path: root/src/indexamajig.c

/*
 * indexamajig.c
 *
 * Index patterns, output hkl+intensity etc.
 *
 * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
 *                  a research centre of the Helmholtz Association.
 * Copyright © 2012 Richard Kirian
 * Copyright © 2012 Lorenzo Galli
 *
 * Authors:
 *   2010-2012 Thomas White <taw@physics.org>
 *   2011      Richard Kirian
 *   2012      Lorenzo Galli
 *   2012      Chunhong Yoon
 *
 * This file is part of CrystFEL.
 *
 * CrystFEL is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * CrystFEL is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
 *
 */


#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 <hdf5.h>
#include <gsl/gsl_errno.h>
#include <pthread.h>
#include <sys/wait.h>
#include <fcntl.h>

#ifdef HAVE_CLOCK_GETTIME
#include <time.h>
#else
#include <sys/time.h>
#endif

#include <crystfel/utils.h>
#include <crystfel/hdf5-file.h>
#include <crystfel/index.h>
#include <crystfel/peaks.h>
#include <crystfel/detector.h>
#include <crystfel/filters.h>
#include <crystfel/thread-pool.h>
#include <crystfel/beam-parameters.h>
#include <crystfel/geometry.h>
#include <crystfel/stream.h>
#include <crystfel/reflist-utils.h>


/* Write statistics at APPROXIMATELY this interval */
#define STATS_EVERY_N_SECONDS (5)

#define LINE_LENGTH 1024

#define BUFFER PIPE_BUF

enum {
	PEAK_ZAEF,
	PEAK_HDF5,
};


/* Information about the indexing process which is common to all patterns */
struct static_index_args
{
	UnitCell *cell;
	int config_cmfilter;
	int config_noisefilter;
	int config_verbose;
	int stream_flags;         /* What goes into the output? */
	int config_satcorr;
	int config_closer;
	int config_insane;
	int config_bgsub;
	float threshold;
	float min_gradient;
	float min_snr;
	double min_int_snr;
	struct detector *det;
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
	int peaks;                /* Peak detection method */
	int cellr;
	float tols[4];
	struct beam_params *beam;
	const char *element;
	const char *hdf5_peak_path;
	double ir_inn;
	double ir_mid;
	double ir_out;

	/* Output stream */
	pthread_mutex_t *output_mutex;  /* Protects the output stream */
	FILE *ofh;
	const struct copy_hdf5_field *copyme;
	char *outfile;
};


/* Information about the indexing process for one pattern */
struct index_args
{
	/* "Input" */
	char *filename;
	struct static_index_args static_args;

	/* "Output" */
	int indexable;
};


/* Information needed to choose the next task and dispatch it */
struct queue_args
{
	FILE *fh;
	char *prefix;
	int config_basename;
	struct static_index_args static_args;

	char *use_this_one_instead;

	int n_indexable;
	int n_processed;
	int n_indexable_last_stats;
	int n_processed_last_stats;
	int t_last_stats;
	int updateReader;
};


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Process and index 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>  Write output stream to this file. '-' for stdout.\n"
"                           Default: indexamajig.stream\n"
"\n"
"     --indexing=<methods> Use 'methods' for indexing.  Provide one or more\n"
"                           methods separated by commas.  Choose from:\n"
"                            none     : no indexing (default)\n"
"                            dirax    : invoke DirAx\n"
"                            mosflm   : invoke MOSFLM (DPS)\n"
"                            reax     : DPS algorithm with known unit cell\n"
" -g. --geometry=<file>    Get detector geometry from file.\n"
" -b, --beam=<file>        Get beam parameters from file (provides nominal\n"
"                           wavelength value if no per-shot value is found in\n"
"                           the HDF5 files.\n"
" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
"                           Default: 'molecule.pdb'.\n"
"     --basename           Remove the directory parts of the filenames.\n"
" -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
"     --peaks=<method>     Use 'method' for finding peaks.  Choose from:\n"
"                           zaef  : Use Zaefferer (2000) gradient detection.\n"
"                                    This is the default method.\n"
"                           hdf5  : Get from a table in HDF5 file.\n"
"     --hdf5-peaks=<p>     Find peaks table in HDF5 file here.\n"
"                           Default: /processing/hitfinder/peakinfo\n"
"\n\n"
"You can control what information is included in the output stream using\n"
"' --record=<flag1>,<flag2>,<flag3>' and so on.  Possible flags are:\n\n"
" integrated        Include a list of reflection intensities, produced by\n"
"                    integrating around predicted peak locations.\n"
"\n"
" peaks             Include peak locations and intensities from the peak\n"
"                    search.\n"
"\n"
" peaksifindexed    As 'peaks', but only if the pattern could be indexed.\n"
"\n"
" peaksifnotindexed As 'peaks', but only if the pattern could NOT be indexed.\n"
"\n\n"
"The default is '--record=integrated'.\n"
"\n\n"
"For more control over the process, you might need:\n\n"
"  --cell-reduction=<m>  Use <m> as the cell reduction method. Choose from:\n"
"                         none    : no matching, just use the raw cell.\n"
"                         reduce  : full cell reduction.\n"
"                         compare : match by at most changing the order of\n"
"                                   the indices.\n"
"                         compare_ab : compare 'a' and 'b' lengths only.\n"
"    --tolerance=<tol>   Set the tolerances for cell reduction.\n"
"                          Default: 5,5,5,1.5.\n"
"    --filter-cm         Perform common-mode noise subtraction on images\n"
"                         before proceeding.  Intensities will be extracted\n"
"                         from the image as it is after this processing.\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.  Intensity measurement will\n"
"                         be performed on the image as it was before this.\n"
"    --no-sat-corr       Don't correct values of saturated peaks using a\n"
"                         table included in the HDF5 file.\n"
"    --threshold=<n>     Only accept peaks above <n> ADU.  Default: 800.\n"
"    --min-gradient=<n>  Minimum gradient for Zaefferer peak search.\n"
"                         Default: 100,000.\n"
"    --min-snr=<n>       Minimum signal-to-noise ratio for peaks.\n"
"                         Default: 5.\n"
"    --min-integration-snr=<n> Minimum signal-to-noise ratio for peaks\n"
"                         during integration. Default: -infinity.\n"
"    --int-radius=<r>    Set the integration radii.  Default: 4,5,7.\n"
"-e, --image=<element>   Use this image from the HDF5 file.\n"
"                          Example: /data/data0.\n"
"                          Default: The first one found.\n"
"\n"
"\nFor time-resolved stuff, you might want to use:\n\n"
"     --copy-hdf5-field <f>  Copy the value of field <f> into the stream. You\n"
"                             can use this option as many times as you need.\n"
"\n"
"\nOptions for greater performance or verbosity:\n\n"
"     --verbose            Be verbose about indexing.\n"
" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
"\n"
"\nOptions you probably won't need:\n\n"
"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
"     --closer-peak        Don't integrate from the location of a nearby peak\n"
"                           instead of the predicted spot.  Don't use.\n"
"     --insane             Don't check that the reduced cell accounts for at\n"
"                           least 10%% of the located peaks.\n"
"     --no-bg-sub          Don't subtract local background estimates from\n"
"                           integrated intensities.\n"
"\n"
"\nYou can tune the CPU affinities for enhanced performance on NUMA machines:\n"
"\n"
"     --cpus=<n>           Specify number of CPUs.  This is NOT the same as\n"
"                           giving the number of analyses to run in parallel.\n"
"     --cpugroup=<n>       Batch threads in groups of this size.\n"
"     --cpuoffset=<n>      Start using CPUs at this group number.\n"
);
}


// Get next pattern in .lst
char* get_pattern(FILE *fh) {
    char *rval;
    char line[LINE_LENGTH];
    rval = fgets(line, LINE_LENGTH - 1, fh);
    if (ferror(fh)) {
        printf("Read error\n");
        rval = NULL;
    }
    return rval;
}


static void process_image(void *qp, void *pp, int cookie)
{
	struct index_args *pargs = pp;
	struct queue_args *qargs = qp;
	float *data_for_measurement;
	size_t data_size;
	UnitCell *cell = qargs->static_args.cell;
	int config_cmfilter = qargs->static_args.config_cmfilter;
	int config_noisefilter = qargs->static_args.config_noisefilter;
	int config_verbose = qargs->static_args.config_verbose;
	IndexingMethod *indm = qargs->static_args.indm;
	struct beam_params *beam = qargs->static_args.beam;
	int r, check;
	struct hdfile *hdfile;
	char *outfile = qargs->static_args.outfile;

	struct image image;
	image.features = NULL;
	image.data = NULL;
	image.flags = NULL;
	image.indexed_cell = NULL;
	image.det = copy_geom(qargs->static_args.det);
	image.copyme = qargs->static_args.copyme;
	image.beam = beam;
	image.id = cookie; // MUST SET ID FOR MOSFLM TO WORK PROPERLY

	if (beam == NULL) {
		ERROR("Warning: no beam parameters file.\n");
		ERROR("I'm going to assume 1 ADU per photon, which is almost");
		ERROR(" certainly wrong.  Peak sigmas will be incorrect.\n");
	}

	char *filename = NULL;
	char *imagename = pargs->filename;
	chomp(imagename);
	filename = malloc(strlen(qargs->prefix) + strlen(imagename) + 1);
	snprintf(filename, LINE_LENGTH - 1, "%s%s", qargs->prefix, imagename);
	image.filename = filename;
	hdfile = hdfile_open(filename);
	if (hdfile == NULL) return;

	r = hdfile_set_first_image(hdfile, "/"); // Need this to read hdf5 files
	if (r) {
		ERROR("Couldn't select first path\n");
		hdfile_close(hdfile);
		return;
	}

	check = hdf5_read(hdfile, &image, 1);
	if (check == 1) {
		hdfile_close(hdfile);
		return;
	}

	if ((image.width != image.det->max_fs + 1)
		|| (image.height != image.det->max_ss + 1)) {
		ERROR("Image size doesn't match geometry size"
			" - rejecting image.\n");
		ERROR("Image size: %i,%i.  Geometry size: %i,%i\n",
		image.width, image.height,
		image.det->max_fs + 1, image.det->max_ss + 1);
		hdfile_close(hdfile);
		free_detector_geometry(image.det);
		return;
	}

	if (image.lambda < 0.0) {
		if (beam != NULL) {
			ERROR("Using nominal photon energy of %.2f eV\n",
			beam->photon_energy);
			image.lambda = ph_en_to_lambda(
			eV_to_J(beam->photon_energy));
		} else {
			ERROR("No wavelength in file, so you need to give "
				"a beam parameters file with -b.\n");
			hdfile_close(hdfile);
			free_detector_geometry(image.det);
			return;
		}
	}
	fill_in_values(image.det, hdfile);

	if (config_cmfilter) {
		filter_cm(&image);
	}

	// Take snapshot of image after CM subtraction but before
	// the aggressive noise filter. 
	data_size = image.width * image.height * sizeof (float);
	data_for_measurement = malloc(data_size);

	if (config_noisefilter) {
		filter_noise(&image, data_for_measurement);
	} else {
		memcpy(data_for_measurement, image.data, data_size);
	}

	switch (qargs->static_args.peaks) {
		case PEAK_HDF5:
		// Get peaks from HDF5
			if (get_peaks(&image, hdfile,
				qargs->static_args.hdf5_peak_path)) {
				ERROR("Failed to get peaks from HDF5 file.\n");
			}
			break;
		case PEAK_ZAEF:
			search_peaks(&image, qargs->static_args.threshold,
							qargs->static_args.min_gradient,
							qargs->static_args.min_snr,
							qargs->static_args.ir_inn,
							qargs->static_args.ir_mid,
							qargs->static_args.ir_out);
			break;
	}

	/* Get rid of noise-filtered version at this point
	 * - it was strictly for the purposes of peak detection. */
	free(image.data);
	image.data = data_for_measurement;

	/* Calculate orientation matrix (by magic) */
	image.div = beam->divergence;
	image.bw = beam->bandwidth;
	image.profile_radius = 0.0001e9;

	/* RUN INDEXING HERE */
	index_pattern(&image, cell, indm, qargs->static_args.cellr,
					config_verbose, qargs->static_args.ipriv,
					qargs->static_args.config_insane, qargs->static_args.tols);

	if (image.indexed_cell != NULL) {
		pargs->indexable = 1;
		image.reflections = find_intersections(&image,
				image.indexed_cell);
		if (image.reflections != NULL) {
			integrate_reflections(&image,
							qargs->static_args.config_closer,
							qargs->static_args.config_bgsub,
							qargs->static_args.min_int_snr,
							qargs->static_args.ir_inn,
							qargs->static_args.ir_mid,
							qargs->static_args.ir_out);
		}
	} else {
		image.reflections = NULL;
	}

	/* Write Lock */
	struct flock fl = {F_WRLCK, SEEK_SET, 0, 0, 0};
	int fd;
	fl.l_pid = getpid();

	char *outfilename = NULL;
	chomp(outfile);
	outfilename = malloc(strlen(outfile) + 1);
	snprintf(outfilename, LINE_LENGTH - 1, "%s", outfile);
	if ((fd = open(outfilename, O_WRONLY)) == -1) {
		perror("Error on opening\n");
		exit(1);
	}
	if (fcntl(fd, F_SETLKW, &fl) == -1) {
		perror("Error on setting lock wait\n");
		exit(1);
	}

	/* LOCKED! Write chunk */
	FILE *fh;
	fh = fopen(outfilename, "a");
	if (fh == NULL) {
		perror("Error inside lock\n");
	}
	write_chunk(fh, &image, hdfile, qargs->static_args.stream_flags);
	fclose(fh);

	/* Unlock stream for other processes */
	fl.l_type = F_UNLCK; /* set to unlock same region */
	if (fcntl(fd, F_SETLK, &fl) == -1) {
		perror("fcntl");
		exit(1);
	}
	close(fd);

	qargs->n_indexable += pargs->indexable;
	qargs->n_processed++;

	/* Only free cell if found */
	cell_free(image.indexed_cell);

	reflist_free(image.reflections);
	free(image.data);
	if ( image.flags != NULL ) free(image.flags);
	image_feature_list_free(image.features);
	hdfile_close(hdfile);
	free_detector_geometry(image.det);
}


#ifdef HAVE_CLOCK_GETTIME

static time_t get_monotonic_seconds()
{
	struct timespec tp;
	clock_gettime(CLOCK_MONOTONIC, &tp);
	return tp.tv_sec;
}

#else

/* Fallback version of the above.  The time according to gettimeofday() is not
 * monotonic, so measuring intervals based on it will screw up if there's a
 * timezone change (e.g. daylight savings) while the program is running. */
static time_t get_monotonic_seconds()
{
	struct timeval tp;
	gettimeofday(&tp, NULL);
	return tp.tv_sec;
}

#endif


static int parse_cell_reduction(const char *scellr, int *err,
                                int *reduction_needs_cell)
{
	*err = 0;
	if ( strcmp(scellr, "none") == 0 ) {
		*reduction_needs_cell = 0;
		return CELLR_NONE;
	} else if ( strcmp(scellr, "reduce") == 0) {
		*reduction_needs_cell = 1;
		return CELLR_REDUCE;
	} else if ( strcmp(scellr, "compare") == 0) {
		*reduction_needs_cell = 1;
		return CELLR_COMPARE;
	} else if ( strcmp(scellr, "compare_ab") == 0) {
		*reduction_needs_cell = 1;
		return CELLR_COMPARE_AB;
	} else {
		*err = 1;
		*reduction_needs_cell = 0;
		return CELLR_NONE;
	}
}


int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
	char *outfile = NULL;
	FILE *fh;
	FILE *ofh;
	char *rval = NULL;
	int config_noindex = 0;
	int config_cmfilter = 0;
	int config_noisefilter = 0;
	int config_verbose = 0;
	int config_satcorr = 1;
	int config_checkprefix = 1;
	int config_closer = 0;
	int config_insane = 0;
	int config_bgsub = 1;
	int config_basename = 0;
	float threshold = 800.0;
	float min_gradient = 100000.0;
	float min_snr = 5.0;
	double min_int_snr = -INFINITY;
	struct detector *det;
	char *geometry = NULL;
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
	int indexer_needs_cell;
	int reduction_needs_cell;
	char *indm_str = NULL;
	UnitCell *cell;
	char *pdb = NULL;
	char *prefix = NULL;
	char *speaks = NULL;
	char *scellr = NULL;
	char *toler = NULL;
	float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */
	int cellr;
	int peaks;
	int nProcesses = 1;
	char *prepare_line;
	char prepare_filename[LINE_LENGTH];
	struct queue_args qargs;
	struct index_args pargs;
	struct beam_params *beam = NULL;
	char *element = NULL;
	double nominal_photon_energy;
	int stream_flags = STREAM_INTEGRATED;
	int cpu_num = 0;
	int cpu_groupsize = 1;
	int cpu_offset = 0;
	char *endptr;
	char *hdf5_peak_path = NULL;
	struct copy_hdf5_field *copyme;
	char *intrad = NULL;
	float ir_inn = 4.0;
	float ir_mid = 5.0;
	float ir_out = 7.0;

	copyme = new_copy_hdf5_field_list();
	if ( copyme == NULL ) {
		ERROR("Couldn't allocate HDF5 field list.\n");
		return 1;
	}

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
		{"output",             1, NULL,               'o'},
		{"no-index",           0, &config_noindex,     1},
		{"indexing",           1, NULL,               'z'},
		{"geometry",           1, NULL,               'g'},
		{"beam",               1, NULL,               'b'},
		{"filter-cm",          0, &config_cmfilter,    1},
		{"filter-noise",       0, &config_noisefilter, 1},
		{"verbose",            0, &config_verbose,     1},
		{"pdb",                1, NULL,               'p'},
		{"prefix",             1, NULL,               'x'},
		{"no-sat-corr",        0, &config_satcorr,     0},
		{"sat-corr",           0, &config_satcorr,     1}, /* Compat */
		{"threshold",          1, NULL,               't'},
		{"no-check-prefix",    0, &config_checkprefix, 0},
		{"no-closer-peak",     0, &config_closer,      0},
		{"closer-peak",        0, &config_closer,      1},
		{"insane",             0, &config_insane,      1},
		{"image",              1, NULL,               'e'},
		{"basename",           0, &config_basename,    1},
		{"bg-sub",             0, &config_bgsub,       1}, /* Compat */
		{"no-bg-sub",          0, &config_bgsub,       0},

		{"peaks",              1, NULL,                2},
		{"cell-reduction",     1, NULL,                3},
		{"min-gradient",       1, NULL,                4},
		{"record",             1, NULL,                5},
		{"cpus",               1, NULL,                6},
		{"cpugroup",           1, NULL,                7},
		{"cpuoffset",          1, NULL,                8},
		{"hdf5-peaks",         1, NULL,                9},
		{"copy-hdf5-field",    1, NULL,               10},
		{"min-snr",            1, NULL,               11},
		{"min-integration-snr",1, NULL,               12},
		{"tolerance",          1, NULL,               13},
		{"int-radius",         1, NULL,               14},
		{0, 0, NULL, 0}
	};

	/* Short options */
	while ((c = getopt_long(argc, argv, "hi:o:z:p:x:j:g:t:b:e:",
	                        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 'z' :
			indm_str = strdup(optarg);
			break;

			case 'p' :
			pdb = strdup(optarg);
			break;

			case 'x' :
			prefix = strdup(optarg);
			break;

			case 'j' :
			nProcesses = atoi(optarg);
			break;

			case 'g' :
			geometry = strdup(optarg);
			break;

			case 't' :
			threshold = strtof(optarg, NULL);
			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 'e' :
			element = strdup(optarg);
			break;

			case 2 :
			speaks = strdup(optarg);
			break;

			case 3 :
			scellr = strdup(optarg);
			break;

			case 4 :
			min_gradient = strtof(optarg, NULL);
			break;

			case 5 :
			stream_flags = parse_stream_flags(optarg);
			if ( stream_flags < 0 ) return 1;
			break;

			case 6 :
			cpu_num = strtol(optarg, &endptr, 10);
			if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
				ERROR("Invalid number of CPUs ('%s')\n",
				      optarg);
				return 1;
			}
			break;

			case 7 :
			cpu_groupsize = strtol(optarg, &endptr, 10);
			if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
				ERROR("Invalid CPU group size ('%s')\n",
				      optarg);
				return 1;
			}
			if ( cpu_groupsize < 1 ) {
				ERROR("CPU group size cannot be"
				      " less than 1.\n");
				return 1;
			}
			break;

			case 8 :
			cpu_offset = strtol(optarg, &endptr, 10);
			if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
				ERROR("Invalid CPU offset ('%s')\n",
				      optarg);
				return 1;
			}
			if ( cpu_offset < 0 ) {
				ERROR("CPU offset must be positive.\n");
				return 1;
			}
			break;

			case 9 :
			hdf5_peak_path = strdup(optarg);
			break;

			case 10 :
			add_copy_hdf5_field(copyme, optarg);
			break;

			case 11 :
			min_snr = strtof(optarg, NULL);
			break;

			case 12 :
			min_int_snr = strtof(optarg, NULL);
			break;

			case 13 :
			toler = strdup(optarg);
			break;

			case 14 :
			intrad = strdup(optarg);
			break;

			case 0 :
			break;

			default :
			return 1;

		}

	}

	if ( (cpu_num > 0) && (cpu_num % cpu_groupsize != 0) ) {
		ERROR("Number of CPUs must be divisible by"
		      " the CPU group size.\n");
		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 ( outfile == NULL ) {
		outfile = strdup("-");
	}
	if ( strcmp(outfile, "-") == 0 ) {
		ofh = stdout;
	} else {
		ofh = fopen(outfile, "w");
	}
	if ( ofh == NULL ) {
		ERROR("Failed to open output file '%s'\n", outfile);
		return 1;
	}

	if ( hdf5_peak_path == NULL ) {
		hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
	}

	if ( speaks == NULL ) {
		speaks = strdup("zaef");
		STATUS("You didn't specify a peak detection method.\n");
		STATUS("I'm using 'zaef' for you.\n");
	}
	if ( strcmp(speaks, "zaef") == 0 ) {
		peaks = PEAK_ZAEF;
	} else if ( strcmp(speaks, "hdf5") == 0 ) {
		peaks = PEAK_HDF5;
	} else {
		ERROR("Unrecognised peak detection method '%s'\n", speaks);
		return 1;
	}
	free(speaks);

	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

	if ( prefix == NULL ) {
		prefix = strdup("");
	} else {
		if ( config_checkprefix ) {
			prefix = check_prefix(prefix);
		}
	}

	if ( nProcesses == 0 ) {
		ERROR("Invalid number of processes.\n");
		return 1;
	}

	if ( (indm_str == NULL) ||
	     ((indm_str != NULL) && (strcmp(indm_str, "none") == 0)) ) {
		STATUS("Not indexing anything.\n");
		indexer_needs_cell = 0;
		reduction_needs_cell = 0;
		indm = NULL;
		cellr = CELLR_NONE;
	} else {
		if ( indm_str == NULL ) {
			STATUS("You didn't specify an indexing method, so I "
			       " won't try to index anything.\n"
			       "If that isn't what you wanted, re-run with"
			       " --indexing=<method>.\n");
			indm = NULL;
			indexer_needs_cell = 0;
		} else {
			indm = build_indexer_list(indm_str,
			                          &indexer_needs_cell);
			if ( indm == NULL ) {
				ERROR("Invalid indexer list '%s'\n", indm_str);
				return 1;
			}
			free(indm_str);
		}

		reduction_needs_cell = 0;
		if ( scellr == NULL ) {
			STATUS("You didn't specify a cell reduction method, so"
			       " I'm going to use 'reduce'.\n");
			cellr = CELLR_REDUCE;
			reduction_needs_cell = 1;
		} else {
			int err;
			cellr = parse_cell_reduction(scellr, &err,
			                             &reduction_needs_cell);
			if ( err ) {
				ERROR("Unrecognised cell reduction '%s'\n",
			              scellr);
				return 1;
			}
			free(scellr);
		}
	}

	/* No indexing -> no reduction */
	if ( indm == NULL ) reduction_needs_cell = 0;

	if ( toler != NULL ) {
		int ttt;
		ttt = sscanf(toler, "%f,%f,%f,%f",
		             &tols[0], &tols[1], &tols[2], &tols[3] );
		if ( ttt != 4 ) {
			ERROR("Invalid parameters for '--tolerance'\n");
			return 1;
		}
	}

	if ( intrad != NULL ) {
		int r;
		r = sscanf(intrad, "%f,%f,%f", &ir_inn, &ir_mid, &ir_out);
		if ( r != 3 ) {
			ERROR("Invalid parameters for '--int-radius'\n");
			return 1;
		}
	} else {
		STATUS("WARNING: You did not specify --int-radius.\n");
		STATUS("WARNING: I will use the default values, which are"
		       " probably not appropriate for your patterns.\n");
	}

	if ( geometry == NULL ) {
		ERROR("You need to specify a geometry file with --geometry\n");
		return 1;
	}

	det = get_detector_geometry(geometry);
	if ( det == NULL ) {
		ERROR("Failed to read detector geometry from '%s'\n", geometry);
		return 1;
	}
	free(geometry);

	if ( reduction_needs_cell || indexer_needs_cell ) {
		cell = load_cell_from_pdb(pdb);
		if ( cell == NULL ) {
			ERROR("Couldn't read unit cell (from %s)\n", pdb);
			return 1;
		}
	} else {
		STATUS("No cell needed for these choices of indexing"
		       " and reduction.\n");
		cell = NULL;
	}
	free(pdb);

	write_stream_header(ofh, argc, argv);

	if ( beam != NULL ) {
		nominal_photon_energy = beam->photon_energy;
	} else {
		STATUS("No beam parameters file was given, so I'm taking the"
		       " nominal photon energy to be 2 keV.\n");
		nominal_photon_energy = 2000.0;
	}

	if ( beam == NULL ) {
		ERROR("Warning: no beam parameters file.\n");
		ERROR("I'm going to assume 1 ADU per photon, which is almost");
		ERROR(" certainly wrong.  Peak sigmas will be incorrect.\n");
	}

	/* Get first filename and use it to set up the indexing */
	prepare_line = malloc(LINE_LENGTH*sizeof(char));
	rval = fgets(prepare_line, LINE_LENGTH-1, fh);
	if ( rval == NULL ) {
		ERROR("Failed to get filename to prepare indexing.\n");
		return 1;
	}
	chomp(prepare_line);
	if ( config_basename ) {
		char *tmp;
		tmp = safe_basename(prepare_line);
		free(prepare_line);
		prepare_line = tmp;
	}
	snprintf(prepare_filename, LINE_LENGTH-1, "%s%s", prefix, prepare_line);
	qargs.use_this_one_instead = prepare_line;

	/* Prepare the indexer */
	if ( indm != NULL ) {
		ipriv = prepare_indexing(indm, cell, prepare_filename, det,
		                         nominal_photon_energy);
		if ( ipriv == NULL ) {
			ERROR("Failed to prepare indexing.\n");
			return 1;
		}
	} else {
		ipriv = NULL;
	}

	gsl_set_error_handler_off();

	qargs.static_args.cell = cell;
	qargs.static_args.config_cmfilter = config_cmfilter;
	qargs.static_args.config_noisefilter = config_noisefilter;
	qargs.static_args.config_verbose = config_verbose;
	qargs.static_args.config_satcorr = config_satcorr;
	qargs.static_args.config_closer = config_closer;
	qargs.static_args.config_insane = config_insane;
	qargs.static_args.config_bgsub = config_bgsub;
	qargs.static_args.cellr = cellr;
	qargs.static_args.tols[0] = tols[0];
	qargs.static_args.tols[1] = tols[1];
	qargs.static_args.tols[2] = tols[2];
	qargs.static_args.tols[3] = tols[3];
	qargs.static_args.threshold = threshold;
	qargs.static_args.min_gradient = min_gradient;
	qargs.static_args.min_snr = min_snr;
	qargs.static_args.min_int_snr = min_int_snr;
	qargs.static_args.det = det;
	qargs.static_args.indm = indm;
	qargs.static_args.ipriv = ipriv;
	qargs.static_args.peaks = peaks;
	qargs.static_args.ofh = ofh;
	qargs.static_args.beam = beam;
	qargs.static_args.element = element;
	qargs.static_args.stream_flags = stream_flags;
	qargs.static_args.hdf5_peak_path = hdf5_peak_path;
	qargs.static_args.copyme = copyme;
	qargs.static_args.ir_inn = ir_inn;
	qargs.static_args.ir_mid = ir_mid;
	qargs.static_args.ir_out = ir_out;

	qargs.fh = fh;
	qargs.prefix = prefix;
	qargs.config_basename = config_basename;
	qargs.n_indexable = 0;
	qargs.n_processed = 0;
	qargs.n_indexable_last_stats = 0;
	qargs.n_processed_last_stats = 0;
	qargs.updateReader = 0; /* first process updates */
	qargs.t_last_stats = get_monotonic_seconds();

	/* Read .lst file */
	register int i;
	rewind(fh); /* make sure to read from start */

	/* Clear output file content */
	char *myOutfilename = NULL;
	chomp(prefix);
	chomp(outfile);
	myOutfilename = malloc(strlen(outfile) + 1);
	snprintf(myOutfilename, LINE_LENGTH - 1, "%s", outfile);
	FILE *tfh;
	tfh = fopen(myOutfilename, "a+");
	if (tfh == NULL) {
		ERROR("No output filename\n");
	}
	fclose(tfh);
	qargs.static_args.outfile = outfile;
	int ready_fd;
	int buff_count;
	fd_set fdset,tmpset;
	char buffR[BUFFER], buffW[BUFFER];
	int fd_pipeIn[nProcesses][2]; /* Process0 In */
	int fd_pipeOut[nProcesses][2]; /* Process0 Out */
	unsigned int opts;

	FD_ZERO(&fdset); /* clear the fd_set */
	/* set pipeIn as non-blocking */
	for ( i=0; i<nProcesses; i++ ) {
		opts = fcntl(fd_pipeIn[i][0], F_GETFL);
		fcntl(fd_pipeIn[i][0], F_SETFL, opts | O_NONBLOCK);
	}

	/**** PIPING ****/
	for ( i=0; i<nProcesses; i++ ) {
		pipe(fd_pipeIn[i]);
		pipe(fd_pipeOut[i]);
	}

	int max_fd = 0;
	for ( i=0; i<nProcesses; i++ ) {
		FD_SET(fd_pipeIn[i][0], &fdset);
		if (fd_pipeIn[i][0] > max_fd) { /* find max_fd */
			max_fd = fd_pipeIn[i][0];
		}
	}
	max_fd = max_fd+1;
	/* copy file set to tmpset */
	memcpy((void *) &tmpset,(void *) &fdset, sizeof(fd_set));

	/**** FORKING ****/	
	int power = 10; /* 2^power must be larger than nProcesses */
	int pid[power];
	double num = 0;
	int batchNum = 0;
	/* Fork 2^power times */
	for ( i=0; i<power; i++ ) {
		pid[i] = fork();
	}
	/* Assign id */
	for ( i=0; i<power; i++ ) {
		if (pid[i] == 0) { /* keep parents and kill off children */
			num += pow(2, i);
		}
	}
	/* Kill if batchNum too high */
	if (num >= nProcesses + 1) {
		exit(0); /* kill */
	}
	batchNum = (int) num;

	/**** PLUMBING ****/
	if (batchNum == qargs.updateReader) {
		for ( i=0; i<nProcesses; i++ ) {
			close(fd_pipeIn[i][1]); /* close all write pipes In */
			close(fd_pipeOut[i][0]); /* close all read pipes Out */
		}
	} else {
		for ( i=0; i<nProcesses; i++ ) {
			if (i == batchNum - 1) { /* batchNum = 1,2,3 ... */
				close(fd_pipeIn[i][0]); /* close read pipe In */
				close(fd_pipeOut[i][1]); /* close write pipe Out */
			} else {
				close(fd_pipeIn[i][0]); // close remaining pipes In
				close(fd_pipeIn[i][1]);
				close(fd_pipeOut[i][0]); // close remaining pipes Out
				close(fd_pipeOut[i][1]);
			}
		}
	}
	/**** INDEXING ****/
	double tStart, tEnd;
	tStart = get_monotonic_seconds();
	int allDone = 0;
	if (batchNum == qargs.updateReader){
		char *nextImage = NULL;
		for ( i=0; i<nProcesses; i++ ) { /* Send out image to all processes*/
			nextImage = get_pattern(fh);
			buff_count = sprintf(buffW, "%s",nextImage);
			write (fd_pipeOut[i][1], buffW, buff_count);
		}
		int nFinished = 0;
		while (!allDone) {
			/* select from file set for reading */
			if ((ready_fd = select(max_fd,&fdset,NULL,NULL,NULL)) < 0)
				perror("select");
			if (ready_fd > 0) {
				for ( i=0; i<nProcesses; i++ ) {
					/* is in file set that raised flag? */
					if (FD_ISSET(fd_pipeIn[i][0],&fdset)) { 
						/* read from pipe and return number of bytes read */
						if ((buff_count=read(fd_pipeIn[i][0],&buffR,BUFFER))<0) {
							perror("read");
						} else {
							qargs.n_indexable += atoi(buffR); 
							qargs.n_processed++;
							/* write to pipe */
							if ((nextImage = get_pattern(fh)) == NULL){
								nFinished++; /* no more images */
								if ( nFinished == nProcesses )
									allDone = 1; /* EXIT */
							} else {
								/* send out image */
								buff_count = sprintf(buffW, "%s",nextImage);
								if (write (fd_pipeOut[i][1], buffW, buff_count)<0)
									perror("write pipe");
							}
						}
					}
				}
			}
			/* file set is modified, so copy original from tmpset */
			memcpy((void *) &fdset,(void *) &tmpset, sizeof(fd_set));

			/* Update to screen */
			double tNow = get_monotonic_seconds();
			if ( tNow >= qargs.t_last_stats+STATS_EVERY_N_SECONDS ) {
					STATUS("%i out of %i indexed so far,"
				    " %i out of %i since the last message.\n\n",
				    qargs.n_indexable, qargs.n_processed,
				    qargs.n_indexable - qargs.n_indexable_last_stats,
				    qargs.n_processed - qargs.n_processed_last_stats);

					qargs.n_indexable_last_stats = qargs.n_indexable;
					qargs.n_processed_last_stats = qargs.n_processed;
					qargs.t_last_stats = tNow;
			}
		}
		/* close my pipes */
		for ( i=0; i<nProcesses; i++ ) {
			close(fd_pipeIn[i][0]); 
			close(fd_pipeOut[i][1]);
		}
		tEnd = get_monotonic_seconds();
		printf("Compute Time: %.2fs\n", tEnd - tStart);
	} else {
		while(!allDone){
			/* read from pipe and return number of bytes read */
			if ((buff_count=read(fd_pipeOut[batchNum-1][0],&buffR,BUFFER))<0) {
				perror("read1");
			} else if (buff_count > 0) {
				/* process image */
				pargs.filename = buffR;
				pargs.indexable = 0;
				process_image(&qargs, &pargs, batchNum);
				/* request another image */
				buff_count = sprintf(buffW, "%d\n", pargs.indexable);
				if(write (fd_pipeIn[batchNum-1][1], buffW, buff_count)<0)
					perror("write P0");
			} else if (buff_count == 0) {
				allDone = 1; /* EXIT */
			}
		}
		/* close my pipes */
		close(fd_pipeIn[batchNum-1][1]);
		close(fd_pipeOut[batchNum-1][0]);
	}

	cleanup_indexing(ipriv);

	free(indm);
	free(ipriv);
	free(prefix);
	free_detector_geometry(det);
	free(beam);
	free(element);
	free(hdf5_peak_path);
	free_copy_hdf5_field_list(copyme);
	cell_free(cell);
	if ( fh != stdin ) fclose(fh);
	if ( ofh != stdout ) fclose(ofh);

	if (batchNum == qargs.updateReader) {
		STATUS("There were %i images, of which %i could be indexed.\n",
				qargs.n_processed, qargs.n_indexable);
	}
	return 0;
}