src/calibrate-detector.c -> src/calibrate_detector.c in line with convention

1 files changed, 479 insertions, 0 deletions

diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
new file mode 100644
index 00000000..3dc57e4b
--- /dev/null
+++ b/src/calibrate_detector.c
@@ -0,0 +1,479 @@
+/*
+ * calibrate-detector.c
+ *
+ * Detector calibration
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#define _GNU_SOURCE 1
+#include <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <pthread.h>
+#include <sys/time.h>
+
+#include "utils.h"
+#include "hdf5-file.h"
+#include "filters.h"
+#include "peaks.h"
+
+
+#define INTEGRATION_RADIUS (10)
+#define MAX_THREADS (96)
+
+
+typedef enum
+{
+	SUM_THRESHOLD,
+	SUM_PEAKS
+} SumMethod;
+
+struct process_args
+{
+	char *filename;
+	int id;
+	int config_cmfilter;
+	int config_noisefilter;
+	double *sum;
+	int w;
+	int h;
+	SumMethod sum_method;
+};
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s [options]\n\n", s);
+	printf(
+"Calibrate detector geometry from FEL diffraction images.\n"
+"\n"
+"  -h, --help              Display this help message.\n"
+"\n"
+"  -i, --input=<filename>  Specify file containing list of images to process.\n"
+"                           '-' means stdin, which is the default.\n"
+"  -o, --output=<filename> Output filename for summed image in HDF5 format.\n"
+"                           Default: summed.h5.\n"
+"\n"
+"  -s, --sum=<method>      Use this method for summation.  Choose from:\n"
+"                           peaks : sum 10px radius circles around peaks.\n"
+"                           threshold : sum thresholded images.\n"
+"      --filter-cm         Perform common-mode noise subtraction on images\n"
+"                           before proceeding.\n"
+"      --filter-noise      Apply an aggressive noise filter which sets all\n"
+"                           pixels in each 3x3 region to zero if any of them\n"
+"                           have negative values.\n"
+"  -j <n>                  Run <n> analyses in parallel.  Default 1.\n");
+}
+
+
+static void sum_peaks(struct image *image, double *sum)
+{
+	int x, y, i;
+	int w = image->width;
+	const int lim = INTEGRATION_RADIUS * INTEGRATION_RADIUS;
+
+	search_peaks(image);
+
+	for ( i=0; i<image_feature_count(image->features); i++ ) {
+
+		struct imagefeature *f = image_get_feature(image->features, i);
+		int xp, yp;
+
+		/* This is not an error. */
+		if ( f == NULL ) continue;
+
+		xp = f->x;
+		yp = f->y;
+
+		for ( x=-INTEGRATION_RADIUS; x<+INTEGRATION_RADIUS; x++ ) {
+		for ( y=-INTEGRATION_RADIUS; y<+INTEGRATION_RADIUS; y++ ) {
+
+			/* Circular mask */
+			if ( x*x + y*y > lim ) continue;
+
+			if ( ((x+xp)>=image->width) || ((x+xp)<0) ) continue;
+			if ( ((y+yp)>=image->height) || ((y+yp)<0) ) continue;
+
+			float val = image->data[(x+xp)+w*(y+yp)];
+			sum[(x+xp)+w*(y+yp)] += val;
+
+		}
+		}
+
+	}
+}
+
+
+static void sum_threshold(struct image *image, double *sum)
+{
+	int x, y;
+
+	for ( x=0; x<image->width; x++ ) {
+	for ( y=0; y<image->height; y++ ) {
+		float val = image->data[x+image->width*y];
+		if ( val > 400.0 ) {
+			sum[x+image->width*y] += val;
+		}
+	}
+	}
+}
+
+
+static void *process_image(void *pargsv)
+{
+	struct process_args *pargs = pargsv;
+	struct hdfile *hdfile;
+	struct image image;
+
+	image.features = NULL;
+	image.data = NULL;
+	image.flags = NULL;
+	image.indexed_cell = NULL;
+	image.id = pargs->id;
+	image.filename = pargs->filename;
+	image.hits = NULL;
+	image.n_hits = 0;
+	image.det = NULL;
+
+	/* View head-on (unit cell is tilted) */
+	image.orientation.w = 1.0;
+	image.orientation.x = 0.0;
+	image.orientation.y = 0.0;
+	image.orientation.z = 0.0;
+
+	STATUS("Processing '%s'\n", pargs->filename);
+
+	hdfile = hdfile_open(pargs->filename);
+	if ( hdfile == NULL ) {
+		return NULL;
+	} else if ( hdfile_set_first_image(hdfile, "/") ) {
+		ERROR("Couldn't select path\n");
+		hdfile_close(hdfile);
+		return NULL;
+	}
+
+	hdf5_read(hdfile, &image);
+
+	if ( pargs->config_cmfilter ) {
+		filter_cm(&image);
+	}
+
+	if ( pargs->config_noisefilter ) {
+		filter_noise(&image, NULL);
+	}
+
+	if ( (pargs->w != image.width) || (pargs->h != image.height) ) {
+		ERROR("Wrong image size.\n");
+		goto out;
+	}
+
+	switch ( pargs->sum_method ) {
+
+	case SUM_THRESHOLD :
+		sum_threshold(&image, pargs->sum);
+		break;
+
+	case SUM_PEAKS :
+		sum_peaks(&image, pargs->sum);
+		break;
+
+	}
+
+out:
+	free(image.data);
+	if ( image.flags != NULL ) free(image.flags);
+	hdfile_close(hdfile);
+
+	return NULL;
+}
+
+
+static void dump_to_file(struct process_args *worker_args[], int nthreads,
+                         int w, int h, int n)
+{
+	int i;
+	double *total;
+	char outfile[256];
+
+	total = calloc(w*h, sizeof(double));
+
+	/* Add the individual sums to the 0th sum */
+	for ( i=0; i<nthreads; i++ ) {
+
+		int x, y;
+
+		for ( x=0; x<w; x++ ) {
+		for ( y=0; y<h; y++ ) {
+			double val = worker_args[i]->sum[x+w*y];
+			total[x+w*y] += val;
+		}
+		}
+
+	}
+
+	snprintf(outfile, 255, "sum-%i.h5", n);
+
+	hdf5_write(outfile, total, w, h, H5T_NATIVE_DOUBLE);
+}
+
+
+int main(int argc, char *argv[])
+{
+	int c;
+	char *filename = NULL;
+	char *outfile = NULL;
+	FILE *fh;
+	char *rval = NULL;
+	int n_images;
+	int config_cmfilter = 0;
+	int config_noisefilter = 0;
+	char *prefix = NULL;
+	char *sum_str = NULL;
+	SumMethod sum;
+	int nthreads = 1;
+	pthread_t workers[MAX_THREADS];
+	struct process_args *worker_args[MAX_THREADS];
+	int worker_active[MAX_THREADS];
+	int i;
+	const int w = 1024;  /* FIXME! */
+	const int h = 1024;  /* FIXME! */
+
+	/* Long options */
+	const struct option longopts[] = {
+		{"help",               0, NULL,               'h'},
+		{"input",              1, NULL,               'i'},
+		{"output",             1, NULL,               'o'},
+		{"filter-cm",          0, &config_cmfilter,    1},
+		{"filter-noise",       0, &config_noisefilter, 1},
+		{"prefix",             1, NULL,               'x'},
+		{"sum",                1, NULL,               's'},
+		{0, 0, NULL, 0}
+	};
+
+	/* Short options */
+	while ((c = getopt_long(argc, argv, "hi:x:j:o:",
+	                        longopts, NULL)) != -1) {
+
+		switch (c) {
+		case 'h' :
+			show_help(argv[0]);
+			return 0;
+
+		case 'i' :
+			filename = strdup(optarg);
+			break;
+
+		case 'o' :
+			outfile = strdup(optarg);
+			break;
+
+		case 'x' :
+			prefix = strdup(optarg);
+			break;
+
+		case 'j' :
+			nthreads = atoi(optarg);
+			break;
+
+		case 's' :
+			sum_str = strdup(optarg);
+			break;
+
+		case 0 :
+			break;
+
+		default :
+			return 1;
+		}
+
+	}
+
+	if ( filename == NULL ) {
+		filename = strdup("-");
+	}
+	if ( strcmp(filename, "-") == 0 ) {
+		fh = stdin;
+	} else {
+		fh = fopen(filename, "r");
+	}
+	if ( fh == NULL ) {
+		ERROR("Failed to open input file '%s'\n", filename);
+		return 1;
+	}
+	free(filename);
+
+	if ( sum_str == NULL ) {
+		STATUS("You didn't specify a summation method, so I'm using"
+		       " the 'peaks' method, which gives the best results.\n");
+		sum = SUM_PEAKS;
+	} else if ( strcmp(sum_str, "peaks") == 0 ) {
+		sum = SUM_PEAKS;
+	} else if ( strcmp(sum_str, "threshold") == 0) {
+		sum = SUM_THRESHOLD;
+	} else {
+		ERROR("Unrecognised summation method '%s'\n", sum_str);
+		return 1;
+	}
+	free(sum_str);
+
+	if ( prefix == NULL ) {
+		prefix = strdup("");
+	}
+
+	if ( outfile == NULL ) {
+		outfile = strdup("summed.h5");
+	}
+
+	if ( (nthreads == 0) || (nthreads > MAX_THREADS) ) {
+		ERROR("Invalid number of threads.\n");
+		return 1;
+	}
+
+	/* Initialise worker arguments */
+	for ( i=0; i<nthreads; i++ ) {
+
+		worker_args[i] = malloc(sizeof(struct process_args));
+		worker_args[i]->filename = malloc(1024);
+		worker_args[i]->sum = calloc(w*h, sizeof(double));
+		worker_active[i] = 0;
+
+		worker_args[i]->w = w;
+		worker_args[i]->h = h;
+		worker_args[i]->sum_method = sum;
+
+	}
+
+	n_images = 0;
+
+	/* Initially, fire off the full number of threads */
+	for ( i=0; i<nthreads; i++ ) {
+
+		char line[1024];
+		struct process_args *pargs;
+		int r;
+
+		pargs = worker_args[i];
+
+		rval = fgets(line, 1023, fh);
+		if ( rval == NULL ) continue;
+		chomp(line);
+		snprintf(pargs->filename, 1023, "%s%s", prefix, line);
+
+		n_images++;
+
+		pargs->config_cmfilter = config_cmfilter;
+		pargs->config_noisefilter = config_noisefilter;
+
+		worker_active[i] = 1;
+		r = pthread_create(&workers[i], NULL, process_image, pargs);
+		if ( r != 0 ) {
+			worker_active[i] = 0;
+			ERROR("Couldn't start thread %i\n", i);
+		}
+
+	}
+
+	/* Start new threads as old ones finish */
+	do {
+
+		int i;
+
+		for ( i=0; i<nthreads; i++ ) {
+
+			char line[1024];
+			int r;
+			struct timespec t;
+			struct timeval tv;
+			struct process_args *pargs;
+
+			if ( !worker_active[i] ) continue;
+
+			pargs = worker_args[i];
+
+			gettimeofday(&tv, NULL);
+			t.tv_sec = tv.tv_sec;
+			t.tv_nsec = tv.tv_usec * 1000 + 20000;
+
+			r = pthread_timedjoin_np(workers[i], NULL, &t);
+			if ( r != 0 ) continue; /* Not ready yet */
+
+			worker_active[i] = 0;
+
+			rval = fgets(line, 1023, fh);
+			if ( rval == NULL ) break;
+			chomp(line);
+			snprintf(pargs->filename, 1023, "%s%s", prefix, line);
+
+			worker_active[i] = 1;
+			r = pthread_create(&workers[i], NULL, process_image, pargs);
+			if ( r != 0 ) {
+				worker_active[i] = 0;
+				ERROR("Couldn't start thread %i\n", i);
+			}
+
+			n_images++;
+			STATUS("Done %i images\n", n_images);
+
+			if ( n_images % 1000 == 0 ) {
+				dump_to_file(worker_args, nthreads, w, h, n_images);
+			}
+		}
+
+	} while ( rval != NULL );
+
+	/* Catch all remaining threads */
+	for ( i=0; i<nthreads; i++ ) {
+
+		if ( !worker_active[i] ) goto free;
+
+		pthread_join(workers[i], NULL);
+
+		worker_active[i] = 0;
+
+	free:
+		if ( worker_args[i]->filename != NULL ) {
+			free(worker_args[i]->filename);
+		}
+
+	}
+
+	/* Add the individual sums to the 0th sum */
+	for ( i=1; i<nthreads; i++ ) {
+
+		int x, y;
+
+		for ( x=0; x<w; x++ ) {
+		for ( y=0; y<h; y++ ) {
+			double val = worker_args[i]->sum[x+w*y];
+			worker_args[0]->sum[x+w*y] += val;
+		}
+		}
+		free(worker_args[i]->sum);
+		free(worker_args[i]);
+
+	}
+
+	hdf5_write(outfile, worker_args[0]->sum, w, h, H5T_NATIVE_DOUBLE);
+
+	free(worker_args[0]->sum);
+	free(worker_args[0]);
+	free(prefix);
+	free(outfile);
+	fclose(fh);
+
+	STATUS("There were %i images.\n", n_images);
+
+	return 0;
+}