"facetron" is now known as "partialator"

1 files changed, 486 insertions, 0 deletions

diff --git a/src/partialator.c b/src/partialator.c
new file mode 100644
index 00000000..c023fcde
--- /dev/null
+++ b/src/partialator.c
@@ -0,0 +1,486 @@
+/*
+ * partialator.c
+ *
+ * Scaling and post refinement for coherent nanocrystallography
+ *
+ * (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 <assert.h>
+#include <pthread.h>
+
+#include "utils.h"
+#include "hdf5-file.h"
+#include "symmetry.h"
+#include "reflections.h"
+#include "stream.h"
+#include "geometry.h"
+#include "peaks.h"
+#include "thread-pool.h"
+#include "beam-parameters.h"
+#include "post-refinement.h"
+#include "hrs-scaling.h"
+
+
+/* Maximum number of iterations of NLSq to do for each image per macrocycle. */
+#define MAX_CYCLES (100)
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s [options]\n\n", s);
+	printf(
+"Scaling and post refinement for coherent nanocrystallography.\n"
+"\n"
+"  -h, --help                 Display this help message.\n"
+"\n"
+"  -i, --input=<filename>     Specify the name of the input 'stream'.\n"
+"                              (must be a file, not e.g. stdin)\n"
+"  -o, --output=<filename>    Output filename.  Default: facetron.hkl.\n"
+"  -g. --geometry=<file>      Get detector geometry from file.\n"
+"  -b, --beam=<file>          Get beam parameters from file, which provides\n"
+"                              initial values for parameters, and nominal\n"
+"                              wavelengths if no per-shot value is found in \n"
+"                              an HDF5 file.\n"
+"  -x, --prefix=<p>           Prefix filenames from input file with <p>.\n"
+"      --basename             Remove the directory parts of the filenames.\n"
+"      --no-check-prefix      Don't attempt to correct the --prefix.\n"
+"  -y, --symmetry=<sym>       Merge according to symmetry <sym>.\n"
+"  -n, --iterations=<n>       Run <n> cycles of scaling and post-refinement.\n"
+"\n"
+"  -j <n>                     Run <n> analyses in parallel.\n");
+}
+
+
+struct refine_args
+{
+	const char *sym;
+	ReflItemList *obs;
+	double *i_full;
+	struct image *image;
+	FILE *graph;
+	FILE *pgraph;
+};
+
+
+static void refine_image(int mytask, void *tasks)
+{
+	struct refine_args *all_args = tasks;
+	struct refine_args *pargs = &all_args[mytask];
+	struct image *image = pargs->image;
+	double nominal_photon_energy = pargs->image->beam->photon_energy;
+	struct hdfile *hdfile;
+	struct cpeak *spots;
+	int n, i;
+	double dev, last_dev;
+
+	hdfile = hdfile_open(image->filename);
+	if ( hdfile == NULL ) {
+		ERROR("Couldn't open '%s'\n", image->filename);
+		return;
+	} else if ( hdfile_set_image(hdfile, "/data/data0") ) {
+		ERROR("Couldn't select path\n");
+		hdfile_close(hdfile);
+		return;
+	}
+
+	if ( hdf5_read(hdfile, pargs->image, 0, nominal_photon_energy) ) {
+		ERROR("Couldn't read '%s'\n", image->filename);
+		hdfile_close(hdfile);
+		return;
+	}
+
+	double a, b, c, al, be, ga;
+	cell_get_parameters(image->indexed_cell, &a, &b, &c, &al, &be, &ga);
+	STATUS("Initial cell: %5.2f %5.2f %5.2f nm %5.2f %5.2f %5.2f deg\n",
+	       a/1.0e-9, b/1.0e-9, c/1.0e-9,
+	       rad2deg(al), rad2deg(be), rad2deg(ga));
+
+	spots = find_intersections(image, image->indexed_cell, &n, 0);
+	dev = +INFINITY;
+	i = 0;
+	do {
+		last_dev = dev;
+		dev = pr_iterate(image, pargs->i_full, pargs->sym, &spots, &n);
+		STATUS("Iteration %2i: mean dev = %5.2f\n", i, dev);
+		i++;
+	} while ( (fabs(last_dev - dev) > 1.0) && (i < MAX_CYCLES) );
+	mean_partial_dev(image, spots, n, pargs->sym,
+	                 pargs->i_full, pargs->graph);
+	if ( pargs->pgraph ) {
+		fprintf(pargs->pgraph, "%5i %5.2f\n", mytask, dev);
+	}
+
+	free(image->data);
+	if ( image->flags != NULL ) free(image->flags);
+	hdfile_close(hdfile);
+	free(spots);
+
+	/* Muppet proofing */
+	image->data = NULL;
+	image->flags = NULL;
+}
+
+
+static void refine_all(struct image *images, int n_total_patterns,
+                       struct detector *det, const char *sym,
+                       ReflItemList *obs, double *i_full, int nthreads,
+                       FILE *graph, FILE *pgraph)
+{
+	struct refine_args *tasks;
+	int i;
+
+	tasks = malloc(n_total_patterns * sizeof(struct refine_args));
+	for ( i=0; i<n_total_patterns; i++ ) {
+
+		tasks[i].sym = sym;
+		tasks[i].obs = obs;
+		tasks[i].i_full = i_full;
+		tasks[i].image = &images[i];
+		tasks[i].graph = graph;
+		tasks[i].pgraph = pgraph;
+
+	}
+
+	run_thread_range(n_total_patterns, nthreads, "Refining",
+	                 refine_image, tasks);
+
+	free(tasks);
+}
+
+
+static void integrate_image(struct image *image)
+{
+	struct cpeak *spots;
+	int j, n;
+	struct hdfile *hdfile;
+	double nominal_photon_energy = image->beam->photon_energy;
+
+	hdfile = hdfile_open(image->filename);
+	if ( hdfile == NULL ) {
+		ERROR("Couldn't open '%s'\n", image->filename);
+		return;
+	} else if ( hdfile_set_image(hdfile, "/data/data0") ) {
+		ERROR("Couldn't select path\n");
+		hdfile_close(hdfile);
+		return;
+	}
+
+	if ( hdf5_read(hdfile, image, 0, nominal_photon_energy) ) {
+		ERROR("Couldn't read '%s'\n", image->filename);
+		hdfile_close(hdfile);
+		return;
+	}
+
+	/* Figure out which spots should appear in this pattern */
+	spots = find_intersections(image, image->indexed_cell, &n, 0);
+
+	/* For each reflection, estimate the partiality */
+	for ( j=0; j<n; j++ ) {
+
+		signed int h, k, l;
+		float i_partial;
+		float xc, yc;
+
+		h = spots[j].h;
+		k = spots[j].k;
+		l = spots[j].l;
+
+		/* Don't attempt to use spots with very small
+		 * partialities, since it won't be accurate. */
+		if ( spots[j].p < 0.1 ) continue;
+
+		/* Actual measurement of this reflection from this
+		 * pattern? */
+		/* FIXME: Coordinates aren't whole numbers */
+		if ( integrate_peak(image, spots[j].x, spots[j].y,
+		                    &xc, &yc, &i_partial, NULL, NULL,
+		                    1, 1, 0) ) {
+			continue;
+		}
+
+	}
+
+	free(image->data);
+	if ( image->flags != NULL ) free(image->flags);
+	hdfile_close(hdfile);
+	image->cpeaks = spots;
+
+	/* Muppet proofing */
+	image->data = NULL;
+	image->flags = NULL;
+}
+
+
+int main(int argc, char *argv[])
+{
+	int c;
+	char *infile = NULL;
+	char *outfile = NULL;
+	char *geomfile = NULL;
+	char *prefix = NULL;
+	char *sym = NULL;
+	FILE *fh;
+	int nthreads = 1;
+	int config_basename = 0;
+	int config_checkprefix = 1;
+	struct detector *det;
+	double *i_full;
+	unsigned int *cts;
+	ReflItemList *obs;
+	int i;
+	int n_total_patterns;
+	struct image *images;
+	int n_iter = 10;
+	struct beam_params *beam = 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'},
+		{"prefix",             1, NULL,               'x'},
+		{"basename",           0, &config_basename,    1},
+		{"no-check-prefix",    0, &config_checkprefix, 0},
+		{"symmetry",           1, NULL,               'y'},
+		{"iterations",         1, NULL,               'n'},
+		{0, 0, NULL, 0}
+	};
+
+	/* Short options */
+	while ((c = getopt_long(argc, argv, "hi:g:x:j:y:o:b:",
+	                        longopts, NULL)) != -1)
+	{
+
+		switch (c) {
+		case 'h' :
+			show_help(argv[0]);
+			return 0;
+
+		case 'i' :
+			infile = strdup(optarg);
+			break;
+
+		case 'g' :
+			geomfile = strdup(optarg);
+			break;
+
+		case 'x' :
+			prefix = strdup(optarg);
+			break;
+
+		case 'j' :
+			nthreads = atoi(optarg);
+			break;
+
+		case 'y' :
+			sym = strdup(optarg);
+			break;
+
+		case 'o' :
+			outfile = strdup(optarg);
+			break;
+
+		case 'n' :
+			n_iter = atoi(optarg);
+			break;
+
+		case 'b' :
+			beam = get_beam_parameters(optarg);
+			if ( beam == NULL ) {
+				ERROR("Failed to load beam parameters"
+				      " from '%s'\n", optarg);
+				return 1;
+			}
+			break;
+
+		case 0 :
+			break;
+
+		default :
+			return 1;
+		}
+
+	}
+
+	/* Sanitise input filename and open */
+	if ( infile == NULL ) {
+		infile = strdup("-");
+	}
+	if ( strcmp(infile, "-") == 0 ) {
+		fh = stdin;
+	} else {
+		fh = fopen(infile, "r");
+	}
+	if ( fh == NULL ) {
+		ERROR("Failed to open input file '%s'\n", infile);
+		return 1;
+	}
+	free(infile);
+
+	/* Sanitise output filename */
+	if ( outfile == NULL ) {
+		outfile = strdup("facetron.hkl");
+	}
+
+	/* Sanitise prefix */
+	if ( prefix == NULL ) {
+		prefix = strdup("");
+	} else {
+		if ( config_checkprefix ) {
+			prefix = check_prefix(prefix);
+		}
+	}
+
+	if ( sym == NULL ) sym = strdup("1");
+
+	/* Get detector geometry */
+	det = get_detector_geometry(geomfile);
+	if ( det == NULL ) {
+		ERROR("Failed to read detector geometry from '%s'\n", geomfile);
+		return 1;
+	}
+	free(geomfile);
+
+	if ( beam == NULL ) {
+		ERROR("You must provide a beam parameters file.\n");
+		return 1;
+	}
+
+	/* Prepare for iteration */
+	i_full = new_list_intensity();
+	obs = new_items();
+
+	n_total_patterns = count_patterns(fh);
+	STATUS("There are %i patterns to process\n", n_total_patterns);
+
+	images = malloc(n_total_patterns * sizeof(struct image));
+	if ( images == NULL ) {
+		ERROR("Couldn't allocate memory for images.\n");
+		return 1;
+	}
+
+	/* Fill in what we know about the images so far */
+	rewind(fh);
+	for ( i=0; i<n_total_patterns; i++ ) {
+
+		UnitCell *cell;
+		char *filename;
+		char *fnamereal;
+
+		if ( find_chunk(fh, &cell, &filename) == 1 ) {
+			ERROR("Couldn't get all of the filenames and cells"
+			      " from the input stream.\n");
+			return 1;
+		}
+
+		images[i].indexed_cell = cell;
+
+		/* Mangle the filename now */
+		if ( config_basename ) {
+			char *tmp;
+			tmp = safe_basename(filename);
+			free(filename);
+			filename = tmp;
+		}
+		fnamereal = malloc(1024);
+		snprintf(fnamereal, 1023, "%s%s", prefix, filename);
+		free(filename);
+
+		images[i].filename = fnamereal;
+		images[i].div = beam->divergence;
+		images[i].bw = beam->bandwidth;
+		images[i].det = det;
+		images[i].beam = beam;
+		images[i].osf = 1.0;
+		images[i].profile_radius = 0.005e9;
+
+		/* Muppet proofing */
+		images[i].data = NULL;
+		images[i].flags = NULL;
+
+		/* Get reflections from this image */
+		integrate_image(&images[i]);
+
+		progress_bar(i, n_total_patterns-1, "Loading pattern data");
+
+	}
+	fclose(fh);
+	free(prefix);
+
+	cts = new_list_count();
+
+	/* Make initial estimates */
+	STATUS("Performing initial scaling.\n");
+	scale_intensities(images, n_total_patterns, sym);
+
+	/* Iterate */
+	for ( i=0; i<n_iter; i++ ) {
+
+		FILE *fhg;
+		FILE *fhp;
+		char filename[1024];
+
+		STATUS("Post refinement iteration %i of %i\n", i+1, n_iter);
+
+		snprintf(filename, 1023, "p-iteration-%i.dat", i+1);
+		fhg = fopen(filename, "w");
+		if ( fhg == NULL ) {
+			ERROR("Failed to open '%s'\n", filename);
+			/* Nothing will be written later */
+		}
+
+		snprintf(filename, 1023, "g-iteration-%i.dat", i+1);
+		fhp = fopen(filename, "w");
+		if ( fhp == NULL ) {
+			ERROR("Failed to open '%s'\n", filename);
+			/* Nothing will be written later */
+		}
+
+		/* Refine the geometry of all patterns to get the best fit */
+		refine_all(images, n_total_patterns, det, sym, obs, i_full,
+		           nthreads, fhg, fhp);
+
+		/* Re-estimate all the full intensities */
+		scale_intensities(images, n_total_patterns, sym);
+
+		fclose(fhg);
+		fclose(fhp);
+	}
+
+	/* Output results */
+	write_reflections(outfile, obs, i_full, NULL, NULL, cts, NULL);
+
+	/* Clean up */
+	free(i_full);
+	delete_items(obs);
+	free(sym);
+	free(outfile);
+	free(det->panels);
+	free(det);
+	free(beam);
+	free(cts);
+	for ( i=0; i<n_total_patterns; i++ ) {
+		cell_free(images[i].indexed_cell);
+		free(images[i].filename);
+	}
+	free(images);
+
+	return 0;
+}