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/*
* process_image.c
*
* The processing pipeline for one image
*
* Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2013 Thomas White <taw@physics.org>
*
* 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 <stdlib.h>
#include <hdf5.h>
#include <gsl/gsl_errno.h>
#include <unistd.h>
#include "utils.h"
#include "hdf5-file.h"
#include "index.h"
#include "peaks.h"
#include "detector.h"
#include "filters.h"
#include "thread-pool.h"
#include "beam-parameters.h"
#include "geometry.h"
#include "stream.h"
#include "reflist-utils.h"
#include "process_image.h"
#include "integration.h"
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
Stream *st, int cookie, const char *tmpdir)
{
float *data_for_measurement;
size_t data_size;
int check;
struct hdfile *hdfile;
struct image image;
int i;
int r;
char *rn;
image.features = NULL;
image.data = NULL;
image.flags = NULL;
image.copyme = iargs->copyme;
image.id = cookie;
image.filename = pargs->filename;
image.beam = iargs->beam;
image.det = iargs->det;
image.crystals = NULL;
image.n_crystals = 0;
hdfile = hdfile_open(image.filename);
if ( hdfile == NULL ) return;
if ( iargs->element != NULL ) {
int r;
r = hdfile_set_image(hdfile, iargs->element);
if ( r ) {
ERROR("Couldn't select path '%s'\n", iargs->element);
hdfile_close(hdfile);
return;
}
} else {
int r;
r = hdfile_set_first_image(hdfile, "/");
if ( r ) {
ERROR("Couldn't select first path\n");
hdfile_close(hdfile);
return;
}
}
check = hdf5_read(hdfile, &image, 1);
if ( check ) {
hdfile_close(hdfile);
return;
}
/* Take snapshot of image after CM subtraction but before applying
* horrible noise filters to it */
data_size = image.width * image.height * sizeof(float);
data_for_measurement = malloc(data_size);
memcpy(data_for_measurement, image.data, data_size);
if ( iargs->median_filter > 0 ) {
filter_median(&image, iargs->median_filter);
}
if ( iargs->noisefilter ) {
filter_noise(&image);
}
switch ( iargs->peaks ) {
case PEAK_HDF5:
/* Get peaks from HDF5 */
if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) {
ERROR("Failed to get peaks from HDF5 file.\n");
}
if ( !iargs->no_revalidate ) {
validate_peaks(&image, iargs->min_snr,
iargs->ir_inn, iargs->ir_mid,
iargs->ir_out, iargs->use_saturated);
}
break;
case PEAK_ZAEF:
search_peaks(&image, iargs->threshold,
iargs->min_gradient, iargs->min_snr,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
iargs->use_saturated);
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;
rn = get_current_dir_name();
r = chdir(tmpdir);
if ( r ) {
ERROR("Failed to chdir to temporary folder: %s\n",
strerror(errno));
return;
}
/* Index the pattern */
index_pattern(&image, iargs->indm, iargs->ipriv);
r = chdir(rn);
if ( r ) {
ERROR("Failed to chdir: %s\n", strerror(errno));
return;
}
pargs->n_crystals = image.n_crystals;
/* Default beam parameters */
image.div = image.beam->divergence;
image.bw = image.beam->bandwidth;
/* Integrate each crystal's diffraction spots */
for ( i=0; i<image.n_crystals; i++ ) {
/* Set default crystal parameter(s) */
crystal_set_profile_radius(image.crystals[i],
image.beam->profile_radius);
crystal_set_mosaicity(image.crystals[i], 0.0); /* radians */
crystal_set_image(image.crystals[i], &image);
}
/* Integrate all the crystals at once - need all the crystals so that
* overlaps can be detected. */
integrate_all(&image, iargs->int_meth,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out);
write_chunk(st, &image, hdfile,
iargs->stream_peaks, iargs->stream_refls);
for ( i=0; i<image.n_crystals; i++ ) {
cell_free(crystal_get_cell(image.crystals[i]));
reflist_free(crystal_get_reflections(image.crystals[i]));
crystal_free(image.crystals[i]);
}
free(image.crystals);
for ( i=0; i<image.det->n_panels; i++ ) {
free(image.dp[i]);
free(image.bad[i]);
}
free(image.dp);
free(image.bad);
free(image.data);
if ( image.flags != NULL ) free(image.flags);
image_feature_list_free(image.features);
hdfile_close(hdfile);
}
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