diff options
| -rw-r--r-- | doc/man/indexamajig.1 | 33 | ||||
| -rw-r--r-- | libcrystfel/Makefile.am | 6 | ||||
| -rw-r--r-- | libcrystfel/src/peakfinder8.c | 1233 | ||||
| -rw-r--r-- | libcrystfel/src/peakfinder8.h | 50 | ||||
| -rw-r--r-- | libcrystfel/src/peaks.c | 28 | ||||
| -rw-r--r-- | libcrystfel/src/peaks.h | 14 | ||||
| -rw-r--r-- | src/indexamajig.c | 87 | ||||
| -rw-r--r-- | src/process_image.c | 24 | ||||
| -rw-r--r-- | src/process_image.h | 11 |
9 files changed, 1454 insertions, 32 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index d7f59f9d..8619fd92 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -47,6 +47,8 @@ You can control the peak detection on the command line. Firstly, you can choose If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search after Zaefferer (2000). You can control the overall threshold and minimum squared gradient for finding a peak using \fB--threshold\fR and \fB--min-gradient\fR. The threshold has arbitrary units matching the pixel values in the data, and the minimum gradient has the equivalent squared units. Peaks will be rejected if the 'foot point' is further away from the 'summit' of the peak by more than the inner integration radius (see below). They will also be rejected if the peak is closer than twice the inner integration radius from another peak. +If you instead use \fB--peaks=peakfinder8\fR, indexamajig will user the "peakfinder8" peak finding algorithm describerd in Barty et al. (2014). Pixels above a radius-dependent intensity threshold are considered as candidate peaks (although the user sets an absolute minimum threshold for candidate peaks). Peaks are then only accepted if their signal to noise level over the local background is sufficiently high. Peaks can include multiple pixels and the user can reject a peak if it includes too many or too few. The distance of a peak from the center of the detector can also be used as a filtering criterion. Please notice that the peakfinder8 will not report more than 2048 peaks for each panel: any additional peak is ignored. + You can suppress peak detection altogether for a panel in the geometry file by specifying the "no_index" value for the panel as non-zero. @@ -270,7 +272,7 @@ This option is here for historical purposes only, to disable a correction which .PD 0 .IP \fB--threshold=\fR\fIthres\fR .PD -Set the overall threshold for peak detection using \fB--peaks=zaef\fR to \fIthres\fR, which has the same units as the detector data. The default is \fB--threshold=800\fR. +Set the overall threshold for peak detection using \fB--peaks=zaef\fR or \fB--peaks=peakfinder8\fR to \fIthres\fR, which has the same units as the detector data. The default is \fB--threshold=800\fR. .PD 0 .IP \fB--min-gradient=\fR\fIgrad\fR @@ -280,12 +282,37 @@ Set the square of the gradient threshold for peak detection using \fB--peaks=zae .PD 0 .IP \fB--min-snr=\fR\fIsnr\fR .PD -Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR. The default is \fB--min-snr=5\fR. +Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR or \fB--peaks=peakfinder8\fR. The default is \fB--min-snr=5\fR. + +.PD 0 +.IP \fB--min-pix-count=\fR\fIcnt\fR +.PD +Accepts peaks only if they include more than \fR\fIcnt\fR pixels, when using \fB--peaks=peakfinder8\fR. The default is \fB--min-pix-count=2\fR. + +.PD 0 +.IP \fB--max-pix-count=\fR\fIcnt\fR +.PD +Accepts peaks only if they include less than \fR\fIcnt\fR pixels, when using \fB--peaks=peakfinder8\fR. The default is \fB--max-pix-count=200\fR. + +.PD 0 +.IP \fB--local-bg-radius=\fR\fIr\fR +.PD +Radius (in pixels) used for the estimation of the local background when using \fB--peaks=peakfinder8\fR. The default is \fB--local-bg-radius=3\fR. + +.PD 0 +.IP \fB--min-res=\fR\fIpx\fR +.PD +Only accept peaks if they lay at more than \fR\fIpx\fR pixels from the center of the detector when using \fB--peaks=peakfinder8\fR. The default is \fB--min-res=0\fR. + +.PD 0 +.IP \fB--max-res=\fR\fIpx\fR +.PD +Only accept peaks if they lay at less than \fR\fIpx\fR pixels from the center of the detector when using \fB--peaks=peakfinder8\fR. The default is \fB--max-res=1200\fR. .PD 0 .IP \fB--copy-hdf5-field=\fR\fIpath\fR .PD -Copy the information from \fIpath\fR in the HDF5 file into the output stream. The information must be a single scalar value. This option is sometimes useful to allow data to be separated after indexing according to some condition such the presence of an optical pump pulse. You can give this option as many times as you need to copy multiple bits of information. +Copy the information from \fR\fIpath\fR in the HDF5 file into the output stream. The information must be a single scalar value. This option is sometimes useful to allow data to be separated after indexing according to some condition such the presence of an optical pump pulse. You can give this option as many times as you need to copy multiple bits of information. .PD 0 .IP "\fB-j\fR \fIn\fR" diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am index d7142f6a..8af82552 100644 --- a/libcrystfel/Makefile.am +++ b/libcrystfel/Makefile.am @@ -10,7 +10,8 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \ src/render.c src/index.c src/dirax.c src/mosflm.c \ src/cell-utils.c src/integer_matrix.c src/crystal.c \ src/xds.c src/integration.c src/predict-refine.c \ - src/histogram.c src/events.c src/felix.c + src/histogram.c src/events.c src/felix.c \ + src/peakfinder8.c if HAVE_FFTW libcrystfel_la_SOURCES += src/asdf.c @@ -30,7 +31,8 @@ libcrystfel_la_include_HEADERS = ${top_srcdir}/version.h \ src/integer_matrix.h src/crystal.h \ src/xds.h src/predict-refine.h \ src/integration.h src/histogram.h \ - src/events.h src/asdf.h src/felix.h + src/events.h src/asdf.h src/felix.h \ + src/peakfinder8.h AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -Wall AM_CPPFLAGS += -I$(top_srcdir)/lib @LIBCRYSTFEL_CFLAGS@ diff --git a/libcrystfel/src/peakfinder8.c b/libcrystfel/src/peakfinder8.c new file mode 100644 index 00000000..f6e70223 --- /dev/null +++ b/libcrystfel/src/peakfinder8.c @@ -0,0 +1,1233 @@ +/* + * peakfinder8.c + * + * The peakfinder8 algorithm + * + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2017 Valerio Mariani <valerio.mariani@desy.de> + * 2017 Anton Barty <anton.barty@desy.de> + * 2017 Oleksandr Yefanov <oleksandr.yefanov@desy.de> + * + * 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 <math.h> +#include <stdlib.h> + +#include "peakfinder8.h" + + +struct radius_maps +{ + float **r_maps; + int n_rmaps; +}; + + +struct peakfinder_mask +{ + char **masks; + int n_masks; +}; + + +struct radial_stats +{ + float *roffset; + float *rthreshold; + float *rsigma; + int *rcount; + int n_rad_bins; +}; + + +struct peakfinder_panel_data +{ + float **panel_data; + int *panel_h; + int *panel_w; + int num_panels; +}; + + +struct peakfinder_intern_data +{ + char *pix_in_peak_map; + int *infs; + int *inss; + int *peak_pixels; +}; + + +struct peakfinder_peak_data +{ + int num_found_peaks; + int *npix; + float *com_fs; + float *com_ss; + int *com_index; + float *tot_i; + float *max_i; + float *sigma; + float *snr; +}; + + +static double compute_r_sigma(float *rsigma, int *rcount, float *roffset, + int i) +{ + return sqrt(rsigma[i] / rcount[i] - + ((roffset[i] / rcount[i]) * + (roffset[i] / rcount[i]))); +} + + +static void update_radial_stats(float *roffset, float *rsigma, int *rcount, + float value, int curr_radius) +{ + roffset[curr_radius] += value; + rsigma[curr_radius] += (value * value); + rcount[curr_radius] += 1; +} + + +static float get_radius(struct panel p, float fs, float ss) +{ + float x, y; + + /* Calculate 3D position of given position, in m */ + x = (p.cnx + fs * p.fsx + ss * p.ssx); + y = (p.cny + fs * p.fsy + ss * p.ssy); + + return sqrt(x * x + y * y); +} + + +static struct radius_maps *compute_radius_maps(struct detector *det) +{ + int i, u, iss, ifs; + struct panel p; + struct radius_maps *rm = NULL; + + rm = (struct radius_maps *)malloc(sizeof(struct radius_maps)); + if ( rm == NULL ) { + return NULL; + } + + rm->r_maps = (float **)malloc(det->n_panels*sizeof(float*)); + if ( rm->r_maps == NULL ) { + free(rm); + return NULL; + } + + rm->n_rmaps = det->n_panels; + + for( i=0 ; i<det->n_panels ; i++ ) { + + p = det->panels[i]; + rm->r_maps[i] = (float *)malloc(p.h*p.w*sizeof(float)); + + if ( rm->r_maps[i] == NULL ) { + for ( u = 0; u<i; u++ ) { + free(rm->r_maps[u]); + } + free(rm); + return NULL; + } + + for ( iss=0 ; iss<p.h ; iss++ ) { + for ( ifs=0; ifs<p.w; ifs++ ) { + + int rmi; + + rmi = ifs + p.w * iss; + + rm->r_maps[i][rmi] = get_radius(p, ifs, iss); + } + } + + } + + return rm; +} + + +static void free_radius_maps(struct radius_maps *r_maps) +{ + int i; + + for ( i=0 ; i<r_maps->n_rmaps ; i++ ) { + free(r_maps->r_maps[i]); + } + free(r_maps->r_maps); + free(r_maps); +} + + +static struct peakfinder_mask *create_peakfinder_mask(struct image *img, + struct radius_maps *rmps, + int min_res, + int max_res) +{ + int i; + struct peakfinder_mask *msk; + + msk = (struct peakfinder_mask *)malloc(sizeof(struct peakfinder_mask)); + msk->masks =(char **) malloc(img->det->n_panels*sizeof(char*)); + msk->n_masks = img->det->n_panels; + for ( i=0; i<img->det->n_panels; i++) { + + struct panel p; + int iss, ifs; + + p = img->det->panels[i]; + + msk->masks[i] = (char *)calloc(p.w*p.h,sizeof(char)); + + for ( iss=0 ; iss<p.h ; iss++ ) { + for ( ifs=0 ; ifs<p.w ; ifs++ ) { + + int idx; + + idx = ifs + iss*p.w; + + if ( rmps->r_maps[i][idx] < max_res + && rmps->r_maps[i][idx] > min_res ) { + + if (! ( ( img->bad != NULL ) + && ( img->bad[i] != NULL ) + && ( img->bad[i][idx] != 0 ) ) ) { + msk->masks[i][idx] = 1; + } + + } + + } + } + } + return msk; +} + + +static void free_peakfinder_mask(struct peakfinder_mask * pfmask) +{ + int i; + + for ( i=0 ; i<pfmask->n_masks ; i++ ) { + free(pfmask->masks[i]); + } + free(pfmask->masks); + free(pfmask); +} + + +static int compute_num_radial_bins(int num_panels, int *w, int *h, + float **r_maps) +{ + + float max_r; + int max_r_int; + int m; + + max_r = -1e9; + + for ( m=0 ; m<num_panels ; m++ ) { + + int ifs, iss; + int pidx; + + for ( iss=0 ; iss<h[m] ; iss++ ) { + for ( ifs=0 ; ifs<w[m] ; ifs++ ) { + pidx = iss * w[m] + ifs; + if ( r_maps[m][pidx] > max_r ) { + max_r = r_maps[m][pidx]; + } + } + } + } + + max_r_int = (int)ceil(max_r) + 1; + + return max_r_int; +} + + +static struct peakfinder_panel_data *allocate_panel_data(int num_panels) +{ + + struct peakfinder_panel_data *pfdata; + + + pfdata = (struct peakfinder_panel_data *)malloc( + sizeof(struct peakfinder_panel_data)); + if ( pfdata == NULL ) { + return NULL; + } + + pfdata->panel_h = (int *)malloc(num_panels*sizeof(int)); + if ( pfdata->panel_h == NULL ) { + free(pfdata); + return NULL; + } + + pfdata->panel_w = (int *)malloc(num_panels*sizeof(int)); + if ( pfdata->panel_w == NULL ) { + free(pfdata->panel_h); + free(pfdata); + return NULL; + } + + pfdata->panel_data = (float **)malloc(num_panels*sizeof(float*)); + if ( pfdata->panel_data == NULL ) { + free(pfdata->panel_w); + free(pfdata->panel_h); + free(pfdata); + return NULL; + } + + pfdata->num_panels = num_panels; + + return pfdata; +} + + +static void free_panel_data(struct peakfinder_panel_data *pfdata) +{ + free(pfdata->panel_data); + free(pfdata->panel_w); + free(pfdata->panel_h); + free(pfdata); +} + + +static struct radial_stats *allocate_radial_stats(int num_rad_bins) +{ + struct radial_stats *rstats; + + rstats = (struct radial_stats *)malloc(sizeof(struct radial_stats)); + if ( rstats == NULL ) { + return NULL; + } + + rstats->roffset = (float *)malloc(num_rad_bins*sizeof(float)); + if ( rstats->roffset == NULL ) { + free(rstats); + return NULL; + } + + rstats->rthreshold = (float *)malloc(num_rad_bins*sizeof(float)); + if ( rstats->rthreshold == NULL ) { + free(rstats); + free(rstats->roffset); + return NULL; + } + + rstats->rsigma = (float *)malloc(num_rad_bins*sizeof(float)); + if ( rstats->rsigma == NULL ) { + free(rstats); + free(rstats->roffset); + free(rstats->rthreshold); + return NULL; + } + + rstats->rcount = (int *)malloc(num_rad_bins*sizeof(int)); + if ( rstats->rcount == NULL ) { + free(rstats); + free(rstats->roffset); + free(rstats->rthreshold); + free(rstats->rsigma); + return NULL; + } + + rstats->n_rad_bins = num_rad_bins; + + return rstats; +} + + +static void free_radial_stats(struct radial_stats *rstats) +{ + free(rstats->roffset); + free(rstats->rthreshold); + free(rstats->rsigma); + free(rstats->rcount); + free(rstats); +} + + +static void fill_radial_bins(float *data, + int w, + int h, + float *r_map, + char *mask, + float *rthreshold, + float *roffset, + float *rsigma, + int *rcount) +{ + int iss, ifs; + int pidx; + + int curr_r; + float value; + + for ( iss = 0; iss<h ; iss++ ) { + + for ( ifs = 0; ifs<w ; ifs++ ) { + + pidx = iss * w + ifs; + + if ( mask[pidx] != 0 ) { + + curr_r = (int)rint(r_map[pidx]); + + value = data[pidx]; + + if ( value < rthreshold[curr_r ] ) { + + update_radial_stats(roffset, + rsigma, + rcount, + value, + curr_r); + } + } + } + } +} + + +static void compute_radial_stats(float *rthreshold, + float *roffset, + float *rsigma, + int *rcount, + int num_rad_bins, + float min_snr, + float acd_threshold) +{ + + int ri; + float this_offset, this_sigma; + + for ( ri=0 ; ri<num_rad_bins ; ri++ ) { + + if ( rcount[ri] == 0 ) { + roffset[ri] = 0; + rsigma[ri] = 0; + rthreshold[ri] = 1e9; + } else { + this_offset = roffset[ri]/rcount[ri]; + + this_sigma = compute_r_sigma(rsigma, + rcount, + roffset, + ri); + + roffset[ri] = this_offset; + rsigma[ri] = this_sigma; + + rthreshold[ri] = roffset[ri] + + min_snr*rsigma[ri]; + + if ( rthreshold[ri] < acd_threshold ) { + rthreshold[ri] = acd_threshold; + } + } + } + +} + + +struct peakfinder_peak_data *allocate_peak_data(int max_num_peaks) +{ + struct peakfinder_peak_data *pkdata; + + pkdata = (struct peakfinder_peak_data*)malloc( + sizeof(struct peakfinder_peak_data)); + if ( pkdata == NULL ) { + return NULL; + } + + pkdata->npix = (int *)malloc(max_num_peaks*sizeof(int)); + if ( pkdata->npix == NULL ) { + free(pkdata); + free(pkdata->npix); + return NULL; + } + + pkdata->com_fs = (float *)malloc(max_num_peaks*sizeof(float)); + if ( pkdata->com_fs == NULL ) { + free(pkdata->npix); + free(pkdata); + return NULL; + } + + pkdata->com_ss = (float *)malloc(max_num_peaks*sizeof(float)); + if ( pkdata->com_ss == NULL ) { + free(pkdata->npix); + free(pkdata->com_fs); + free(pkdata); + return NULL; + } + + pkdata->com_index = (int *)malloc(max_num_peaks*sizeof(int)); + if ( pkdata->com_ss == NULL ) { + free(pkdata->npix); + free(pkdata->com_fs); + free(pkdata->com_ss); + free(pkdata); + return NULL; + } + + + pkdata->tot_i = (float *)malloc(max_num_peaks*sizeof(float)); + if ( pkdata->tot_i == NULL ) { + free(pkdata->npix); + free(pkdata->com_fs); + free(pkdata->com_ss); + free(pkdata->com_index); + free(pkdata); + return NULL; + } + + pkdata->max_i = (float *)malloc(max_num_peaks*sizeof(float)); + if ( pkdata->max_i == NULL ) { + free(pkdata->npix); + free(pkdata->com_fs); + free(pkdata->com_ss); + free(pkdata->com_index); + free(pkdata->tot_i); + free(pkdata); + return NULL; + } + + pkdata->sigma = (float *)malloc(max_num_peaks*sizeof(float)); + if ( pkdata->sigma == NULL ) { + free(pkdata->npix); + free(pkdata->com_fs); + free(pkdata->com_ss); + free(pkdata->com_index); + free(pkdata->tot_i); + free(pkdata->max_i); + free(pkdata); + return NULL; + } + + pkdata->snr = (float *)malloc(max_num_peaks*sizeof(float)); + if ( pkdata->snr == NULL ) { + free(pkdata->npix); + free(pkdata->com_fs); + free(pkdata->com_ss); + free(pkdata->com_index); + free(pkdata->tot_i); + free(pkdata->max_i); + free(pkdata->sigma); + free(pkdata); + return NULL; + } + + return pkdata; +} + + +static void free_peak_data(struct peakfinder_peak_data *pkdata) +{ + free(pkdata->npix); + free(pkdata->com_fs); + free(pkdata->com_ss); + free(pkdata->com_index); + free(pkdata->tot_i); + free(pkdata->max_i); + free(pkdata->sigma); + free(pkdata->snr); + free(pkdata); +} + + +static struct peakfinder_intern_data *allocate_peakfinder_intern_data( + int data_size, int max_pix_count) +{ + + struct peakfinder_intern_data *intern_data; + + intern_data = (struct peakfinder_intern_data *)malloc( + sizeof(struct peakfinder_intern_data)); + if ( intern_data == NULL ) { + return NULL; + } + + intern_data->pix_in_peak_map =(char *)calloc(data_size, sizeof(char)); + if ( intern_data->pix_in_peak_map == NULL ) { + free(intern_data); + return NULL; + } + + intern_data->infs =(int *)calloc(data_size, sizeof(int)); + if ( intern_data->infs == NULL ) { + free(intern_data->pix_in_peak_map); + free(intern_data); + return NULL; + } + + intern_data->inss =(int *)calloc(data_size, sizeof(int)); + if ( intern_data->inss == NULL ) { + free(intern_data->pix_in_peak_map); + free(intern_data->infs); + free(intern_data); + return NULL; + } + + intern_data->peak_pixels =(int *)calloc(max_pix_count, sizeof(int)); + if ( intern_data->peak_pixels == NULL ) { + free(intern_data->pix_in_peak_map); + free(intern_data->infs); + free(intern_data->inss); + free(intern_data); + return NULL; + } + + return intern_data; +} + + +static void free_peakfinder_intern_data(struct peakfinder_intern_data *pfid) +{ + free(pfid->peak_pixels); + free(pfid->pix_in_peak_map); + free(pfid->infs); + free(pfid->inss); + free(pfid); +} + + +static void peak_search(int p, struct peakfinder_intern_data *pfinter, + float *copy, char *mask, float *r_map, + float *rthreshold, float *roffset, + int *num_pix_in_peak, int asic_size_fs, + int asic_size_ss, int aifs, int aiss, + int num_pix_fs, float *sum_com_fs, + float *sum_com_ss, float *sum_i, int max_pix_count) +{ + + int k, pi; + int curr_radius; + float curr_threshold; + int curr_fs; + int curr_ss; + float curr_i; + + int search_fs[9] = { 0, -1, 0, 1, -1, 1, -1, 0, 1 }; + int search_ss[9] = { 0, -1, -1, -1, 0, 0, 1, 1, 1 }; + int search_n = 9; + + for ( k=0; k<search_n; k++ ) { + + if ( (pfinter->infs[p] + search_fs[k]) < 0 ) + continue; + if ( (pfinter->infs[p] + search_fs[k]) >= asic_size_fs ) + continue; + if ( (pfinter->inss[p] + search_ss[k]) < 0 ) + continue; + if ( (pfinter->inss[p] + search_ss[k]) >= asic_size_ss ) + continue; + + curr_fs = pfinter->infs[p] + search_fs[k] + aifs * asic_size_fs; + curr_ss = pfinter->inss[p] + search_ss[k] + aiss * asic_size_ss; + pi = curr_fs + curr_ss * num_pix_fs; + + curr_radius = (int)rint(r_map[pi]); + curr_threshold = rthreshold[curr_radius]; + + if ( copy[pi] > curr_threshold + && pfinter->pix_in_peak_map[pi] == 0 + && mask[pi] != 0 ) + { + + + curr_i = copy[pi] - roffset[curr_radius]; + + *sum_i += curr_i; + *sum_com_fs += curr_i * ((float)curr_fs); + *sum_com_ss += curr_i * ((float)curr_ss); + + pfinter->inss[*num_pix_in_peak] = pfinter->inss[p] + + search_ss[k]; + pfinter->infs[*num_pix_in_peak] = pfinter->infs[p] + + search_fs[k]; + + pfinter->pix_in_peak_map[pi] = 1; + if ( *num_pix_in_peak < max_pix_count ) { + pfinter->peak_pixels[*num_pix_in_peak] = pi; + } + *num_pix_in_peak = *num_pix_in_peak+1; + } + } +} + + +static void search_in_ring(int ring_width, int com_fs_int, int com_ss_int, + float *copy, float *r_map, + float *rthreshold, float *roffset, + char *pix_in_peak_map, char *mask, int asic_size_fs, + int asic_size_ss, int aifs, int aiss, + int num_pix_fs,float *local_sigma, + float *local_offset, float *background_max_i, + int com_idx, int local_bg_radius) +{ + int ssj, fsi; + float pix_radius; + int curr_fs, curr_ss; + int pi; + int curr_radius; + float curr_threshold; + float curr_i; + + int np_sigma; + int np_counted; + int local_radius; + + float sum_i; + float sum_i_squared; + + ring_width = 2 * local_bg_radius; + + sum_i = 0; + sum_i_squared = 0; + np_sigma = 0; + np_counted = 0; + local_radius = 0; + + for ( ssj = -ring_width ; ssj<ring_width ; ssj++ ) { + for ( fsi = -ring_width ; fsi<ring_width ; fsi++ ) { + + if ( (com_fs_int + fsi) < 0 ) + continue; + if ( (com_fs_int + fsi) >= asic_size_fs ) + continue; + if ( (com_ss_int + ssj) < 0 ) + continue; + if ( (com_ss_int + ssj) >= asic_size_ss ) + continue; + + pix_radius = sqrt(fsi * fsi + ssj * ssj); + if ( pix_radius>ring_width ) + continue; + + curr_fs = com_fs_int +fsi + aifs * asic_size_fs; + curr_ss = com_ss_int +ssj + aiss * asic_size_ss; + pi = curr_fs + curr_ss * num_pix_fs; + + curr_radius = rint(r_map[pi]); + curr_threshold = rthreshold[curr_radius]; + curr_i = copy[pi]; + + if ( copy[pi] < curr_threshold + && pix_in_peak_map[pi] == 0 + && mask[pi] != 0 ) { + + np_sigma++; + sum_i += curr_i; + sum_i_squared += (curr_i * curr_i); + + if ( curr_i > *background_max_i ) { + *background_max_i = curr_i; + } + } + np_counted += 1; + } + } + + if ( np_sigma != 0 ) { + *local_offset = sum_i / np_sigma; + *local_sigma = sqrt(sum_i_squared / np_sigma - + ((sum_i / np_sigma) * (sum_i / np_sigma))); + } else { + + local_radius = rint(r_map[(int)rint(com_idx)]); + *local_offset = roffset[local_radius]; + *local_sigma = 0.01; + } +} + + +static void process_panel(int asic_size_fs, int asic_size_ss, int num_pix_fs, + int aiss, int aifs, float *rthreshold, + float *roffset, int *peak_count, + float *copy, struct peakfinder_intern_data *pfinter, + float *r_map, char *mask, int *npix, float *com_fs, + float *com_ss, int *com_index, float *tot_i, + float *max_i, float *sigma, float *snr, + int min_pix_count, int max_pix_count, + int local_bg_radius, float min_snr, int max_n_peaks) +{ + int pxss, pxfs; + int num_pix_in_peak; + + for ( pxss=1 ; pxss<asic_size_ss-1 ; pxss++ ) { + for ( pxfs=1 ; pxfs<asic_size_fs-1 ; pxfs++ ) { + + float curr_thresh; + int pxidx; + int curr_rad; + + pxidx = (pxss + aiss * asic_size_ss) * + num_pix_fs + pxfs + + aifs * asic_size_fs; + + curr_rad = (int)rint(r_map[pxidx]); + curr_thresh = rthreshold[curr_rad]; + + if ( copy[pxidx] > curr_thresh + && pfinter->pix_in_peak_map[pxidx] == 0 ) { + + float sum_com_fs, sum_com_ss; + float sum_i; + float peak_com_fs, peak_com_ss; + float peak_com_fs_int, peak_com_ss_int; + float peak_tot_i, pk_tot_i_raw; + float peak_max_i, pk_max_i_raw; + float peak_snr; + float local_sigma, local_offset; + float background_max_i; + float f_background_thresh; + int lt_num_pix_in_pk; + int ring_width; + int peak_idx; + int com_idx; + int p; + + pfinter->infs[0] = pxfs; + pfinter->inss[0] = pxss; + pfinter->peak_pixels[0] = pxidx; + num_pix_in_peak = 1; + + sum_i = 0; + sum_com_fs = 0; + sum_com_ss = 0; + + do { + lt_num_pix_in_pk = num_pix_in_peak; + + for ( p=0; p<num_pix_in_peak; p++ ) { + peak_search(p, + pfinter, copy, mask, + r_map, + rthreshold, + roffset, + &num_pix_in_peak, + asic_size_fs, + asic_size_ss, + aifs, aiss, + num_pix_fs, + &sum_com_fs, + &sum_com_ss, + &sum_i, + max_pix_count); + } + + } while ( lt_num_pix_in_pk != num_pix_in_peak ); + + if ( num_pix_in_peak < min_pix_count + || num_pix_in_peak > max_pix_count) { + continue; + } + + peak_com_fs = sum_com_fs / fabs(sum_i); + peak_com_ss = sum_com_ss / fabs(sum_i); + + com_idx = rint(peak_com_fs) + + rint(peak_com_ss) * num_pix_fs; + + peak_com_fs_int = (int)rint(peak_com_fs) - + aifs * asic_size_fs; + peak_com_ss_int = (int)rint(peak_com_ss) - + aiss * asic_size_ss; + + local_sigma = 0.0; + local_offset = 0.0; + background_max_i = 0.0; + + ring_width = 2 * local_bg_radius; + + search_in_ring(ring_width, peak_com_fs_int, + peak_com_ss_int, + copy, r_map, rthreshold, + roffset, + pfinter->pix_in_peak_map, + mask, asic_size_fs, + asic_size_ss, + aifs, aiss, + num_pix_fs, + &local_sigma, + &local_offset, + &background_max_i, + com_idx, local_bg_radius); + + peak_tot_i = 0; + pk_tot_i_raw = 0; + peak_max_i = 0; + pk_max_i_raw = 0; + sum_com_fs = 0; + sum_com_ss = 0; + + for ( peak_idx = 1 ; + peak_idx < num_pix_in_peak + && peak_idx <= max_pix_count ; + peak_idx++ ) { + + int curr_idx; + float curr_i; + float curr_i_raw; + int curr_fs, curr_ss; + + // BUG HERE, I THINK. PEAK_PIXELS + // HAS SIZE MAX_PIX_COUNT, BUT + // IN THE FOLLOWING LINE PEAK_IDX + // CAN HAVE VALUE EXACTLY MAX_PEAK_COUNT + // (SEE THE FOR LOOP ABOVE) + curr_idx = + pfinter->peak_pixels[peak_idx]; + + curr_i_raw = copy[curr_idx]; + curr_i = curr_i_raw - local_offset; + + peak_tot_i += curr_i; + pk_tot_i_raw += curr_i_raw; + + curr_fs = curr_idx % asic_size_fs; + curr_ss = curr_idx / asic_size_fs; + sum_com_fs += curr_i * ((float)curr_fs); + sum_com_ss += curr_i * ((float)curr_ss); + + if ( curr_i_raw > pk_max_i_raw ) + pk_max_i_raw = curr_i_raw; + if ( curr_i > peak_max_i ) + peak_max_i = curr_i; + } + + + peak_com_fs = sum_com_fs / fabs(peak_tot_i); + peak_com_ss = sum_com_ss / fabs(peak_tot_i); + + peak_snr = peak_tot_i / local_sigma; + + if (peak_snr < min_snr) { + continue; + } + + f_background_thresh = 1; + f_background_thresh *= + background_max_i - local_offset; + if (peak_max_i < f_background_thresh) { + continue; + } + + if ( num_pix_in_peak >= min_pix_count + && num_pix_in_peak <= max_pix_count ) { + + int peak_com_idx; + + if ( peak_tot_i == 0 ) { + continue; + } + + peak_com_idx = rint(peak_com_fs) + + rint(peak_com_ss) * + asic_size_fs; + + if ( *peak_count < max_n_peaks ) { + + int pidx; + pidx = *peak_count; + + npix[pidx] = num_pix_in_peak; + com_fs[pidx] = peak_com_fs; + com_ss[pidx] = peak_com_ss; + com_index[pidx] = peak_com_idx; + tot_i[pidx] = peak_tot_i; + max_i[pidx] = peak_max_i; + sigma[pidx] = local_sigma; + snr[pidx] = peak_snr; + *peak_count = *peak_count + 1; + } else { + *peak_count = *peak_count + 1; + } + } + } + } + } +} + + +static int peakfinder8_base(float *roffset, float *rthreshold, + float *data, char *mask, float *r_map, + int asic_size_fs, int num_asics_fs, + int asic_size_ss, int num_asics_ss, + int max_n_peaks, int *num_found_peaks, + int *npix, float *com_fs, + float *com_ss, int *com_index, float *tot_i, + float *max_i, float *sigma, float *snr, + int min_pix_count, int max_pix_count, + int local_bg_radius, float min_snr) +{ + int num_pix_fs, num_pix_ss, num_pix_tot; + int i, aifs, aiss; + int peak_count; + float *copy; + struct peakfinder_intern_data *pfinter; + + num_pix_fs = asic_size_fs * num_asics_fs; + num_pix_ss = asic_size_ss * num_asics_ss; + num_pix_tot = num_pix_fs * num_pix_ss; + + copy = (float *)calloc(num_pix_tot, sizeof(float)); + if ( copy == NULL ) { + return 1; + } + + memcpy(copy, data, num_pix_tot*sizeof(float)); + + for (i = 0; i < num_pix_tot; i++) { + copy[i] *= mask[i]; + } + + pfinter = allocate_peakfinder_intern_data(num_pix_tot, max_pix_count); + if ( pfinter == NULL ) { + free(copy); + return 1; + } + + peak_count = 0; + + for ( aiss=0 ; aiss<num_asics_ss ; aiss++ ) { + for ( aifs=0 ; aifs<num_asics_fs ; aifs++ ) { + + process_panel(asic_size_fs, asic_size_ss, num_pix_fs, + aiss, aifs, rthreshold, roffset, + &peak_count, copy, pfinter, r_map, mask, + npix, com_fs, com_ss, com_index, tot_i, + max_i, sigma, snr, min_pix_count, + max_pix_count, local_bg_radius, min_snr, + max_n_peaks); + } + } + *num_found_peaks = peak_count; + + free_peakfinder_intern_data(pfinter); + free(copy); + + return 0; +} + + +int peakfinder8(struct image *img, int max_n_peaks, + float threshold, float min_snr, + int min_pix_count, int max_pix_count, + int local_bg_radius, int min_res, + int max_res, int use_saturated) +{ + struct radius_maps *rmaps; + struct peakfinder_mask *pfmask; + struct peakfinder_panel_data *pfdata; + struct radial_stats *rstats; + struct peakfinder_peak_data *pkdata; + int num_rad_bins; + int pi; + int i, it_counter; + int num_found_peaks; + int remaining_max_num_peaks; + int iterations; + + iterations = 5; + + if ( img-> det == NULL) { + return 1; + } + + rmaps = compute_radius_maps(img->det); + if ( rmaps == NULL ) { + return 1; + } + + pfmask = create_peakfinder_mask(img, rmaps, min_res, max_res); + if ( pfmask == NULL ) { + free_radius_maps(rmaps); + return 1; + } + + pfdata = allocate_panel_data(img->det->n_panels); + if ( pfdata == NULL) { + free_radius_maps(rmaps); + free_peakfinder_mask(pfmask); + return 1; + } + + for ( pi=0 ; pi<img->det->n_panels ; pi++ ) { + pfdata->panel_h[pi] = img->det->panels[pi].h; + pfdata->panel_w[pi] = img->det->panels[pi].w; + pfdata->panel_data[pi] = img->dp[pi]; + pfdata->num_panels = img->det->n_panels; + } + + num_rad_bins = compute_num_radial_bins(img->det->n_panels, + pfdata->panel_w, + pfdata->panel_h, + rmaps->r_maps); + + rstats = allocate_radial_stats(num_rad_bins); + if ( rstats == NULL ) { + free_radius_maps(rmaps); + free_peakfinder_mask(pfmask); + free_panel_data(pfdata); + return 1; + } + + for ( i=0 ; i<rstats->n_rad_bins ; i++) { + rstats->rthreshold[i] = 1e9; + } + + for ( it_counter=0 ; it_counter<iterations ; it_counter++ ) { + + for ( i=0; i<num_rad_bins; i++ ) { + rstats->roffset[i] = 0; + rstats->rsigma[i] = 0; + rstats->rcount[i] = 0; + } + + for ( pi=0 ; pi<pfdata->num_panels ; pi++ ) { + + fill_radial_bins(pfdata->panel_data[pi], + pfdata->panel_w[pi], + pfdata->panel_h[pi], + rmaps->r_maps[pi], + pfmask->masks[pi], + rstats->rthreshold, + rstats->roffset, + rstats->rsigma, + rstats->rcount); + + } + + compute_radial_stats(rstats->rthreshold, + rstats->roffset, + rstats->rsigma, + rstats->rcount, + num_rad_bins, + min_snr, + threshold); + + } + + pkdata = allocate_peak_data(max_n_peaks); + if ( pkdata == NULL ) { + free_radius_maps(rmaps); + free_peakfinder_mask(pfmask); + free_panel_data(pfdata); + free_radial_stats(rstats); + return 1; + } + + remaining_max_num_peaks = max_n_peaks; + + for ( pi=0 ; pi<img->det->n_panels ; pi++) { + + int peaks_to_add; + int pki; + int ret; + + num_found_peaks = 0; + + if ( img->det->panels[pi].no_index ) { + continue; + } + + ret = peakfinder8_base(rstats->roffset, + rstats->rthreshold, + pfdata->panel_data[pi], + pfmask->masks[pi], + rmaps->r_maps[pi], + pfdata->panel_w[pi], 1, + pfdata->panel_h[pi], 1, + max_n_peaks, + &num_found_peaks, + pkdata->npix, + pkdata->com_fs, + pkdata->com_ss, + pkdata->com_index, + pkdata->tot_i, + pkdata->max_i, + pkdata->sigma, + pkdata->snr, + min_pix_count, + max_pix_count, + local_bg_radius, + min_snr); + + if ( ret != 0 ) { + free_radius_maps(rmaps); + free_peakfinder_mask(pfmask); + free_panel_data(pfdata); + free_radial_stats(rstats); + return 1; + } + + peaks_to_add = num_found_peaks; + + if ( num_found_peaks > remaining_max_num_peaks ) { + peaks_to_add = remaining_max_num_peaks; + } + + remaining_max_num_peaks -= peaks_to_add; + + for ( pki=0 ; pki<peaks_to_add ; pki++ ) { + + struct panel *p; + + p = &img->det->panels[pi]; + + img->num_peaks += 1; + if ( pkdata->max_i[pki] > p->max_adu ) { + img->num_saturated_peaks++; + if ( !use_saturated ) { + continue; + } + } + + image_add_feature(img->features, + pkdata->com_fs[pki], + pkdata->com_ss[pki], + p, + img, + pkdata->tot_i[pki], + NULL); + } + } + + free_radius_maps(rmaps); + free_peakfinder_mask(pfmask); + free_panel_data(pfdata); + free_radial_stats(rstats); + free_peak_data(pkdata); + return 0; +} diff --git a/libcrystfel/src/peakfinder8.h b/libcrystfel/src/peakfinder8.h new file mode 100644 index 00000000..483eebdf --- /dev/null +++ b/libcrystfel/src/peakfinder8.h @@ -0,0 +1,50 @@ +/* + * peakfinder8.h + * + * The peakfinder8 algorithm + * + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2017 Valerio Mariani <valerio.mariani@desy.de> + * 2017 Anton Barty <anton.barty@desy.de> + * 2017 Oleksandr Yefanov <oleksandr.yefanov@desy.de> + * + * 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/>. + * + */ + +#ifndef PEAKFINDER8_H +#define PEAKFINDER8_H + +#include "image.h" + +#ifdef __cplusplus +extern "C" { +#endif + +extern int peakfinder8(struct image *img, int max_n_peaks, + float threshold, float min_snr, + int mix_pix_count, int max_pix_count, + int local_bg_radius, int min_res, + int max_res, int use_saturated); + +#ifdef __cplusplus +} +#endif + +#endif // PEAKFINDER8_H diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c index cb2a9f5a..28c79538 100644 --- a/libcrystfel/src/peaks.c +++ b/libcrystfel/src/peaks.c @@ -3,7 +3,7 @@ * * Peak search and other image analysis * - * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * @@ -12,6 +12,7 @@ * 2012 Kenneth Beyerlein <kenneth.beyerlein@desy.de> * 2011 Andrew Martin <andrew.martin@desy.de> * 2011 Richard Kirian + * 2017 Valerio Mariani <valerio.mariani@desy.de> * * This file is part of CrystFEL. * @@ -52,6 +53,7 @@ #include "reflist-utils.h" #include "cell-utils.h" #include "geometry.h" +#include "peakfinder8.h" static int cull_peaks_in_panel(struct image *image, struct panel *p) @@ -517,8 +519,8 @@ static void search_peaks_in_panel(struct image *image, float threshold, void search_peaks(struct image *image, float threshold, float min_gradient, - float min_snr, double ir_inn, double ir_mid, double ir_out, - int use_saturated) + float min_snr, double ir_inn, double ir_mid, + double ir_out, int use_saturated) { int i; @@ -541,6 +543,26 @@ void search_peaks(struct image *image, float threshold, float min_gradient, } +int search_peaks_peakfinder8(struct image *image, int max_n_peaks, + float threshold, float min_snr, + int min_pix_count, int max_pix_count, + int local_bg_radius, int min_res, + int max_res, int use_saturated) +{ + if ( image->features != NULL ) { + image_feature_list_free(image->features); + } + image->features = image_feature_list_new(); + image->num_peaks = 0; + image->num_saturated_peaks = 0; + + return peakfinder8(image, max_n_peaks, threshold, min_snr, + min_pix_count, max_pix_count, + local_bg_radius, min_res, + max_res, use_saturated); +} + + int peak_sanity_check(struct image *image, Crystal **crystals, int n_cryst) { int n_feat = 0; diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h index ba724419..a5095127 100644 --- a/libcrystfel/src/peaks.h +++ b/libcrystfel/src/peaks.h @@ -3,11 +3,12 @@ * * Peak search and other image analysis * - * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: * 2010-2015 Thomas White <taw@physics.org> + * 2017 Valerio Mariani <valerio.mariani@desy.de> * * This file is part of CrystFEL. * @@ -45,9 +46,14 @@ extern "C" { extern int *make_BgMask(struct image *image, struct panel *p, double ir_inn); extern void search_peaks(struct image *image, float threshold, - float min_gradient, float min_snr, - double ir_inn, double ir_mid, double ir_out, - int use_saturated); + float min_gradient, float min_snr, double ir_inn, + double ir_mid, double ir_out, int use_saturated); + +extern int search_peaks_peakfinder8(struct image *image, int max_n_peaks, + float threshold, float min_snr, + int mix_pix_count, int max_pix_count, + int local_bg_radius, int min_res, + int max_res, int use_saturated); extern int peak_sanity_check(struct image *image, Crystal **crystals, int n_cryst); diff --git a/src/indexamajig.c b/src/indexamajig.c index 82a15e21..6300f7ff 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -13,6 +13,7 @@ * 2011 Richard Kirian * 2012 Lorenzo Galli * 2012 Chunhong Yoon + * 2017 Valerio Mariani <valerio.mariani@desy.de> * * This file is part of CrystFEL. * @@ -88,6 +89,7 @@ static void show_help(const char *s) " --peaks=<method> Use 'method' for finding peaks. Choose from:\n" " zaef : Use Zaefferer (2000) gradient detection.\n" " This is the default method.\n" +" peakfinder8: Use Peakfinder8 algorithm.\n" " hdf5 : Get from a table in HDF5 file.\n" " cxi : Get from CXI format HDF5 file.\n" " --hdf5-peaks=<p> Find peaks table in HDF5 file here.\n" @@ -95,23 +97,42 @@ static void show_help(const char *s) " --integration=<meth> Perform final pattern integration using <meth>.\n" "\n\n" "For more control over the process, you might need:\n\n" -" --tolerance=<tol> Set the tolerances for cell comparison.\n" -" Default: 5,5,5,1.5.\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" -" --median-filter=<n> Apply a median filter to the image data. Intensity\n" -" measurement will be performed on the image as it\n" -" was before this. The side length of the median\n" -" filter box will be 2<n>+1. Default: 0 (no filter).\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 squared gradient for Zaefferer peak search.\n" -" Default: 100,000.\n" -" --min-snr=<n> Minimum signal-to-noise ratio for peaks.\n" -" Default: 5.\n" +" --tolerance=<tol> Set the tolerances for cell comparison.\n" +" Default: 5,5,5,1.5.\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" +" --median-filter=<n> Apply a median filter to the image data. Intensity\n" +" measurement will be performed on the image as it\n" +" was before this. The side length of the median\n" +" filter box will be 2<n>+1.\n" +" Default: 0 (no filter).\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 in both the\n" +" Zaefferer and Peakfinder8 algorithms." +" Default: 800.\n" +" --min-gradient=<n> Minimum squared gradient for Zaefferer peak\n" +" search. Default: 100,000.\n" +" --min-snr=<n> Minimum signal-to-noise ratio for peaks, with both" +" Zaefferer and Peakfinder8 algorithms.\n" +" Default: 5.\n" +" --min-pix-count=<n> Only accept peaks if they include more than <n>" +" pixels, in the Peakfinder8 algorithm." +" Default: 2.\n" +" --max-pix-count=<n> Only accept peaks if they include less than <n>" +" pixels, in the Peakfinder8 algorithm." +" Default: 200.\n" +" --local-bg-radius=<n> Radius (in pixels) to use for the estimation of\n" +" local background in the Peakfinder8 algorithm.\n" +" Default: 3.\n" +" --min-res=<n> Only accept peaks if they lay at more than <n>\n" +" pixels from the center of the detector, int the\n" +" peakfinder8 algorithm. Default: 0.\n" +" --max-res=<n> Only accept peaks if they lay at less than <n>\n" +" pixels from the center of the detector, int the\n" +" peakfinder8 algorithm. Default: 1200.\n" " --check-hdf5-snr Check SNR for peaks from --peaks=hdf5.\n" " --peak-radius=<r> Integration radii for peak search.\n" " --int-radius=<r> Set the integration radii. Default: 4,5,7.\n" @@ -212,6 +233,11 @@ int main(int argc, char *argv[]) iargs.threshold = 800.0; iargs.min_gradient = 100000.0; iargs.min_snr = 5.0; + iargs.min_pix_count = 2; + iargs.max_pix_count = 200; + iargs.min_res = 0; + iargs.max_res = 1200; + iargs.local_bg_radius = 3; iargs.check_hdf5_snr = 0; iargs.det = NULL; iargs.peaks = PEAK_ZAEF; @@ -303,6 +329,11 @@ int main(int argc, char *argv[]) {"fix-bandwidth", 1, NULL, 23}, {"fix-divergence", 1, NULL, 24}, {"felix-options", 1, NULL, 25}, + {"min-pix-count", 1, NULL, 26}, + {"max-pix-count", 1, NULL, 27}, + {"local-bg-radius", 1, NULL, 28}, + {"min-res", 1, NULL, 29}, + {"max-res", 1, NULL, 30}, {0, 0, NULL, 0} }; @@ -486,6 +517,26 @@ int main(int argc, char *argv[]) } break; + case 26: + iargs.min_pix_count = atoi(optarg); + break; + + case 27: + iargs.max_pix_count = atoi(optarg); + break; + + case 28: + iargs.local_bg_radius = atoi(optarg); + break; + + case 29: + iargs.min_res = atoi(optarg); + break; + + case 30: + iargs.max_res = atoi(optarg); + break; + case 0 : break; @@ -538,6 +589,8 @@ int main(int argc, char *argv[]) } if ( strcmp(speaks, "zaef") == 0 ) { iargs.peaks = PEAK_ZAEF; + } else if ( strcmp(speaks, "peakfinder8") == 0 ) { + iargs.peaks = PEAK_PEAKFINDER8; } else if ( strcmp(speaks, "hdf5") == 0 ) { iargs.peaks = PEAK_HDF5; } else if ( strcmp(speaks, "cxi") == 0 ) { diff --git a/src/process_image.c b/src/process_image.c index f3629e0e..e6e6d22a 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. * @@ -191,6 +191,28 @@ 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); diff --git a/src/process_image.h b/src/process_image.h index 57be255c..bc8b31fd 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -3,12 +3,12 @@ * * The processing pipeline for one image * - * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: * 2010-2016 Thomas White <taw@physics.org> - * 2014 Valerio Mariani + * 2014-2017 Valerio Mariani <valerio.mariani@desy.de> * * This file is part of CrystFEL. * @@ -42,6 +42,7 @@ struct index_args; enum { + PEAK_PEAKFINDER8, PEAK_ZAEF, PEAK_HDF5, PEAK_CXI, @@ -72,6 +73,12 @@ struct index_args float ir_inn; float ir_mid; float ir_out; + int min_res; + int max_res; + int max_n_peaks; + int min_pix_count; + int max_pix_count; + int local_bg_radius; struct copy_hdf5_field *copyme; int integrate_saturated; int use_saturated; |