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Diffstat (limited to 'src/process_image.c')
| -rw-r--r-- | src/process_image.c | 231 |
1 files changed, 231 insertions, 0 deletions
diff --git a/src/process_image.c b/src/process_image.c new file mode 100644 index 00000000..010054c8 --- /dev/null +++ b/src/process_image.c @@ -0,0 +1,231 @@ +/* + * 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 "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" + + +void process_image(const struct index_args *iargs, struct pattern_args *pargs, + Stream *st, int cookie) +{ + float *data_for_measurement; + size_t data_size; + int check; + struct hdfile *hdfile; + struct image image; + int i; + char filename[1024]; + + /* Prefix to jump out of temporary folder */ + if ( pargs->filename[0] != '/' ) { + snprintf(filename, 1023, "../../%s", pargs->filename); + } else { + snprintf(filename, 1023, "%s", pargs->filename); + } + + image.features = NULL; + image.data = NULL; + image.flags = NULL; + image.copyme = iargs->copyme; + image.id = cookie; + image.filename = pargs->filename; /* Relative to top level */ + image.beam = iargs->beam; + image.det = iargs->det; + image.crystals = NULL; + image.n_crystals = 0; + + hdfile = hdfile_open(filename); /* Relative to temporary folder */ + 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; + } + + 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); + return; + } + + fill_in_values(image.det, hdfile); + fill_in_beam_parameters(image.beam, hdfile); + + image.lambda = ph_en_to_lambda(eV_to_J(image.beam->photon_energy)); + + if ( (image.beam->photon_energy < 0.0) || (image.lambda > 1000) ) { + /* Error message covers a silly value in the beam file or in + * the HDF5 file. */ + ERROR("Nonsensical wavelength (%e m or %e eV) value for %s.\n", + image.lambda, image.beam->photon_energy, image.filename); + hdfile_close(hdfile); + return; + } + + if ( iargs->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 ( iargs->noisefilter ) { + filter_noise(&image, data_for_measurement); + } else { + memcpy(data_for_measurement, image.data, data_size); + } + + 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_int_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; + + /* Index the pattern */ + index_pattern(&image, iargs->indm, iargs->ipriv); + + 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++ ) { + + RefList *reflections; + + /* Set default crystal parameter(s) */ + crystal_set_profile_radius(image.crystals[i], + image.beam->profile_radius); + + if ( iargs->integrate_found ) { + reflections = select_intersections(&image, + image.crystals[i]); + } else { + reflections = find_intersections(&image, + image.crystals[i]); + } + + crystal_set_reflections(image.crystals[i], reflections); + + } + + /* Integrate all the crystals at once - need all the crystals so that + * overlaps can be detected. */ + integrate_reflections(&image, iargs->closer, + iargs->bgsub, + iargs->min_int_snr, + iargs->ir_inn, + iargs->ir_mid, + iargs->ir_out, + iargs->integrate_saturated, + iargs->res_cutoff); + + write_chunk(st, &image, hdfile, + iargs->stream_peaks, iargs->stream_refls); + + for ( i=0; i<image.n_crystals; i++ ) { + crystal_free(image.crystals[i]); + } + + free(image.data); + if ( image.flags != NULL ) free(image.flags); + image_feature_list_free(image.features); + hdfile_close(hdfile); +} |