_to_histogram(fs, ss, intensity,
+ image, info, histdata);
+ }
+ }
+ }
+ return 0;
+}
+
+static unsigned int process_hkl(struct image *image, char *sym, UnitCell *cell,
+ struct histogram_info *info, struct bin_stats *histdata,
+ int q_scaling,unsigned int processing_total, int use_redundency)
+{
+ Reflection *refl;
+ RefListIterator *iter;
+ unsigned int i = 0;
+ unsigned int n_peaks = 0;
+ int h,k,l,redundancy;
+ double q, intensity;
+ for ( refl = first_refl((*image).reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
+ i++;
+ progress_bar(i, processing_total, "Processing");
+ get_indices(refl, &h, &k, &l);
+ intensity = get_intensity(refl);
+ if (use_redundency == 1) {
+ redundancy = get_redundancy(refl);
+ } else {
+ redundancy = num_equivs(h, k, l, sym);
+ }
+ /*note: resolution returns 1/d/2 in m */
+ q = 2.0 * resolution(cell, h, k, l);
+ //sigma = get_esd_intensity(refl);
+ add_hkl_to_histogram(q, intensity, redundancy,
+ q_scaling, info, histdata);
+ n_peaks+=redundancy;
+ }
+ return n_peaks;
+}
+
+static unsigned int process_stream_reflection(FILE *fh, struct image *image,
+ struct histogram_info *info, struct bin_stats *histdata,
+ unsigned int processing_total, unsigned int *n_patterns)
+{
+ int rval;
+ unsigned int i = 0;
+ unsigned int n_peaks = 0;
+ Reflection *refl;
+ RefListIterator *iter;
+ double intensity, fs_double, ss_double;
+ do {
+ /* Get data from next chunk */
+ rval = read_chunk(fh, image);
+ if ( rval ) continue;
+ i++;
+ progress_bar(i, processing_total, "Processing");
+ // check if the pattern indexed, if so use those peaks
+ if ((*image).reflections != NULL) {
+ (*n_patterns)++; //inc number of patterns used
+ for ( refl = first_refl((*image).reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
+ /* note added fs_double as fs is an int */
+ intensity = get_intensity(refl);
+ get_detector_pos(refl, &fs_double, &ss_double);
+ if(add_peak_to_histogram(fs_double, ss_double,
+ intensity, image, info, histdata) == 0) {
+ n_peaks++;
+ }
+ }
+ }
+ free((*image).filename);
+ reflist_free((*image).reflections);
+ image_feature_list_free((*image).features);
+ cell_free((*image).indexed_cell);
+ } while (rval == 0);
+ return n_peaks;
+}
+
+static unsigned int process_stream_d(FILE *fh, struct image *image,
+ struct histogram_info *info, struct bin_stats *histdata,
+ unsigned int processing_total, unsigned int *n_patterns)
+{
+ int h, k, l, rval;
+ unsigned int i = 0;
+ unsigned int n_peaks = 0;
+ Reflection *refl;
+ RefListIterator *iter;
+ double intensity, q;
+ do {
+ /* Get data from next chunk */
+ rval = read_chunk(fh, image);
+ if ( rval ) continue;
+ i++;
+ progress_bar(i, processing_total, "Processing");
+ // check if the pattern indexed, if so use those peaks
+ if ((*image).reflections != NULL) {
+ (*n_patterns)++; //inc number of patterns used
+ for ( refl = first_refl((*image).reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
+ get_indices(refl, &h, &k, &l);
+ intensity = get_intensity(refl);
+ /*resolution returns 1/d/2 in nm */
+ q = 2.0 * resolution((*image).indexed_cell, h, k, l);
+ if (add_d_to_histogram(q, intensity, info,
+ histdata) == 0) {
+ n_peaks++;
+ }
+ }
+ }
+ free((*image).filename);
+ reflist_free((*image).reflections);
+ image_feature_list_free((*image).features);
+ cell_free((*image).indexed_cell);
+ } while (rval == 0);
+ return n_peaks;
+}
+
+
+static unsigned int process_stream_hkl(FILE *fh, struct image *image,
+ struct histogram_info *info, struct bin_stats *histdata, UnitCell *cell,
+ unsigned int processing_total, unsigned int *n_patterns)
+{
+ int h, k, l, rval;
+ unsigned int i = 0;
+ unsigned int n_peaks = 0;
+ Reflection *refl;
+ RefListIterator *iter;
+ double intensity, q;
+ do {
+ /* Get data from next chunk */
+ rval = read_chunk(fh, image);
+ if ( rval ) continue;
+ i++;
+ progress_bar(i, processing_total, "Processing");
+ if ((*image).reflections != NULL) {
+ n_patterns++; //inc number of patterns used
+ for ( refl = first_refl((*image).reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
+ get_indices(refl, &h, &k, &l);
+ intensity = get_intensity(refl);
+ q = 2.0 * resolution(cell, h, k, l);
+ if(add_d_to_histogram(q, intensity, info,
+ histdata) == 0) {
+ n_peaks++;
+ }
+ }
+ }
+ free((*image).filename);
+ reflist_free((*image).reflections);
+ image_feature_list_free((*image).features);
+ cell_free((*image).indexed_cell);
+ } while (rval == 0);
+ return n_peaks;
+}
+
+static unsigned int process_stream_peaks(FILE *fh, struct image *image,
+ struct histogram_info *info, struct bin_stats *histdata,
+ unsigned int processing_total, unsigned int *n_patterns, int only_indexed)
+{
+ struct imagefeature *f;
+ int rval;
+ unsigned int i = 0;
+ unsigned int n_peaks = 0;
+ unsigned int j;
+ do {
+ /* Get data from next chunk */
+ rval = read_chunk(fh, image);
+ if ( rval ) continue;
+ i++;
+ progress_bar(i, processing_total, "Processing");
+ if ((*image).features != NULL) {
+ if ((only_indexed == 0) ||
+ ((only_indexed == 1) &&
+ ((*image).reflections != NULL))) {
+ (*n_patterns)++;
+ for (j = 0;
+ j<image_feature_count((*image).features);
+ j++) {
+ f = image_get_feature((*image).features, j);
+ if (in_bad_region((*image).det,
+ (*f).fs,(*f).ss) == 0) {
+ if (add_peak_to_histogram((*f).fs,
+ (*f).ss, (*f).intensity, image,
+ info, histdata) == 0) {
+ n_peaks++;
+ }
+ }
+ }
+ }
+ }
+ free((*image).filename);
+ reflist_free((*image).reflections);
+ image_feature_list_free((*image).features);
+ cell_free((*image).indexed_cell);
+ } while (rval == 0);
+ return n_peaks;
+}
+
+static unsigned int process_stream_h5(FILE *fh, struct image *image,
+ struct histogram_info *info, struct bin_stats *histdata, int config_satcorr,
+ int only_indexed, unsigned int processing_total, unsigned int *n_patterns)
+{
+ int fs, ss, rval;
+ double intensity;
+ unsigned int i = 0;
+ unsigned int n_peaks = 0;
+ struct hdfile *hdfile = NULL;
+ do {
+ /* Get data from next chunk */
+ rval = read_chunk(fh, image);
+ if ( rval ) continue;
+ i++;
+ progress_bar(i, processing_total, "Processing");
+ if ((only_indexed == 0) ||
+ ((only_indexed == 1) &&
+ ((*image).reflections != NULL))) {
+ hdfile = hdfile_open((*image).filename);
+ hdfile_set_image(hdfile, "/data/data");
+ hdf5_read(hdfile, image, config_satcorr);
+ hdfile_close(hdfile);
+ n_patterns++;
+ for ( ss=0; ss<(*image).height; ss++ ) {
+ for ( fs=0; fs<(*image).width; fs++ ) {
+ intensity = (*image).data[fs + (*image).width*ss];
+ if (in_bad_region((*image).det,fs,ss) == 0) {
+ add_peak_to_histogram(fs, ss, intensity,
+ image, info, histdata);
+ }
+ }
+ }
+ }
+ free((*image).data);
+ free((*image).filename);
+ reflist_free((*image).reflections);
+ image_feature_list_free((*image).features);
+ cell_free((*image).indexed_cell);
+ } while (rval == 0);
+ return n_peaks;
+}
static void show_help(const char *s)
{
- printf("Syntax: %s [options] <file.h5>\n\n", s);
+ printf("Syntax: %s [options]\n\n", s);
printf(
"Plot a powder pattern as a 1D graph using the detector geometry.\n"
"\n"
-" -h, --help Display this help message.\n"
-" -g. --geometry=<file> Get detector geometry from file.\n"
-" -i, --input=<file> Input filename.\n"
-" -b, --beam=<file> Get beam parameters (specifically, wavelength)"
-" from file if non present in the HDF5 file.\n"
+" -h, --help Display this help message.\n"
+" -i, --input=<file> Input filename. (*.stream, *.hkl, or *.h5)\n"
+" -o, --output=<file> Output filename. (default stdout)\n"
+" -g. --geometry=<file> Get detector geometry from file.\n"
+" -b, --beam=<file> Get beam parameters (wavelength) from file.\n"
+" -p, --pdb=<file> Get unit cell from PDB file. (.hkl files only)\n"
+" -y, --symmetry=<sym> The symmetry of crystal (.hkl files only)\n"
+" -s, --bins=n Makes histogram wiht n bins (default is 100).\n"
+" --spacing=<type> Use 'type' to select the q spacing.\n"
+" Choose from:\n"
+" linear : linear (default)\n"
+" q2 : even spacing in Wilson plots\n"
+" volume : constant volume spacing\n"
+" --q-max=n The max q to be considered in plot.\n"
+" --q-min=n The min q to be considered in plot.\n"
+" -d, --data=<type> Use to select the kind of stream data in histogram.\n"
+" Choose from:\n"
+" reflection : uses peak positons from indexed\n"
+" reflection \n"
+" hkl : uses the hkl list from indexed\n"
+" reflections (requires pdb file)\n"
+" d : uses the 1/d list from indexed\n"
+" reflections (default)\n"
+" peaks : uses all peaks found from peak\n"
+" search\n"
+" h5 : all points in h5, excluding bad\n"
+" regions\n"
+" --no-sat-corr Don't correct values of saturated peaks using a\n"
+" table included in the HDF5 file.\n"
+" --only-indexed Use wiht -data=peaks or h5 if you want to use the\n"
+" peak list of only indexed patterns\n"
+" --no-q-scaling Use with .hkl files if you want to not scale the\n"
+" powder by 1/q^2\n"
+" --ring-corr Use if you want to scale the powder plot to\n"
+" correct for the fractional area sampled of the\n"
+" powder ring\n"
+" --use-redundency Use with .hkl files if you want to use the number\n"
+" of measurements and not the number of symetrical\n"
+" equivelent reflections as the number of time a\n"
+" reflection occurs in the powder\n"
"\n");
}
-
int main(int argc, char *argv[])
{
- int c;
- struct image image;
- int x, y;
- struct hdfile *hdfile;
+ FILE *fh = NULL;
+ UnitCell *cell = NULL;
+ struct image image;
+ struct hdfile *hdfile = NULL;
+ struct bin_stats *histdata = NULL;
+ struct histogram_info hist_info;
+
+ hist_info.histsize = 100; //default settings
+ hist_info.q_min = -1.0;
+ hist_info.q_max = -1.0;
+ hist_info.spacing = LINEAR;
+ image.lambda = -1.0;
+ image.beam = NULL;
+ image.det = NULL;
+
+ unsigned int n_patterns = 0;
+ unsigned int n_peaks = 0;
+
+ int c, rval, file_type, data_type;
+ int config_satcorr = 1; //true by default
+ int need_geometry = 0; //false
+ int need_beam = 0; //false
+ int need_pdb = 0; //false
+ int only_indexed = 0; //false
+ int q_scaling = 1; //true by default
+ int ring_corr = 0; //false
+ int use_redundency = 0; //false
+ unsigned int i, processing_total;
+
char *filename = NULL;
char *geometry = NULL;
- char *beamf = NULL;
- struct beam_params *beam = NULL;
+ char *beamf = NULL;
+ char *pdb = NULL;
+ char *output = NULL;
+ char *datatype = NULL;
+ char *sym = NULL;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
+ {"output", 1, NULL, 'o'},
{"geometry", 1, NULL, 'g'},
{"beam", 1, NULL, 'b'},
+ {"pdb", 1, NULL, 'p'},
+ {"symmetry", 1, NULL, 'y'},
+ {"bins", 1, NULL, 's'},
+ {"q-max", 1, NULL, 1 },
+ {"q-min", 1, NULL, 2 },
+ {"spacing", 1, NULL, 3 },
+ {"no-sat-corr", 0, &config_satcorr, 0 },
+ {"sat-corr", 0, &config_satcorr, 1 },
+ {"only-indexed", 0, &only_indexed, 1 },
+ {"no-q-scaling", 0, &q_scaling, 0 },
+ {"ring-corr", 0, &ring_corr, 1 },
+ {"use-redundency", 0, &use_redundency, 1 },
+ {"data", 1, NULL, 'd'},
{0, 0, NULL, 0}
};
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:g:", longopts, NULL)) != -1) {
+ while ((c = getopt_long(argc, argv, "hi:o:g:b:p:s:d:y:",
+ longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
- case 0 :
- break;
-
case 'i' :
filename = strdup(optarg);
break;
+ case 'o' :
+ output = strdup(optarg);
+ break;
+
case 'g' :
geometry = strdup(optarg);
break;
@@ -87,65 +635,338 @@ int main(int argc, char *argv[])
beamf = strdup(optarg);
break;
+ case 'p' :
+ pdb = strdup(optarg);
+ break;
+
+ case 'y' :
+ sym = strdup(optarg);
+ break;
+
+ case 's' :
+ hist_info.histsize = atoi(optarg);
+ break;
+
+ case 1 :
+ hist_info.q_max = atof(optarg);
+ break;
+
+ case 2 :
+ hist_info.q_min = atof(optarg);
+ break;
+
+ case 3 :
+ if (strcmp(optarg, "linear") == 0 ) {
+ hist_info.spacing = LINEAR;
+ } else if (strcmp(optarg, "q2") == 0 ) {
+ hist_info.spacing = q2;
+ } else if (strcmp(optarg, "volume") == 0) {
+ hist_info.spacing = VOLUME;
+ } else {
+ ERROR("Failed to read spacing plot type: '%s'\n",
+ optarg);
+ return 1;
+ }
+ break;
+
+ case 'd' :
+ datatype = strdup(optarg);
+ break;
+
+ case 0 :
+ break;
+
default :
return 1;
}
-
}
+ /* Process input file type */
if ( filename == NULL ) {
ERROR("You must specify the input filename with -i\n");
return 1;
+ } else if ( is_stream(filename) == 1 ) { //open .stream file
+ file_type = FILE_STREAM;
+ fh = fopen(filename, "r");
+ if ( fh == NULL ) {
+ ERROR("Failed to open input file\n");
+ return 1;
+ }
+ rval = read_chunk(fh, &image); //read chunk to get wavelength
+ rewind(fh);
+ processing_total = count_patterns(fh);
+ rewind(fh);
+
+ } else if ( H5Fis_hdf5(filename) > 0) { //open .h5 file
+ file_type = FILE_H5;
+ need_geometry = 1; //true
+ hdfile = hdfile_open(filename);
+ hdfile_set_image(hdfile, "/data/data");
+ hdf5_read(hdfile, &image, config_satcorr);
+ hdfile_close(hdfile);
+ processing_total = image.width * image.height;
+ } else {
+ image.reflections = read_reflections(filename);
+ if (image.reflections != NULL) { //open .hkl file
+ file_type = FILE_HKL;
+ need_pdb = 1;
+ processing_total = num_reflections(image.reflections);
+ } else {
+ ERROR("Input file: %s is an invalid type.\n",filename);
+ return 1;
+ }
}
+ free(filename);
- if ( geometry == NULL ) {
- ERROR("You need to specify a geometry file with --geometry\n");
+ /*Process data read type */
+ if ( datatype == NULL ) {
+ data_type = PLOT_D;
+ if ((hist_info.q_min < 0.0) || (hist_info.q_max < 0.0)) {
+ need_geometry = 1;
+ }
+ } else if ( strcmp(datatype, "reflection") == 0 ) {
+ data_type = PLOT_REFL;
+ need_geometry = 1;
+ } else if ( strcmp(datatype, "hkl") == 0 ) {
+ data_type = PLOT_HKL;
+ need_pdb = 1;
+ if ((hist_info.q_min <= 0.0) || (hist_info.q_max <= 0.0)) {
+ need_geometry = 1;
+ }
+ } else if ( strcmp(datatype, "d") == 0 ) {
+ data_type = PLOT_D;
+ if ((hist_info.q_min <= 0.0) || (hist_info.q_max <= 0.0)) {
+ need_geometry = 1;
+ }
+ } else if ( strcmp(datatype, "peaks") == 0 ) {
+ data_type = PLOT_PEAKS;
+ need_geometry = 1;
+ }
+ else if ( strcmp(datatype, "h5") == 0 ) {
+ data_type = PLOT_H5;
+ need_geometry = 1;
+ } else {
+ ERROR("Failed to read data plot type: '%s'\n", datatype);
return 1;
}
- if ( beamf != NULL ) {
- beam = get_beam_parameters(beamf);
- free(beamf);
+ /* logic checks */
+ if ((need_geometry) && (image.lambda < 0.0)) {
+ need_beam = 1;
}
-
- image.det = get_detector_geometry(geometry);
- if ( image.det == NULL ) {
- ERROR("Failed to read detector geometry from '%s'\n", geometry);
+ if ( hist_info.histsize <= 0 ) {
+ ERROR("You need to specify a histogram with more then 0 "
+ "bins\n");
+ return 1;
+ }
+ if (hist_info.q_min > hist_info.q_max) {
+ ERROR("the minimum q value of: %e "
+ "is greator then your max q value of: %e\n",
+ hist_info.q_min, hist_info.q_max);
return 1;
}
+
+ /*get geometry, beam and pdb files and parameters as needed */
+ if (need_geometry) {
+ if (geometry == NULL) {
+ ERROR("You need to specify a geometry file with "
+ "--geometry\n");
+ return 1;
+ } else {
+ image.det = get_detector_geometry(geometry);
+ if ( image.det == NULL ) {
+ ERROR("Failed to read detector geometry "
+ "from '%s'\n", geometry);
+ return 1;
+ }
+ image.width = image.det->max_fs;
+ image.height = image.det->max_ss;
+ }
+ }
free(geometry);
+
+ if (need_beam) {
+ if ( beamf == NULL ) {
+ ERROR("No wavelength in file, so you need to specify "
+ "a beam parameters file with --beam\n");
+ return 1;
+ } else {
+ image.beam = get_beam_parameters(beamf);
+ if ( image.beam == NULL ) {
+ ERROR("Failed to read beam from '%s'\n",
+ beamf);
+ return 1;
+ }
+ image.lambda = ph_en_to_lambda(eV_to_J(
+ image.beam->photon_energy));
+ }
+ }
+ free(beamf);
- hdfile = hdfile_open(filename);
- hdfile_set_image(hdfile, "/data/data");
- hdf5_read(hdfile, &image, 1);
- if ( image.lambda < 0.0 ) {
- if ( beam != NULL ) {
- image.lambda = beam->photon_energy;
+ if (need_pdb) {
+ if (pdb == NULL) {
+ ERROR("You need to specify a pdb file with --pdb.\n");
+ return 1;
} else {
- ERROR("No wavelength in file, so you need to give "
- "a beam parameters file with -b.\n");
+ cell = load_cell_from_pdb(pdb);
+ if ( cell == NULL ) {
+ ERROR("Couldn't read unit cell (from %s)\n",
+ pdb);
+ return 1;
+ }
+ }
+ }
+ free(pdb);
+
+ if ( sym == NULL ) {
+ sym = strdup("1");
+ }
+
+ /* setup histogram info*/
+ if (hist_info.q_min <= 0 ) {
+ hist_info.q_min = smallest_q(&image);
+ }
+ if (hist_info.q_max <= 0 ) {
+ hist_info.q_max = largest_q(&image);
+ }
+ if (hist_info.spacing == LINEAR) {
+ hist_info.q_delta = (hist_info.q_max - hist_info.q_min)/
+ hist_info.histsize;
+ } else if (hist_info.spacing == q2) {
+ hist_info.q_delta = (pow(hist_info.q_max, 2.0) -
+ pow(hist_info.q_min, 2.0)) /
+ hist_info.histsize;
+ } else { //by default must be in VOLUME
+ hist_info.q_delta = (pow(hist_info.q_max, 3.0) -
+ pow(hist_info.q_min, 3.0)) /
+ hist_info.histsize;
+ }
+ /* setup histogram data */
+ histdata = malloc((hist_info.histsize) * sizeof(struct bin_stats));
+ histogram_setup(&hist_info, histdata);
+
+ /* setup ring scaling */
+ if (ring_corr == 1) {
+ if (ring_fraction_calc(&hist_info, histdata, &image) == 1) {
+ ERROR("Detector is not loaded could not correct for"
+ " finiate ring measurement. Do not use --ring-corr\n");
return 1;
}
}
- for ( x=0; x<image.width; x++ ) {
- for ( y=0; y<image.height; y++ ) {
+ /* process reflections based on file type and data type*/
+ switch (file_type) {
+ case FILE_H5 :
+ n_patterns++;
+ n_peaks = process_h5(&image, &hist_info, histdata, processing_total);
+ free(image.data);
+ break;
- double q;
- int intensity;
- struct rvec r;
+ case FILE_HKL :
+ n_patterns++; //inc number of patterns used
+ n_peaks = process_hkl(&image, sym, cell, &hist_info, histdata,
+ q_scaling, processing_total, use_redundency);
+ break;
- r = get_q(&image, x, y, NULL, 1.0/image.lambda);
- q = modulus(r.u, r.v, r.w);
+ case FILE_STREAM :
+ switch (data_type) {
+ case PLOT_REFL :
+ n_peaks = process_stream_reflection(fh, &image,
+ &hist_info, histdata, processing_total,
+ &n_patterns);
+ break;
+ case PLOT_D :
+ n_peaks = process_stream_d(fh, &image, &hist_info,
+ histdata, processing_total,
+ &n_patterns);
+ break;
+ case PLOT_HKL :
+ n_peaks = process_stream_hkl(fh, &image, &hist_info,
+ histdata, cell, processing_total,
+ &n_patterns);
+ break;
+ case PLOT_PEAKS :
+ n_peaks = process_stream_peaks(fh, &image, &hist_info,
+ histdata, processing_total,
+ &n_patterns, only_indexed);
+ break;
+ case PLOT_H5 :
+ n_peaks = process_stream_h5(fh, &image, &hist_info,
+ histdata, config_satcorr, only_indexed,
+ processing_total, &n_patterns);
+ break;
+ default :
+ break;
+ }
+ fclose(fh);
+ break;
- intensity = image.data[x + image.width*y];
+ default :
+ break;
- printf("%5i\t%5i\t%7.3f\t%7i\n", x, y, q/1.0e9, intensity);
+ }
+
+ /* sqrt the variance to get the std_dev */
+
+ for(i=0; i<hist_info.histsize; i++) {
+ if (histdata[i].N > 1) {
+ histdata[i].std_dev = sqrt(histdata[i].std_dev/
+ (histdata[i].N-1));
+ }
+ }
+ if (ring_corr == 1) {
+ for(i=0; i<hist_info.histsize; i++) {
+ histdata[i].N = histdata[i].N /
+ histdata[i].fract;
+ histdata[i].total = histdata[i].total /
+ histdata[i].fract;
+ histdata[i].mean = histdata[i].mean /
+ histdata[i].fract;
+ histdata[i].std_dev = histdata[i].total /
+ histdata[i].fract;
+ }
+ }
+ /* print out the results */
+ if (output != NULL) {
+ fh = fopen(output, "w");
+ if ( fh == NULL ) {
+ ERROR("Failed to open output file\n");
+ return 1;
+ }
+ fprintf(fh,"I read %i patterns with %i peaks\n",
+ n_patterns, n_peaks);
+ fprintf(fh,"q\tN\ttotal\tmean\tstd dev\t std dev of mean\n");
}
+ else {
+ printf("I read %i patterns with %i peaks\n",
+ n_patterns, n_peaks);
+ printf("q\tN\ttotal\tmean\tstd dev\t std dev of mean\n");
+ }
+ for(i=0; i<hist_info.histsize; i++) {
+ if (output != NULL) {
+ fprintf(fh,"%5e\t%i\t%5e\t%5e\t%5e\t%5e\n",
+ histdata[i].q_min, histdata[i].N, histdata[i].total,
+ histdata[i].mean, histdata[i].std_dev,
+ histdata[i].std_dev/sqrt(histdata[i].N));
+ }
+ else {
+ printf("%5e\t%i\t%5e\t%5e\t%5e\t%5e\n",
+ histdata[i].q_min, histdata[i].N, histdata[i].total,
+ histdata[i].mean, histdata[i].std_dev,
+ histdata[i].std_dev/sqrt(histdata[i].N));
+ }
}
- free(beamf);
+ if ( cell != NULL ) cell_free(cell);
+ if ( image.det != NULL ) free(image.det);
+ if ( image.beam != NULL ) free(image.beam);
+ if (output != NULL) {
+ fclose(fh);
+ free(output);
+ }
+ free(histdata);
+ free(sym);
return 0;
}
diff --git a/src/stream.c b/src/stream.c
index 99344404..e3bc3c87 100644
--- a/src/stream.c
+++ b/src/stream.c
@@ -168,7 +168,7 @@ static int read_peaks(FILE *fh, struct image *image)
first = 0;
if ( r == 4 ) {
image_add_feature(image->features, x, y,
- image, 1.0, NULL);
+ image, intensity, NULL);
}
} while ( rval != NULL );
@@ -450,3 +450,22 @@ int skip_some_files(FILE *fh, int n)
return 1;
}
+
+int is_stream(const char *filename) {
+ FILE *fh;
+ char line[1024];
+ char *rval = NULL;
+ fh = fopen(filename, "r");
+ rval = fgets(line, 1023, fh);
+ fclose(fh);
+ if ( rval == NULL ) {
+ return -1;
+ }
+ if ( strncmp(line, "CrystFEL stream format 2.0", 26) == 0 ) {
+ return 1;
+ }
+ else {
+ return 0;
+ }
+ return -1;
+}
diff --git a/src/stream.h b/src/stream.h
index 02a01c48..e4e71728 100644
--- a/src/stream.h
+++ b/src/stream.h
@@ -43,4 +43,6 @@ extern int read_chunk(FILE *fh, struct image *image);
extern int skip_some_files(FILE *fh, int n);
+extern int is_stream(const char *filename);
+
#endif /* STREAM_H */