Rename calibrate_detector to sum_stack, add new calibrate_detector

1 files changed, 412 insertions, 0 deletions

diff --git a/src/sum_stack.c b/src/sum_stack.c
new file mode 100644
index 00000000..8bd5197e
--- /dev/null
+++ b/src/sum_stack.c
@@ -0,0 +1,412 @@
+/*
+ * sum_stack.c
+ *
+ * Sum a stack of images (e.g. for detector calibration)
+ *
+ * (c) 2006-2011 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 <pthread.h>
+
+#include "utils.h"
+#include "hdf5-file.h"
+#include "filters.h"
+#include "peaks.h"
+#include "thread-pool.h"
+
+
+#define INTEGRATION_RADIUS (10)
+
+
+typedef enum
+{
+	SUM_THRESHOLD,
+	SUM_PEAKS
+} SumMethod;
+
+struct sum_args
+{
+	char *filename;
+	int config_cmfilter;
+	int config_noisefilter;
+	double *sum;
+	int w;
+	int h;
+	SumMethod sum_method;
+	double threshold;
+};
+
+
+struct queue_args
+{
+	FILE *fh;
+	char *prefix;
+	int config_cmfilter;
+	int config_noisefilter;
+	double *sum;
+	int w;
+	int h;
+	SumMethod sum_method;
+	double threshold;
+};
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s [options]\n\n", s);
+	printf(
+"Sum 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"
+"  -p, --intermediate=<P>  Stem of filename for intermediate images.\n"
+"                            The filename stem <p> will be postfixed with a\n"
+"                            hyphen, the current number of patterns processed\n"
+"                            and '.h5'.  Such a pattern will be saved after\n"
+"                            every 1000 input patterns.\n"
+"                            If this option is not specified, no intermediate\n"
+"                            patterns will be saved.\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"
+"  -t, --threshold=<n>     Set the threshold if summing using the 'threshold'\n"
+"                           method.\n"
+"\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"
+"\n"
+" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
+" -x, --prefix=<p>         Prefix filenames from input file with 'p'.\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;
+
+	/* FIXME: Get threshold value from command line */
+	search_peaks(image, 800.0, 100000.0);
+
+	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, double threshold)
+{
+	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 > threshold ) {
+			sum[x+image->width*y] += val;
+		}
+	}
+	}
+}
+
+
+static void add_image(void *args, int cookie)
+{
+	struct sum_args *pargs = args;
+	struct hdfile *hdfile;
+	struct image image;
+
+	image.features = NULL;
+	image.data = NULL;
+	image.flags = NULL;
+	image.indexed_cell = NULL;
+	image.filename = pargs->filename;
+	image.det = NULL;
+
+	STATUS("%3i: Processing '%s'\n", cookie, pargs->filename);
+
+	hdfile = hdfile_open(pargs->filename);
+	if ( hdfile == NULL ) {
+		return;
+	} else if ( hdfile_set_first_image(hdfile, "/") ) {
+		ERROR("Couldn't select path\n");
+		hdfile_close(hdfile);
+		return;
+	}
+
+	/* FIXME: Nominal photon energy */
+	hdf5_read(hdfile, &image, 1, 2000.0);
+
+	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, pargs->threshold);
+		break;
+
+	case SUM_PEAKS :
+		sum_peaks(&image, pargs->sum);
+		break;
+
+	}
+
+out:
+	free(image.data);
+	image_feature_list_free(image.features);
+	if ( image.flags != NULL ) free(image.flags);
+	hdfile_close(hdfile);
+
+	free(pargs->filename);
+	free(pargs);
+}
+
+
+static void *get_image(void *qp)
+{
+	char line[1024];
+	struct sum_args *pargs;
+	char *rval;
+	struct queue_args *qargs = qp;
+
+	/* Get the next filename */
+	rval = fgets(line, 1023, qargs->fh);
+	if ( rval == NULL ) return NULL;
+
+	pargs = malloc(sizeof(struct sum_args));
+
+	pargs->w = qargs->w;
+	pargs->h = qargs->h;
+	pargs->sum_method = qargs->sum_method;
+	pargs->threshold = qargs->threshold;
+	pargs->config_cmfilter = qargs->config_cmfilter;
+	pargs->config_noisefilter = qargs->config_noisefilter;
+	pargs->sum = qargs->sum;
+
+	chomp(line);
+	pargs->filename = malloc(strlen(qargs->prefix) + strlen(line) + 1);
+	snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, line);
+
+	return pargs;
+}
+
+
+int main(int argc, char *argv[])
+{
+	int c;
+	char *filename = NULL;
+	char *outfile = NULL;
+	FILE *fh;
+	int n_images = 0;
+	int config_cmfilter = 0;
+	int config_noisefilter = 0;
+	char *prefix = NULL;
+	char *sum_str = NULL;
+	char *intermediate = NULL;
+	double threshold = 400.0;
+	SumMethod sum;
+	int nthreads = 1;
+	struct queue_args qargs;
+	int n_done;
+	const int chunk_size = 1000;
+
+	/* 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'},
+		{"intermediate",       1, NULL,               'p'},
+		{"threshold",          1, NULL,               't'},
+		{0, 0, NULL, 0}
+	};
+
+	/* Short options */
+	while ((c = getopt_long(argc, argv, "hi:x:j:o:s:p:t:",
+	                        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 'p' :
+			intermediate = strdup(optarg);
+			break;
+
+		case 't' :
+			threshold = atof(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  ) {
+		ERROR("Invalid number of threads.\n");
+		return 1;
+	}
+
+	qargs.w = 1024;  /* FIXME! */
+	qargs.h = 1024;  /* FIXME! */
+	qargs.sum_method = sum;
+	qargs.threshold = threshold;
+	qargs.config_cmfilter = config_cmfilter;
+	qargs.config_noisefilter = config_noisefilter;
+	qargs.sum = calloc(qargs.w*qargs.h, sizeof(double));
+	qargs.prefix = prefix;
+	qargs.fh = fh;
+
+	do {
+
+		n_done = run_threads(nthreads, add_image, get_image,
+		                     (void *)&qargs, NULL, chunk_size);
+
+		n_images += n_done;
+
+		/* Write intermediate sum if requested */
+		if ( (intermediate != NULL) && (n_done == chunk_size) ) {
+			char outfile[1024];
+			snprintf(outfile, 1023, "%s-%i.h5",
+			         intermediate, n_images);
+			hdf5_write(outfile, qargs.sum, qargs.w, qargs.h,
+			           H5T_NATIVE_DOUBLE);
+		}
+
+	} while ( n_done == chunk_size );
+
+	/* Write the final output */
+	hdf5_write(outfile, qargs.sum, qargs.w, qargs.h, H5T_NATIVE_DOUBLE);
+
+	free(qargs.sum);
+	free(prefix);
+	free(outfile);
+	if ( intermediate != NULL ) free(intermediate);
+	fclose(fh);
+
+	STATUS("There were %i images.\n", n_images);
+
+	return 0;
+}