diff options
Diffstat (limited to 'src/process_image.c')
| -rw-r--r-- | src/process_image.c | 77 |
1 files changed, 63 insertions, 14 deletions
diff --git a/src/process_image.c b/src/process_image.c index bcaee543..498b3398 100644 --- a/src/process_image.c +++ b/src/process_image.c @@ -8,7 +8,7 @@ * * Authors: * 2010-2017 Thomas White <taw@physics.org> - * 2014 Valerio Mariani + * 2014-2017 Valerio Mariani <valerio.mariani@desy.de> * * This file is part of CrystFEL. * @@ -102,7 +102,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, int serial, struct sb_shm *sb_shared, TimeAccounts *taccs) { int check; - struct hdfile *hdfile; + struct imagefile *imfile; struct image image; int i; int r; @@ -125,15 +125,15 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, time_accounts_set(taccs, TACC_HDF5OPEN); sb_shared->pings[cookie]++; - hdfile = hdfile_open(image.filename); - if ( hdfile == NULL ) { + imfile = imagefile_open(image.filename); + if ( imfile == NULL ) { ERROR("Couldn't open file: %s\n", image.filename); return; } time_accounts_set(taccs, TACC_HDF5READ); sb_shared->pings[cookie]++; - check = hdf5_read2(hdfile, &image, image.event, 0); + check = imagefile_read(imfile, &image, image.event); if ( check ) { return; } @@ -159,8 +159,14 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, sb_shared->pings[cookie]++; switch ( iargs->peaks ) { + struct hdfile *hdfile; + case PEAK_HDF5: - if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) { + 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 ) { @@ -172,8 +178,12 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, break; case PEAK_CXI: - if ( get_peaks_cxi(&image, hdfile, iargs->hdf5_peak_path, - pargs->filename_p_e) ) { + 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 ) { @@ -191,6 +201,28 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, iargs->use_saturated); break; + case PEAK_PEAKFINDER8: + 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; + } restore_image_data(image.dp, image.det, prefilter); @@ -201,7 +233,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, if ( r ) { ERROR("Failed to chdir to temporary folder: %s\n", strerror(errno)); - hdfile_close(hdfile); + imagefile_close(imfile); return; } @@ -217,15 +249,30 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, image.bw = 0.00000001; } + 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); + + if ( iargs->stream_nonhits ) { + goto streamwrite; + } else { + goto out; + } + } + /* Index the pattern */ time_accounts_set(taccs, TACC_INDEXING); - index_pattern_2(&image, iargs->indm, iargs->ipriv, - &sb_shared->pings[cookie]); + index_pattern_2(&image, iargs->ipriv, &sb_shared->pings[cookie]); r = chdir(rn); if ( r ) { ERROR("Failed to chdir: %s\n", strerror(errno)); - hdfile_close(hdfile); + imagefile_close(imfile); return; } free(rn); @@ -261,9 +308,10 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, iargs->int_diag_k, iargs->int_diag_l, &sb_shared->term_lock); +streamwrite: time_accounts_set(taccs, TACC_WRITESTREAM); sb_shared->pings[cookie]++; - ret = write_chunk(st, &image, hdfile, + ret = write_chunk(st, &image, imfile, iargs->stream_peaks, iargs->stream_refls, pargs->filename_p_e->ev); if ( ret != 0 ) { @@ -280,6 +328,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, get_event_string(image.event)); } +out: /* Count crystals which are still good */ time_accounts_set(taccs, TACC_TOTALS); sb_shared->pings[cookie]++; @@ -313,5 +362,5 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, image_feature_list_free(image.features); free_detector_geometry(image.det); - hdfile_close(hdfile); + imagefile_close(imfile); } |