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/*
* process_image.c
*
* The processing pipeline for one image
*
* Copyright © 2012-2019 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2019 Thomas White <taw@physics.org>
* 2014-2017 Valerio Mariani <valerio.mariani@desy.de>
* 2017 Stijn de Graaf
*
* 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 <gsl/gsl_statistics_double.h>
#include <gsl/gsl_sort.h>
#include <unistd.h>
#include <sys/stat.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 "geometry.h"
#include "stream.h"
#include "reflist-utils.h"
#include "process_image.h"
#include "integration.h"
#include "predict-refine.h"
#include "im-sandbox.h"
#include "time-accounts.h"
#include "im-zmq.h"
static float **backup_image_data(float **dp, struct detector *det)
{
float **bu;
int i;
bu = malloc(det->n_panels * sizeof(float *));
if ( bu == NULL ) return NULL;
for ( i=0; i<det->n_panels; i++ ) {
size_t data_size;
data_size = det->panels[i].w * det->panels[i].h * sizeof(float);
bu[i] = malloc(data_size);
if ( bu[i] == NULL ) {
free(bu);
ERROR("Failed to allocate pre-filter backup.\n");
return NULL;
}
memcpy(bu[i], dp[i], data_size);
}
return bu;
}
static void restore_image_data(float **dp, struct detector *det, float **bu)
{
int i;
for ( i=0; i<det->n_panels; i++ ) {
size_t data_size;
data_size = det->panels[i].w * det->panels[i].h * sizeof(float);
memcpy(dp[i], bu[i], data_size);
free(bu[i]);
}
free(bu);
}
static int file_wait_open_read(struct sb_shm *sb_shared, struct image *image,
TimeAccounts *taccs, char *last_task,
signed int wait_for_file, int cookie,
struct imagefile **pimfile)
{
signed int file_wait_time = wait_for_file;
int wait_message_done = 0;
int read_retry_done = 0;
int r;
struct imagefile *imfile;
time_accounts_set(taccs, TACC_WAITFILE);
set_last_task(last_task, "wait for file");
do {
struct stat statbuf;
sb_shared->pings[cookie]++;
r = stat(image->filename, &statbuf);
if ( r ) {
if ( (wait_for_file != 0) && (file_wait_time != 0) ) {
if ( !wait_message_done ) {
STATUS("Waiting for '%s'\n",
image->filename);
wait_message_done = 1;
}
sleep(1);
if ( wait_for_file != -1 ) {
file_wait_time--;
}
continue;
}
ERROR("File %s not found\n", image->filename);
return 1;
}
} while ( r );
time_accounts_set(taccs, TACC_HDF5OPEN);
set_last_task(last_task, "open file");
sb_shared->pings[cookie]++;
do {
imfile = imagefile_open(image->filename);
if ( imfile == NULL ) {
if ( wait_for_file && !read_retry_done ) {
read_retry_done = 1;
r = 1;
STATUS("File '%s' exists but could not be opened."
" Trying again after 10 seconds.\n",
image->filename);
sleep(10);
continue;
}
ERROR("Couldn't open file: %s\n", image->filename);
return 1;
}
time_accounts_set(taccs, TACC_HDF5READ);
set_last_task(last_task, "read file");
sb_shared->pings[cookie]++;
r = imagefile_read(imfile, image, image->event);
if ( r ) {
if ( wait_for_file && !read_retry_done ) {
read_retry_done = 1;
imagefile_close(imfile);
STATUS("File '%s' exists but could not be read."
" Trying again after 10 seconds.\n",
image->filename);
sleep(10);
continue;
}
ERROR("Couldn't open file: %s\n", image->filename);
return 1;
}
} while ( r );
*pimfile = imfile;
return 0;
}
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
Stream *st, int cookie, const char *tmpdir,
int serial, struct sb_shm *sb_shared, TimeAccounts *taccs,
char *last_task)
{
struct imagefile *imfile = NULL;
struct image image;
int i;
int r;
int ret;
char *rn;
float **prefilter;
int any_crystals;
image.features = NULL;
image.copyme = iargs->copyme;
image.id = cookie;
image.beam = iargs->beam;
image.det = copy_geom(iargs->det);
image.crystals = NULL;
image.n_crystals = 0;
image.serial = serial;
image.indexed_by = INDEXING_NONE;
image.filename = pargs->filename_p_e->filename;
image.event = pargs->filename_p_e->ev;
if ( pargs->msgpack_obj != NULL ) {
if ( unpack_msgpack_data(pargs->msgpack_obj, &image,
iargs->no_image_data) ) return;
} else {
if ( file_wait_open_read(sb_shared, &image, taccs, last_task,
iargs->wait_for_file, cookie,
&imfile) ) return;
}
/* Take snapshot of image before applying horrible noise filters */
time_accounts_set(taccs, TACC_FILTER);
set_last_task(last_task, "image filter");
sb_shared->pings[cookie]++;
prefilter = backup_image_data(image.dp, image.det);
if ( iargs->median_filter > 0 ) {
filter_median(&image, iargs->median_filter);
}
if ( iargs->noisefilter ) {
filter_noise(&image);
}
time_accounts_set(taccs, TACC_RESRANGE);
set_last_task(last_task, "resolution range");
sb_shared->pings[cookie]++;
mark_resolution_range_as_bad(&image, iargs->highres, +INFINITY);
time_accounts_set(taccs, TACC_PEAKSEARCH);
sb_shared->pings[cookie]++;
switch ( iargs->peaks ) {
struct hdfile *hdfile;
case PEAK_HDF5:
set_last_task(last_task, "peaksearch:hdf5");
hdfile = imagefile_get_hdfile(imfile);
if ( (hdfile == NULL)
|| (get_peaks_2(&image, hdfile, iargs->hdf5_peak_path,
iargs->half_pixel_shift)) )
{
ERROR("Failed to get peaks from HDF5 file.\n");
}
if ( !iargs->no_revalidate ) {
validate_peaks(&image, iargs->min_snr,
iargs->pk_inn, iargs->pk_mid,
iargs->pk_out, iargs->use_saturated,
iargs->check_hdf5_snr);
}
break;
case PEAK_CXI:
set_last_task(last_task, "peaksearch:cxi");
hdfile = imagefile_get_hdfile(imfile);
if ( (hdfile == NULL)
|| (get_peaks_cxi_2(&image, hdfile, iargs->hdf5_peak_path,
pargs->filename_p_e,
iargs->half_pixel_shift)) )
{
ERROR("Failed to get peaks from CXI file.\n");
}
if ( !iargs->no_revalidate ) {
validate_peaks(&image, iargs->min_snr,
iargs->pk_inn, iargs->pk_mid,
iargs->pk_out, iargs->use_saturated,
iargs->check_hdf5_snr);
}
break;
case PEAK_ZAEF:
set_last_task(last_task, "peaksearch:zaef");
search_peaks(&image, iargs->threshold,
iargs->min_sq_gradient, iargs->min_snr,
iargs->pk_inn, iargs->pk_mid, iargs->pk_out,
iargs->use_saturated);
break;
case PEAK_PEAKFINDER8:
set_last_task(last_task, "peaksearch:pf8");
if ( search_peaks_peakfinder8(&image, 2048,
iargs->threshold,
iargs->min_snr,
iargs->min_pix_count,
iargs->max_pix_count,
iargs->local_bg_radius,
iargs->min_res,
iargs->max_res,
iargs->use_saturated) ) {
if ( image.event != NULL ) {
ERROR("Failed to find peaks in image %s"
"(event %s).\n", image.filename,
get_event_string(image.event));
} else {
ERROR("Failed to find peaks in image %s.",
image.filename);
}
}
break;
case PEAK_PEAKFINDER9:
set_last_task(last_task, "peaksearch:pf9");
if ( search_peaks_peakfinder9(&image,
iargs->min_snr_biggest_pix,
iargs->min_snr_peak_pix,
iargs->min_snr,
iargs->min_sig,
iargs->min_peak_over_neighbour,
iargs->local_bg_radius) )
{
if ( image.event != NULL ) {
ERROR("Failed to find peaks in image %s"
"(event %s).\n", image.filename,
get_event_string(image.event));
} else {
ERROR("Failed to find peaks in image %s.",
image.filename);
}
}
break;
case PEAK_MSGPACK:
get_peaks_msgpack(pargs->msgpack_obj, &image,
iargs->half_pixel_shift);
break;
}
image.peak_resolution = estimate_peak_resolution(image.features,
image.lambda);
restore_image_data(image.dp, image.det, prefilter);
rn = getcwd(NULL, 0);
r = chdir(tmpdir);
if ( r ) {
ERROR("Failed to chdir to temporary folder: %s\n",
strerror(errno));
imagefile_close(imfile);
return;
}
/* Set beam parameters */
if ( iargs->fix_divergence >= 0.0 ) {
image.div = iargs->fix_divergence;
} else {
image.div = 0.0;
}
if ( iargs->fix_bandwidth >= 0.0 ) {
image.bw = iargs->fix_bandwidth;
} else {
image.bw = 0.00000001;
}
/* Set beam spectrum for pink beam data */
if ( iargs->spectrum != NULL ) {
image.spectrum = iargs->spectrum;
}
if ( image_feature_count(image.features) < iargs->min_peaks ) {
r = chdir(rn);
if ( r ) {
ERROR("Failed to chdir: %s\n", strerror(errno));
imagefile_close(imfile);
return;
}
free(rn);
image.hit = 0;
if ( iargs->stream_nonhits ) {
goto streamwrite;
} else {
goto out;
}
}
image.hit = 1;
/* Index the pattern */
time_accounts_set(taccs, TACC_INDEXING);
set_last_task(last_task, "indexing");
index_pattern_3(&image, iargs->ipriv, &sb_shared->pings[cookie],
last_task);
r = chdir(rn);
if ( r ) {
ERROR("Failed to chdir: %s\n", strerror(errno));
imagefile_close(imfile);
return;
}
free(rn);
/* Set beam/crystal parameters */
time_accounts_set(taccs, TACC_PREDPARAMS);
set_last_task(last_task, "prediction params");
if ( iargs->fix_profile_r >= 0.0 ) {
for ( i=0; i<image.n_crystals; i++ ) {
crystal_set_profile_radius(image.crystals[i],
iargs->fix_profile_r);
crystal_set_mosaicity(image.crystals[i], 0.0);
}
} else {
for ( i=0; i<image.n_crystals; i++ ) {
crystal_set_profile_radius(image.crystals[i], 0.02e9);
crystal_set_mosaicity(image.crystals[i], 0.0);
}
}
if ( iargs->fix_profile_r < 0.0 ) {
for ( i=0; i<image.n_crystals; i++ ) {
if ( refine_radius(image.crystals[i], &image) ) {
ERROR("WARNING: Radius determination failed\n");
}
}
}
/* Integrate! */
time_accounts_set(taccs, TACC_INTEGRATION);
set_last_task(last_task, "integration");
sb_shared->pings[cookie]++;
integrate_all_5(&image, iargs->int_meth, PMODEL_XSPHERE,
iargs->push_res,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
iargs->int_diag, iargs->int_diag_h,
iargs->int_diag_k, iargs->int_diag_l,
&sb_shared->term_lock, iargs->overpredict);
streamwrite:
time_accounts_set(taccs, TACC_WRITESTREAM);
set_last_task(last_task, "stream write");
sb_shared->pings[cookie]++;
ret = write_chunk(st, &image, imfile,
iargs->stream_peaks, iargs->stream_refls,
pargs->filename_p_e->ev);
if ( ret != 0 ) {
ERROR("Error writing stream file.\n");
}
int n = 0;
for ( i=0; i<image.n_crystals; i++ ) {
n += crystal_get_num_implausible_reflections(image.crystals[i]);
}
if ( n > 0 ) {
STATUS("WARNING: %i implausibly negative reflection%s in %s "
"%s\n", n, n>1?"s":"", image.filename,
get_event_string(image.event));
}
out:
/* Count crystals which are still good */
time_accounts_set(taccs, TACC_TOTALS);
set_last_task(last_task, "process_image finalisation");
sb_shared->pings[cookie]++;
pthread_mutex_lock(&sb_shared->totals_lock);
any_crystals = 0;
for ( i=0; i<image.n_crystals; i++ ) {
if ( crystal_get_user_flag(image.crystals[i]) == 0 ) {
sb_shared->n_crystals++;
any_crystals = 1;
}
}
sb_shared->n_processed++;
sb_shared->n_hits += image.hit;
sb_shared->n_hadcrystals += any_crystals;
pthread_mutex_unlock(&sb_shared->totals_lock);
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.sat[i]);
}
free(image.dp);
free(image.bad);
free(image.sat);
image_feature_list_free(image.features);
free_detector_geometry(image.det);
if ( imfile != NULL ) imagefile_close(imfile);
}
|