From 6309221fcc3c573cdb20a7c953b8964fb85f78c5 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Thu, 7 Apr 2016 17:36:57 +0200 Subject: No more slab-relative coordinates in libcrystfel --- libcrystfel/src/detector.c | 231 ++++------------ libcrystfel/src/detector.h | 30 +- libcrystfel/src/filters.c | 20 +- libcrystfel/src/geometry.c | 11 +- libcrystfel/src/hdf5-file.c | 577 +++++++-------------------------------- libcrystfel/src/image.c | 32 +-- libcrystfel/src/image.h | 16 +- libcrystfel/src/index.c | 6 +- libcrystfel/src/integration.c | 33 ++- libcrystfel/src/mosflm.c | 20 +- libcrystfel/src/peaks.c | 94 +++---- libcrystfel/src/predict-refine.c | 16 +- libcrystfel/src/stream.c | 74 +++-- libcrystfel/src/xds.c | 20 +- 14 files changed, 312 insertions(+), 868 deletions(-) (limited to 'libcrystfel/src') diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c index 610da657..91fedaf2 100644 --- a/libcrystfel/src/detector.c +++ b/libcrystfel/src/detector.c @@ -3,12 +3,12 @@ * * Detector properties * - * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * * Authors: - * 2009-2015 Thomas White + * 2009-2016 Thomas White * 2014 Valerio Mariani * 2014 Kenneth Beyerlein * 2011 Andrew Aquila @@ -298,39 +298,19 @@ struct rvec get_q_for_panel(struct panel *p, double fs, double ss, } -struct rvec get_q(struct image *image, double fs, double ss, - double *ttp, double k) -{ - struct panel *p; - const unsigned int fsi = fs; - const unsigned int ssi = ss; /* Explicit rounding */ - - /* Determine which panel to use */ - p = find_panel(image->det, fsi, ssi); - assert(p != NULL); - - return get_q_for_panel(p, fs-(double)p->min_fs, ss-(double)p->min_ss, - ttp, k); -} - - -int in_bad_region(struct detector *det, double fs, double ss) +int in_bad_region(struct detector *det, struct panel *p, double fs, double ss) { double rx, ry; - struct panel *p; double xs, ys; int i; - /* Determine which panel to use */ - p = find_panel(det, fs, ss); - /* No panel found -> definitely bad! */ if ( p == NULL ) return 1; /* Convert xs and ys, which are in fast scan/slow scan coordinates, * to x and y */ - xs = (fs-(double)p->min_fs)*p->fsx + (ss-(double)p->min_ss)*p->ssx; - ys = (fs-(double)p->min_fs)*p->fsy + (ss-(double)p->min_ss)*p->ssy; + xs = fs*p->fsx + ss*p->ssx; + ys = fs*p->fsy + ss*p->ssy; rx = xs + p->cnx; ry = ys + p->cny; @@ -348,8 +328,8 @@ int in_bad_region(struct detector *det, double fs, double ss) /* fs/ss bad regions are specified according to the * original coordinates */ - nfs = (fs-p->min_fs) + p->orig_min_fs; - nss = (ss-p->min_ss) + p->orig_min_ss; + nfs = fs + p->orig_min_fs; + nss = ss + p->orig_min_ss; if ( nfs < b->min_fs ) continue; if ( nfs > b->max_fs ) continue; @@ -372,34 +352,6 @@ int in_bad_region(struct detector *det, double fs, double ss) } -double get_tt(struct image *image, double fs, double ss, int *err) -{ - double r, rx, ry; - struct panel *p; - double xs, ys; - - *err = 0; - - p = find_panel(image->det, fs, ss); - if ( p == NULL ) { - *err = 1; - return 0.0; - } - - /* Convert xs and ys, which are in fast scan/slow scan coordinates, - * to x and y */ - xs = (fs-p->min_fs)*p->fsx + (ss-p->min_ss)*p->ssx; - ys = (fs-p->min_fs)*p->fsy + (ss-p->min_ss)*p->ssy; - - rx = (xs + p->cnx) / p->res; - ry = (ys + p->cny) / p->res; - - r = sqrt(pow(rx, 2.0) + pow(ry, 2.0)); - - return atan2(r, p->clen); -} - - int detector_has_clen_references(struct detector *det) { int i; @@ -538,32 +490,6 @@ void record_image(struct image *image, int do_poisson, double background, } -signed int find_panel_number(struct detector *det, double fs, double ss) -{ - int p; - - /* Fractional pixel coordinates are allowed to be a little further along - * than "== max_{f,s}s" for an integer. */ - - for ( p=0; pn_panels; p++ ) { - if ( (fs >= det->panels[p].min_fs) - && (fs < det->panels[p].max_fs+1) - && (ss >= det->panels[p].min_ss) - && (ss < det->panels[p].max_ss+1) ) return p; - } - - return -1; -} - - -struct panel *find_panel(struct detector *det, double fs, double ss) -{ - signed int pn = find_panel_number(det, fs, ss); - if ( pn == -1 ) return NULL; - return &det->panels[pn]; -} - - signed int find_orig_panel_number(struct detector *det, double fs, double ss) { int p; @@ -589,6 +515,18 @@ struct panel *find_orig_panel(struct detector *det, double fs, double ss) } +int panel_number(struct detector *det, struct panel *p) +{ + int pn; + + for ( pn=0; pnn_panels; pn++ ) { + if ( &det->panels[pn] == p ) return pn; + } + + return det->n_panels; +} + + void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev) { int i; @@ -940,13 +878,13 @@ static int parse_field_for_panel(struct panel *panel, const char *key, int reject = 0; if ( strcmp(key, "min_fs") == 0 ) { - panel->min_fs = atof(val); + panel->orig_min_fs = atof(val); } else if ( strcmp(key, "max_fs") == 0 ) { - panel->max_fs = atof(val); + panel->orig_max_fs = atof(val); } else if ( strcmp(key, "min_ss") == 0 ) { - panel->min_ss = atof(val); + panel->orig_min_ss = atof(val); } else if ( strcmp(key, "max_ss") == 0 ) { - panel->max_ss = atof(val); + panel->orig_max_ss = atof(val); } else if ( strcmp(key, "corner_x") == 0 ) { panel->cnx = atof(val); } else if ( strcmp(key, "corner_y") == 0 ) { @@ -1212,16 +1150,13 @@ static void find_min_max_d(struct detector *det) for ( i=0; in_panels; i++ ) { struct panel *p; - double w, h; p = &det->panels[i]; - w = p->max_fs - p->min_fs + 1; - h = p->max_ss - p->min_ss + 1; - check_point(p, 0, 0, &min_d, &max_d, det); - check_point(p, w, 0, &min_d, &max_d, det); - check_point(p, 0, h, &min_d, &max_d, det); - check_point(p, w, h, &min_d, &max_d, det); + check_point(p, 0, 0, &min_d, &max_d, det); + check_point(p, p->w, 0, &min_d, &max_d, det); + check_point(p, 0, p->h, &min_d, &max_d, det); + check_point(p, p->w, p->h, &min_d, &max_d, det); } } @@ -1239,8 +1174,6 @@ struct detector *get_detector_geometry(const char *filename, int reject = 0; int path_dim; int dim_dim; - int curr_ss; - int x, y, max_fs, max_ss; int dim_reject = 0; int dim_dim_reject = 0; struct rg_definition **rg_defl = NULL; @@ -1277,10 +1210,6 @@ struct detector *get_detector_geometry(const char *filename, det->rigid_group_collections = NULL; /* The default defaults... */ - det->defaults.min_fs = -1; - det->defaults.min_ss = -1; - det->defaults.max_fs = -1; - det->defaults.max_ss = -1; det->defaults.orig_min_fs = -1; det->defaults.orig_min_ss = -1; det->defaults.orig_max_fs = -1; @@ -1394,9 +1323,6 @@ struct detector *get_detector_geometry(const char *filename, return NULL; } - max_fs = 0; - max_ss = 0; - path_dim = -1; dim_reject = 0; @@ -1524,32 +1450,24 @@ struct detector *get_detector_geometry(const char *filename, det->dim_dim = dim_dim; - curr_ss = 0; - for ( i=0; in_panels; i++ ) { - if ( det->panels[i].max_fs-det->panels[i].min_fs+1 != - det->panels[0].max_fs-det->panels[0].min_fs+1 ) { - ERROR("All panels should have the same fs extent\n"); - reject = 1; - } - - if ( det->panels[i ].min_fs < 0 ) { + if ( det->panels[i].orig_min_fs < 0 ) { ERROR("Please specify the minimum FS coordinate for" " panel %s\n", det->panels[i].name); reject = 1; } - if ( det->panels[i].max_fs < 0 ) { + if ( det->panels[i].orig_max_fs < 0 ) { ERROR("Please specify the maximum FS coordinate for" " panel %s\n", det->panels[i].name); reject = 1; } - if ( det->panels[i].min_ss < 0 ) { + if ( det->panels[i].orig_min_ss < 0 ) { ERROR("Please specify the minimum SS coordinate for" " panel %s\n", det->panels[i].name); reject = 1; } - if ( det->panels[i].max_ss < 0 ) { + if ( det->panels[i].orig_max_ss < 0 ) { ERROR("Please specify the maximum SS coordinate for" " panel %s\n", det->panels[i].name); reject = 1; @@ -1587,28 +1505,10 @@ struct detector *get_detector_geometry(const char *filename, /* It's not a problem if "no_index" is still zero */ /* The default transformation matrix is at least valid */ - det->panels[i].orig_max_fs = det->panels[i].max_fs; - det->panels[i].orig_min_fs = det->panels[i].min_fs; - det->panels[i].orig_max_ss = det->panels[i].max_ss; - det->panels[i].orig_min_ss = det->panels[i].min_ss; - - det->panels[i].w = - det->panels[i].max_fs-det->panels[i].min_fs+1; - det->panels[i].h = - det->panels[i].max_ss-det->panels[i].min_ss+1; - - det->panels[i].min_fs = 0; - det->panels[i].max_fs = det->panels[i].w-1; - det->panels[i].min_ss = curr_ss; - det->panels[i].max_ss = curr_ss+det->panels[i].h-1; - curr_ss += det->panels[i].h; - - if ( det->panels[i].max_fs > max_fs ) { - max_fs = det->panels[i].max_fs; - } - if ( det->panels[i].max_ss > max_ss ) { - max_ss = det->panels[i].max_ss; - } + det->panels[i].w = det->panels[i].orig_max_fs + - det->panels[i].orig_min_fs+1; + det->panels[i].h = det->panels[i].orig_max_ss + - det->panels[i].orig_min_ss+1; } @@ -1620,20 +1520,6 @@ struct detector *get_detector_geometry(const char *filename, } } - for ( x=0; x<=max_fs; x++ ) { - for ( y=0; y<=max_ss; y++ ) { - if ( find_panel(det, x, y) == NULL ) { - ERROR("Detector geometry invalid: contains gaps.\n"); - reject = 1; - goto out; - } - } - } - -out: - det->max_fs = max_fs; - det->max_ss = max_ss; - free(det->defaults.clen_from); free(det->defaults.data); free(det->defaults.mask); @@ -1744,8 +1630,8 @@ out: p->xss = -p->fsy / d; p->yss = p->fsx / d; - p->w = p->max_fs - p->min_fs + 1; - p->h = p->max_ss - p->min_ss + 1; + p->w = p->orig_max_fs - p->orig_min_fs + 1; + p->h = p->orig_max_ss - p->orig_min_ss + 1; } @@ -1884,7 +1770,7 @@ struct detector *copy_geom(const struct detector *in) } -struct detector *simple_geometry(const struct image *image) +struct detector *simple_geometry(const struct image *image, int w, int h) { struct detector *geom; @@ -1893,16 +1779,12 @@ struct detector *simple_geometry(const struct image *image) geom->n_panels = 1; geom->panels = calloc(1, sizeof(struct panel)); - geom->panels[0].min_fs = 0; - geom->panels[0].max_fs = image->width-1; - geom->panels[0].min_ss = 0; - geom->panels[0].max_ss = image->height-1; geom->panels[0].orig_min_fs = 0; - geom->panels[0].orig_max_fs = image->width-1; + geom->panels[0].orig_max_fs = w-1; geom->panels[0].orig_min_ss = 0; - geom->panels[0].orig_max_ss = image->height-1; - geom->panels[0].cnx = -image->width / 2.0; - geom->panels[0].cny = -image->height / 2.0; + geom->panels[0].orig_max_ss = h-1; + geom->panels[0].cnx = -w / 2.0; + geom->panels[0].cny = -h / 2.0; geom->panels[0].max_adu = INFINITY; geom->panels[0].orig_min_fs = -1; geom->panels[0].orig_max_fs = -1; @@ -1919,8 +1801,8 @@ struct detector *simple_geometry(const struct image *image) geom->panels[0].yfs = 0; geom->panels[0].yss = 1; - geom->panels[0].w = image->width; - geom->panels[0].h = image->height; + geom->panels[0].w = w; + geom->panels[0].h = h; geom->panels[0].mask = NULL; geom->panels[0].data = NULL; @@ -1931,8 +1813,8 @@ struct detector *simple_geometry(const struct image *image) } -int reverse_2d_mapping(double x, double y, double *pfs, double *pss, - struct detector *det) +int reverse_2d_mapping(double x, double y, struct detector *det, + struct panel **pp, double *pfs, double *pss) { int i; @@ -1952,11 +1834,12 @@ int reverse_2d_mapping(double x, double y, double *pfs, double *pss, /* In range? */ if ( fs < 0 ) continue; if ( ss < 0 ) continue; - if ( fs > p->max_fs-p->min_fs ) continue; - if ( ss > p->max_ss-p->min_ss ) continue; + if ( fs > p->w ) continue; + if ( ss > p->h ) continue; - *pfs = fs + p->min_fs; - *pss = ss + p->min_ss; + *pfs = fs; + *pss = ss; + *pp = p; return 0; } @@ -2095,20 +1978,16 @@ void get_pixel_extents(struct detector *det, for ( i=0; in_panels; i++ ) { check_extents(det->panels[i], min_x, min_y, max_x, max_y, - 0.0, - 0.0); + 0.0, 0.0); check_extents(det->panels[i], min_x, min_y, max_x, max_y, - 0.0, - det->panels[i].max_ss-det->panels[i].min_ss+1); + 0.0, det->panels[i].h+1); check_extents(det->panels[i], min_x, min_y, max_x, max_y, - det->panels[i].max_fs-det->panels[i].min_fs+1, - 0.0); + det->panels[i].w+1, 0.0); check_extents(det->panels[i], min_x, min_y, max_x, max_y, - det->panels[i].max_fs-det->panels[i].min_fs+1, - det->panels[i].max_ss-det->panels[i].min_ss+1); + det->panels[i].w+1, det->panels[i].h+1); } diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h index a52d56b7..dad3afe4 100644 --- a/libcrystfel/src/detector.h +++ b/libcrystfel/src/detector.h @@ -3,12 +3,12 @@ * * Detector properties * - * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * * Authors: - * 2009-2015 Thomas White + * 2009-2016 Thomas White * 2011-2012 Richard Kirian * 2014 Valerio Mariani * 2011 Andrew Aquila @@ -84,12 +84,6 @@ struct panel { char name[1024]; /* Name for this panel */ - /* Position of panel in the data block in memory (see below) */ - int min_fs; /* Smallest FS value considered to be in the panel */ - int max_fs; /* Largest FS value considered to be in this panel */ - int min_ss; /* ... and so on */ - int max_ss; - double cnx; /* Location of corner (min_fs,min_ss) in pixels */ double cny; double coffset; @@ -158,9 +152,6 @@ struct detector struct panel *panels; int n_panels; - int max_fs; - int max_ss; /* Size of overall array needed, minus 1 */ - struct badregion *bad; int n_bad; @@ -192,32 +183,31 @@ struct detector }; -extern struct rvec get_q(struct image *image, double fs, double ss, - double *ttp, double k); - extern struct rvec get_q_for_panel(struct panel *p, double fs, double ss, double *ttp, double k); extern double get_tt(struct image *image, double xs, double ys, int *err); -extern int in_bad_region(struct detector *det, double fs, double ss); +extern int in_bad_region(struct detector *det, struct panel *p, + double fs, double ss); extern void record_image(struct image *image, int do_poisson, double background, gsl_rng *rng, double beam_radius, double nphotons); -extern struct panel *find_panel(struct detector *det, double fs, double ss); -extern signed int find_panel_number(struct detector *det, double fs, double ss); extern struct panel *find_orig_panel(struct detector *det, double fs, double ss); + extern signed int find_orig_panel_number(struct detector *det, double fs, double ss); +extern int panel_number(struct detector *det, struct panel *p); + extern struct detector *get_detector_geometry(const char *filename, struct beam_params *beam); extern void free_detector_geometry(struct detector *det); -extern struct detector *simple_geometry(const struct image *image); +extern struct detector *simple_geometry(const struct image *image, int w, int h); extern void get_pixel_extents(struct detector *det, double *min_x, double *min_y, @@ -235,8 +225,8 @@ extern int rigid_group_is_in_collection(struct rg_collection *c, extern struct detector *copy_geom(const struct detector *in); -extern int reverse_2d_mapping(double x, double y, double *pfs, double *pss, - struct detector *det); +extern int reverse_2d_mapping(double x, double y, struct detector *det, + struct panel **pp, double *pfs, double *pss); extern double largest_q(struct image *image); diff --git a/libcrystfel/src/filters.c b/libcrystfel/src/filters.c index c804099e..cbaf6001 100644 --- a/libcrystfel/src/filters.c +++ b/libcrystfel/src/filters.c @@ -3,11 +3,11 @@ * * Image filtering * - * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2010-2015 Thomas White + * 2010-2016 Thomas White * 2013 Anton Barty * * This file is part of CrystFEL. @@ -132,7 +132,6 @@ void filter_median(struct image *image, int size) int counter; int nn; float *buffer; - float *localBg; int pn; if ( size <= 0 ) return; @@ -142,9 +141,8 @@ void filter_median(struct image *image, int size) /* "localBg" is way too big, but guaranteed big enough */ buffer = calloc(nn, sizeof(float)); - localBg = calloc(image->width*image->height, sizeof(float)); - if ( (buffer == NULL) || (localBg == NULL) ) { - ERROR("Failed to allocate LB buffers.\n"); + if ( buffer == NULL ) { + ERROR("Failed to allocate LB buffer.\n"); return; } @@ -155,9 +153,16 @@ void filter_median(struct image *image, int size) int fs, ss; int i; struct panel *p; + float *localBg; p = &image->det->panels[pn]; + localBg = calloc(p->w*p->h, sizeof(float)); + if ( localBg == NULL ) { + ERROR("Failed to allocate LB buffer.\n"); + return; + } + for ( fs=0; fsw; fs++ ) { for ( ss=0; ssh; ss++ ) { @@ -193,8 +198,9 @@ void filter_median(struct image *image, int size) for ( i=0; iw*p->h; i++ ) { image->dp[pn][i] -= localBg[i]; } + + free(localBg); } - free(localBg); free(buffer); } diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c index 4c24f0bf..0f643ebe 100644 --- a/libcrystfel/src/geometry.c +++ b/libcrystfel/src/geometry.c @@ -69,16 +69,13 @@ static int locate_peak_on_panel(double x, double y, double z, double k, fs = p->xfs*plx + p->yfs*ply; ss = p->xss*plx + p->yss*ply; - fs += p->min_fs; - ss += p->min_ss; - *pfs = fs; *pss = ss; /* Now, is this on this panel? */ - if ( fs < p->min_fs ) return 0; - if ( fs > p->max_fs ) return 0; - if ( ss < p->min_ss ) return 0; - if ( ss > p->max_ss ) return 0; + if ( fs < 0 ) return 0; + if ( fs > p->w ) return 0; + if ( ss < 0 ) return 0; + if ( ss > p->h ) return 0; return 1; } diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c index 16fa0e75..95da2353 100644 --- a/libcrystfel/src/hdf5-file.c +++ b/libcrystfel/src/hdf5-file.c @@ -88,9 +88,6 @@ struct hdfile { const char *path; /* Current data path */ - size_t nfs; /* Image width */ - size_t nss; /* Image height */ - hid_t fh; /* HDF file handle */ hid_t dh; /* Dataset handle */ @@ -127,67 +124,12 @@ struct hdfile *hdfile_open(const char *filename) int hdfile_set_image(struct hdfile *f, const char *path, struct panel *p) { - hsize_t *size; - hsize_t *max_size; - hid_t sh; - int sh_dim; - int di; - f->dh = H5Dopen2(f->fh, path, H5P_DEFAULT); if ( f->dh < 0 ) { ERROR("Couldn't open dataset\n"); return -1; } f->data_open = 1; - sh = H5Dget_space(f->dh); - sh_dim = H5Sget_simple_extent_ndims(sh); - - if ( p == NULL ) { - - if ( sh_dim != 2 ) { - ERROR("Dataset is not two-dimensional\n"); - return -1; - } - - } else { - - if ( sh_dim != p->dim_structure->num_dims ) { - ERROR("Dataset dimensionality does not match " - "geometry file\n"); - return -1; - } - - } - - size = malloc(sh_dim*sizeof(hsize_t)); - max_size = malloc(sh_dim*sizeof(hsize_t)); - - H5Sget_simple_extent_dims(sh, size, max_size); - H5Sclose(sh); - - if ( p == NULL ) { - - f->nss = size[0]; - f->nfs = size[1]; - - } else { - - for ( di=0; didim_structure->num_dims; di++ ) { - - if ( p->dim_structure->dims[di] == HYSL_SS ) { - f->nss = size[di]; - } - if ( p->dim_structure->dims[di] == HYSL_FS ) { - f->nfs = size[di]; - } - - } - - } - - free(size); - free(max_size); - return 0; } @@ -441,13 +383,11 @@ int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p, if ( p == NULL ) continue; if ( p->no_index ) continue; - /* Convert coordinates to match rearranged - * panels in memory */ - fs = fs - p->orig_min_fs + p->min_fs; - ss = ss - p->orig_min_ss + p->min_ss; + /* Convert coordinates to panel-relative */ + fs = fs - p->orig_min_fs; + ss = ss - p->orig_min_ss; - image_add_feature(image->features, fs, ss, image, - val, NULL); + image_add_feature(image->features, fs, ss, p, image, val, NULL); } @@ -541,11 +481,11 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p) if ( p == NULL ) continue; if ( p->no_index ) continue; - /* Convert coordinates to match rearranged panels in memory */ - fs = fs - p->orig_min_fs + p->min_fs; - ss = ss - p->orig_min_ss + p->min_ss; + /* Convert coordinates to panel-relative */ + fs = fs - p->orig_min_fs; + ss = ss - p->orig_min_ss; - image_add_feature(image->features, fs, ss, image, val, + image_add_feature(image->features, fs, ss, p, image, val, NULL); } @@ -791,9 +731,6 @@ static void write_location(hid_t fh, struct detector *det, float *data, for ( pi=0; pin_panels; pi++ ) { hsize_t f_offset[2], f_count[2]; - hsize_t m_offset[2], m_count[2]; - hsize_t dimsm[2]; - hid_t memspace; struct panel p; int r; @@ -818,18 +755,7 @@ static void write_location(hid_t fh, struct detector *det, float *data, return; } - m_offset[0] = p.min_ss; - m_offset[1] = p.min_fs; - m_count[0] = p.max_ss - p.min_ss +1; - m_count[1] = p.max_fs - p.min_fs +1; - - dimsm[0] = det->max_ss + 1; - dimsm[1] = det->max_fs + 1; - memspace = H5Screate_simple(2, dimsm, NULL); - - r = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, - m_offset, NULL, m_count, NULL); - r = H5Dwrite(dh, H5T_NATIVE_FLOAT, memspace, + r = H5Dwrite(dh, H5T_NATIVE_FLOAT, H5S_ALL, dh_dataspace, H5P_DEFAULT, data); if ( r < 0 ) { ERROR("Couldn't write data\n"); @@ -837,13 +763,11 @@ static void write_location(hid_t fh, struct detector *det, float *data, H5Dclose(dh); H5Sclose(dh_dataspace); H5Sclose(sh); - H5Sclose(memspace); H5Fclose(fh); return; } H5Sclose(dh_dataspace); - H5Sclose(memspace); } H5Pclose(ph); H5Sclose(sh); @@ -961,34 +885,6 @@ static void write_spectrum(hid_t fh, struct sample *spectrum, int spectrum_size, } -static float *make_array_from_dp(const struct image *image) -{ - int i; - float *data; - - data = malloc(image->width * image->height * sizeof(float)); - if ( data == NULL ) { - ERROR("Failed to allocate data\n"); - return NULL; - } - - for ( i=0; idet->n_panels; i++ ) { - - int fs, ss; - struct panel *p = &image->det->panels[i]; - - for ( ss=0; ssh; ss++ ) { - for ( fs=0; fsw; fs++ ) { - int idx = p->min_fs+fs + image->width*(p->min_ss+ss); - data[idx] = image->dp[i][fs + p->w*ss]; - } - } - } - - return data; -} - - int hdf5_write_image(const char *filename, const struct image *image, char *element) { @@ -998,16 +894,12 @@ int hdf5_write_image(const char *filename, const struct image *image, struct hdf5_write_location *locations; int num_locations; const char *ph_en_loc; - float *data; if ( image->det == NULL ) { ERROR("Geometry not available\n"); return 1; } - data = make_array_from_dp(image); - if ( data == NULL ) return 1; - fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); if ( fh < 0 ) { ERROR("Couldn't create file: %s\n", filename); @@ -1024,7 +916,7 @@ int hdf5_write_image(const char *filename, const struct image *image, &num_locations); for ( li=0; lidet, data, &locations[li]); + write_location(fh, image->det, image->dp[li], &locations[li]); } if ( image->beam == NULL @@ -1047,7 +939,6 @@ int hdf5_write_image(const char *filename, const struct image *image, for ( li=0; lidp = malloc(det->n_panels * sizeof(float *)); - image->bad = malloc(det->n_panels * sizeof(int *)); - image->sat = malloc(det->n_panels * sizeof(float *)); - if ( (image->dp == NULL) || (image->bad == NULL) - || (image->sat == NULL) ) - { - ERROR("Failed to allocate panels.\n"); - return 1; + badmap = malloc(p->w*p->h*sizeof(int)); + if ( badmap == NULL ) { + ERROR("Failed to allocate bad mask for panel %s\n", + p->name); + return NULL; } - for ( pi=0; pin_panels; pi++ ) { - - struct panel *p; - int fs, ss; - - p = &det->panels[pi]; - image->dp[pi] = malloc(p->w*p->h*sizeof(float)); - image->bad[pi] = calloc(p->w*p->h, sizeof(int)); - image->sat[pi] = malloc(p->w*p->h*sizeof(float)); - if ( (image->dp[pi] == NULL) || (image->bad[pi] == NULL) - || (image->sat[pi] == NULL) ) - { - ERROR("Failed to allocate panel\n"); - return 1; - } - - for ( ss=0; ssh; ss++ ) { - for ( fs=0; fsw; fs++ ) { - - int idx; - int cfs, css; - int bad = 0; - - cfs = fs+p->min_fs; - css = ss+p->min_ss; - idx = cfs + css*image->width; - - image->dp[pi][fs+p->w*ss] = data[idx]; + for ( ss=0; ssh; ss++ ) { + for ( fs=0; fsw; fs++ ) { - if ( sat != NULL ) { - image->sat[pi][fs+p->w*ss] = sat[idx]; - } else { - image->sat[pi][fs+p->w*ss] = INFINITY; - } + int bad = 0; + int f; - if ( p->no_index ) bad = 1; - - if ( in_bad_region(det, cfs, css) ) { - bad = 1; - } + if ( p->no_index ) bad = 1; - if ( flags != NULL ) { - - int f; - - f = flags[idx]; + if ( in_bad_region(det, p, fs, ss) ) { + bad = 1; + } - /* Bad if it's missing any of the "good" bits */ - if ( (f & image->det->mask_good) - != image->det->mask_good ) bad = 1; + f = flags[fs+p->w*ss]; - /* Bad if it has any of the "bad" bits. */ - if ( f & image->det->mask_bad ) bad = 1; + /* Bad if it's missing any of the "good" bits */ + if ( (f & det->mask_good) != det->mask_good ) bad = 1; - } - image->bad[pi][fs+p->w*ss] = bad; + /* Bad if it has any of the "bad" bits. */ + if ( f & det->mask_bad ) bad = 1; - } - } + badmap[fs+p->w*ss] = bad; } + } - return 0; + return badmap; } @@ -1448,6 +1299,11 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element, herr_t r; float *buf; int fail; + hsize_t *size; + hsize_t *max_size; + hid_t sh; + int sh_dim; + int w, h; if ( element == NULL ) { fail = hdfile_set_first_image(f, "/"); @@ -1460,13 +1316,26 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element, return 1; } - image->width = f->nfs; - image->height = f->nss; + sh = H5Dget_space(f->dh); + sh_dim = H5Sget_simple_extent_ndims(sh); + + if ( sh_dim != 2 ) { + ERROR("Dataset is not two-dimensional\n"); + return -1; + } - buf = malloc(sizeof(float)*f->nfs*f->nss); + size = malloc(sh_dim*sizeof(hsize_t)); + max_size = malloc(sh_dim*sizeof(hsize_t)); + H5Sget_simple_extent_dims(sh, size, max_size); + H5Sclose(sh); + w = size[1]; + h = size[0]; + free(size); + free(max_size); + buf = malloc(sizeof(float)*w*h); r = H5Dread(f->dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, buf); + H5P_DEFAULT, buf); if ( r < 0 ) { ERROR("Couldn't read data\n"); free(buf); @@ -1476,9 +1345,8 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element, if ( image->det != NULL ) { ERROR("WARNING: hdf5_read() called with geometry structure.\n"); } - image->det = simple_geometry(image); + image->det = simple_geometry(image, w, h); - unpack_panels(image, image->det, buf, NULL, NULL); if ( satcorr ) debodge_saturation(f, image); if ( image->beam != NULL ) { @@ -1501,210 +1369,10 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element, } -static hsize_t *first_two_dims(hsize_t *in, struct dim_structure *ds) -{ - int i, j; - hsize_t *out = malloc(2*sizeof(hsize_t)); - - if ( out == NULL ) return NULL; - - j = 0; - for ( i=0; inum_dims; i++ ) { - if ( (ds->dims[i] == HYSL_FS) || (ds->dims[i] == HYSL_SS) ) { - out[j++] = in[i]; - } - } - return out; -} - - -static int load_mask(struct hdfile *f, struct event *ev, char *mask, - const char *mask_file, - const char *pname, struct image *image, - size_t p_w, size_t sum_p_h, uint16_t *flags, - hsize_t *in_f_offset, hsize_t *in_f_count, - hsize_t *m_offset, hsize_t *m_count, - struct dim_structure *dim_struct) -{ - hid_t mask_dataspace, mask_dh; - int exists; - int check, r; - hid_t memspace; - hsize_t dimsm[2]; - hid_t fh; - hsize_t *f_offset, *f_count; - - if ( mask_file != NULL ) { - - fh = H5Fopen(mask_file, H5F_ACC_RDONLY, H5P_DEFAULT); - if ( fh < 0 ) { - ERROR("Couldn't open mask file '%s'\n", mask_file); - return 1; - } - - /* If we have an external map file, we assume it to be a simple - * 2D job */ - f_offset = first_two_dims(in_f_offset, dim_struct); - f_count = first_two_dims(in_f_count, dim_struct); - - } else { - fh = f->fh; - f_offset = in_f_offset; - f_count = in_f_count; - } - - if ( ev != NULL ) { - mask = retrieve_full_path(ev, mask); - } - - exists = check_path_existence(fh, mask); - if ( !exists ) { - ERROR("Cannot find flags for panel %s\n", pname); - goto err; - } - - mask_dh = H5Dopen2(fh, mask, H5P_DEFAULT); - if ( mask_dh <= 0 ) { - ERROR("Couldn't open flags for panel %s\n", pname); - goto err; - } - - mask_dataspace = H5Dget_space(mask_dh); - check = H5Sselect_hyperslab(mask_dataspace, H5S_SELECT_SET, - f_offset, NULL, f_count, NULL); - if ( check < 0 ) { - ERROR("Error selecting mask dataspace for panel %s\n", pname); - goto err; - } - - dimsm[0] = sum_p_h; - dimsm[1] = p_w; - memspace = H5Screate_simple(2, dimsm, NULL); - check = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, - m_offset, NULL, m_count, NULL); - if ( check < 0 ) { - ERROR("Error selecting memory dataspace for panel %s\n", pname); - goto err; - } - - r = H5Dread(mask_dh, H5T_NATIVE_UINT16, memspace, - mask_dataspace, H5P_DEFAULT, flags); - if ( r < 0 ) { - ERROR("Couldn't read flags for panel %s\n", pname); - goto err; - } - - H5Sclose(mask_dataspace); - H5Dclose(mask_dh); - if ( ev != NULL ) free(mask); - - return 0; - -err: - if ( mask_file != NULL ) H5Fclose(fh); - if ( ev != NULL ) free(mask); - return 1; -} - - -static int load_satmap(struct hdfile *f, struct event *ev, char *satmap, - const char *satmap_file, - const char *pname, struct image *image, - size_t p_w, size_t sum_p_h, float *smap, - hsize_t *in_f_offset, hsize_t *in_f_count, - hsize_t *m_offset, hsize_t *m_count, - struct dim_structure *dim_struct) -{ - hid_t satmap_dataspace, satmap_dh; - int exists; - int check, r; - hid_t memspace; - hsize_t dimsm[2]; - hid_t fh; - hsize_t *f_offset, *f_count; - - if ( satmap_file != NULL ) { - - fh = H5Fopen(satmap_file, H5F_ACC_RDONLY, H5P_DEFAULT); - if ( fh < 0 ) { - ERROR("Couldn't open satmap file '%s'\n", satmap_file); - return 1; - } - - /* If we have an external map file, we assume it to be a simple - * 2D job */ - f_offset = first_two_dims(in_f_offset, dim_struct); - f_count = first_two_dims(in_f_count, dim_struct); - - } else { - fh = f->fh; - f_offset = in_f_offset; - f_count = in_f_count; - } - - if ( ev != NULL ) { - satmap = retrieve_full_path(ev, satmap); - } - - exists = check_path_existence(fh, satmap); - if ( !exists ) { - ERROR("Cannot find satmap for panel %s\n", pname); - goto err; - } - - satmap_dh = H5Dopen2(fh, satmap, H5P_DEFAULT); - if ( satmap_dh <= 0 ) { - ERROR("Couldn't open satmap for panel %s\n", pname); - goto err; - } - - satmap_dataspace = H5Dget_space(satmap_dh); - check = H5Sselect_hyperslab(satmap_dataspace, H5S_SELECT_SET, - f_offset, NULL, f_count, NULL); - if ( check < 0 ) { - ERROR("Error selecting satmap dataspace for panel %s\n", pname); - goto err; - } - - dimsm[0] = sum_p_h; - dimsm[1] = p_w; - memspace = H5Screate_simple(2, dimsm, NULL); - check = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, - m_offset, NULL, m_count, NULL); - if ( check < 0 ) { - ERROR("Error selecting memory dataspace for panel %s\n", pname); - goto err; - } - - r = H5Dread(satmap_dh, H5T_NATIVE_FLOAT, memspace, - satmap_dataspace, H5P_DEFAULT, smap); - if ( r < 0 ) { - ERROR("Couldn't read satmap for panel %s\n", pname); - goto err; - } - - H5Sclose(satmap_dataspace); - H5Dclose(satmap_dh); - if ( ev != NULL ) free(satmap); - - return 0; - -err: - if ( satmap_file != NULL ) H5Fclose(fh); - if ( ev != NULL ) free(satmap); - return 1; -} - - int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, int satcorr) { herr_t r; - float *buf; - uint16_t *flags; - float *smap; - int sum_p_h; - int p_w; int pi; int i; @@ -1713,51 +1381,21 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, return 1; } - p_w = image->det->panels[0].w; - sum_p_h = 0; - - for ( pi=0; pidet->n_panels; pi++ ) { - - if ( image->det->panels[pi].w != p_w ) { - ERROR("Panels must have the same width."); - return 1; - } - - sum_p_h += image->det->panels[pi].h; - - } - - buf = malloc(sizeof(float)*p_w*sum_p_h); - if ( buf == NULL ) { - ERROR("Failed to allocate memory for image\n"); - return 1; - } - image->width = p_w; - image->height = sum_p_h; - - flags = calloc(p_w*sum_p_h,sizeof(uint16_t)); - if ( flags == NULL ) { - ERROR("Failed to allocate memory for flags\n"); - return 1; - } - - smap = calloc(p_w*sum_p_h,sizeof(float)); - if ( smap == NULL ) { - ERROR("Failed to allocate memory for satmap\n"); + image->dp = malloc(image->det->n_panels*sizeof(float *)); + image->bad = malloc(image->det->n_panels*sizeof(int *)); + image->sat = malloc(image->det->n_panels*sizeof(float *)); + if ( (image->dp==NULL) || (image->bad==NULL) || (image->sat==NULL) ) { + ERROR("Failed to allocate data arrays.\n"); return 1; } - for ( i=0; idet->n_panels; pi++ ) { - int data_width, data_height; hsize_t *f_offset, *f_count; int hsi; struct dim_structure *hsd; - hsize_t m_offset[2], m_count[2]; - hsize_t dimsm[2]; herr_t check; - hid_t dataspace, memspace; + hid_t dataspace; int fail; struct panel *p; @@ -1807,25 +1445,14 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, return 1; } - data_width = f->nfs; - data_height = f->nss; - - if ( (data_width < p->w ) - || (data_height < p->h) ) - { - ERROR("Data size doesn't match panel geometry size" - " - rejecting image.\n"); - ERROR("Panel name: %s. Data size: %i,%i. " - "Geometry size: %i,%i\n", - p->name, data_width, data_height, p->w, p->h); - return 1; - } - + /* Determine where to read the data from in the file */ hsd = image->det->panels[pi].dim_structure; - f_offset = malloc(hsd->num_dims*sizeof(hsize_t)); f_count = malloc(hsd->num_dims*sizeof(hsize_t)); - + if ( (f_offset == NULL) || (f_count == NULL ) ) { + ERROR("Failed to allocate offset or count.\n"); + return 1; + } for ( hsi=0; hsinum_dims; hsi++ ) { if ( hsd->dims[hsi] == HYSL_FS ) { @@ -1844,76 +1471,74 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, } + /* Set up dataspace for file */ dataspace = H5Dget_space(f->dh); check = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, f_offset, NULL, f_count, NULL); if ( check < 0 ) { ERROR("Error selecting file dataspace for panel %s\n", p->name); - free(buf); return 1; } - m_offset[0] = p->min_ss; - m_offset[1] = p->min_fs; - m_count[0] = p->max_ss - p->min_ss +1; - m_count[1] = p->max_fs - p->min_fs +1; - dimsm[0] = sum_p_h; - dimsm[1] = p_w; - memspace = H5Screate_simple(2, dimsm, NULL); - check = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, - m_offset, NULL, m_count, NULL); - if ( check < 0 ) { - ERROR("Error selecting memory dataspace for panel %s\n", - p->name); - free(buf); + image->dp[pi] = malloc(p->w*p->h*sizeof(float)); + image->sat[pi] = malloc(p->w*p->h*sizeof(float)); + if ( (image->dp[pi] == NULL) || (image->sat[pi] == NULL) ) { + ERROR("Failed to allocate panel %s\n", p->name); free(f_offset); free(f_count); return 1; } + for ( i=0; iw*p->h; i++ ) image->sat[pi][i] = INFINITY; - r = H5Dread(f->dh, H5T_NATIVE_FLOAT, memspace, dataspace, - H5P_DEFAULT, buf); + r = H5Dread(f->dh, H5T_NATIVE_FLOAT, H5S_ALL, dataspace, + H5P_DEFAULT, image->dp[pi]); if ( r < 0 ) { ERROR("Couldn't read data for panel %s\n", p->name); - free(buf); free(f_offset); free(f_count); return 1; } - H5Dclose(f->dh); - f->data_open = 0; - H5Sclose(dataspace); - H5Sclose(memspace); if ( p->mask != NULL ) { - if ( load_mask(f, ev, p->mask, p->mask_file, p->name, - image, p_w, sum_p_h, flags, - f_offset, f_count, m_offset, m_count, - hsd) ) { - ERROR("Error loading bad pixel mask!\n"); + int *flags = malloc(p->w*p->h*sizeof(int)); + r = H5Dread(f->dh, H5T_NATIVE_FLOAT, H5S_ALL, dataspace, + H5P_DEFAULT, flags); + if ( r < 0 ) { + ERROR("Couldn't read flags for panel %s\n", + p->name); + free(f_offset); + free(f_count); + return 1; } + image->bad[pi] = make_badmask(flags, p, image->det); + } else { + image->bad[pi] = calloc(p->w*p->h, sizeof(int)); } if ( p->satmap != NULL ) { - if ( load_satmap(f, ev, p->satmap, p->satmap_file, - p->name, image, p_w, sum_p_h, smap, - f_offset, f_count, m_offset, m_count, - hsd) ) - { - ERROR("Error loading saturation map!\n"); + r = H5Dread(f->dh, H5T_NATIVE_FLOAT, H5S_ALL, dataspace, + H5P_DEFAULT, image->sat[pi]); + if ( r < 0 ) { + ERROR("Couldn't read satmap for panel %s\n", + p->name); + free(f_offset); + free(f_count); + return 1; } } + H5Sclose(dataspace); free(f_offset); free(f_count); } + H5Dclose(f->dh); + f->data_open = 0; fill_in_values(image->det, f, ev); - unpack_panels(image, image->det, buf, flags, smap); if ( satcorr ) debodge_saturation(f, image); if ( image->beam != NULL ) { @@ -1932,10 +1557,6 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev, fill_in_adu(image); - free(buf); - free(flags); - free(smap); - return 0; } diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c index 82ad8f7e..7bb4cede 100644 --- a/libcrystfel/src/image.c +++ b/libcrystfel/src/image.c @@ -3,12 +3,12 @@ * * Handle images and image features * - * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: * 2014 Kenneth Beyerlein - * 2011-2014 Thomas White + * 2011-2016 Thomas White * * This file is part of CrystFEL. * @@ -59,6 +59,7 @@ struct _imagefeaturelist void image_add_feature(ImageFeatureList *flist, double fs, double ss, + struct panel *p, struct image *parent, double intensity, const char *name) { if ( flist->features ) { @@ -72,6 +73,7 @@ void image_add_feature(ImageFeatureList *flist, double fs, double ss, flist->features[flist->n_features].fs = fs; flist->features[flist->n_features].ss = ss; + flist->features[flist->n_features].p = p; flist->features[flist->n_features].intensity = intensity; flist->features[flist->n_features].parent = parent; flist->features[flist->n_features].name = name; @@ -145,27 +147,17 @@ void image_feature_list_free(ImageFeatureList *flist) struct imagefeature *image_feature_closest(ImageFeatureList *flist, double fs, double ss, - double *d, int *idx, - struct detector *det) + struct panel *p, double *d, int *idx) { int i; double dmin = +HUGE_VAL; int closest = 0; - struct panel *p1; - - p1 = find_panel(det, fs, ss); for ( i=0; in_features; i++ ) { double ds; - struct panel *p2; - p2 = find_panel(det, flist->features[i].fs, - flist->features[i].ss); - - if ( p1 != p2 ) { - continue; - } + if ( p != flist->features[i].p ) continue; ds = distance(flist->features[i].fs, flist->features[i].ss, fs, ss); @@ -189,19 +181,16 @@ struct imagefeature *image_feature_closest(ImageFeatureList *flist, Reflection *image_reflection_closest(RefList *rlist, - double fs, double ss, + double fs, double ss, struct panel *p, struct detector *det, double *d) { double dmin = HUGE_VAL; Reflection *closest = NULL; - struct panel *p1; Reflection *refl; RefListIterator *iter; - p1 = find_panel(det, fs, ss); - for ( refl = first_refl(rlist, &iter); refl != NULL; refl = next_refl(refl, iter) ) @@ -211,12 +200,9 @@ Reflection *image_reflection_closest(RefList *rlist, double rfs, rss; get_detector_pos(refl, &rfs, &rss); + p2 = get_panel(refl); - p2 = find_panel(det, rfs, rss); - - if ( p1 != p2 ) { - continue; - } + if ( p != p2 ) continue; ds = distance(rfs, rss, fs, ss); diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index ddbfc9dc..89c01785 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -3,11 +3,11 @@ * * Handle images and image features * - * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2009-2013 Thomas White + * 2009-2016 Thomas White * 2014 Valerio Mariani * * @@ -73,7 +73,7 @@ struct imagefeature { struct image *parent; double fs; double ss; - char *pn; + struct panel *p; double intensity; /* Reciprocal space coordinates (m^-1 of course) of this feature */ @@ -188,9 +188,6 @@ struct image { double div; /* Divergence in radians */ double bw; /* Bandwidth as a fraction */ - int width; - int height; - /* Detected peaks */ long long int num_peaks; long long int num_saturated_peaks; @@ -208,6 +205,7 @@ extern ImageFeatureList *image_feature_list_new(void); extern void image_feature_list_free(ImageFeatureList *flist); extern void image_add_feature(ImageFeatureList *flist, double x, double y, + struct panel *p, struct image *parent, double intensity, const char *name); @@ -215,10 +213,12 @@ extern void image_remove_feature(ImageFeatureList *flist, int idx); extern struct imagefeature *image_feature_closest(ImageFeatureList *flist, double fs, double ss, - double *d, int *idx, - struct detector *det); + struct panel *p, + double *d, int *idx); + extern Reflection *image_reflection_closest(RefList *rlist, double fs, double ss, + struct panel *p, struct detector *det, double *d); diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index 6b530b61..c8c86414 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -224,7 +224,8 @@ void map_all_peaks(struct image *image) f = image_get_feature(image->features, i); if ( f == NULL ) continue; - r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda); + r = get_q_for_panel(f->p, f->fs, f->ss, + NULL, 1.0/image->lambda); f->rx = r.u; f->ry = r.v; f->rz = r.w; } @@ -352,7 +353,8 @@ static int delete_explained_peaks(struct image *image, Crystal *cr) nspots++; /* Reciprocal space position of found peak */ - q = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda); + q = get_q_for_panel(f->p, f->fs, f->ss, + NULL, 1.0/image->lambda); /* Decimal and fractional Miller indices of nearest * reciprocal lattice point */ diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c index 7380f836..d50f8d6b 100644 --- a/libcrystfel/src/integration.c +++ b/libcrystfel/src/integration.c @@ -3,11 +3,11 @@ * * Integration of intensities * - * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2010-2014 Thomas White + * 2010-2016 Thomas White * * This file is part of CrystFEL. * @@ -271,8 +271,8 @@ static void show_peak_box(struct intcontext *ic, struct peak_box *bx, get_indices(bx->refl, &h, &k, &l); get_detector_pos(bx->refl, &fs, &ss); /* Convert coordinates to match arrangement of panels in HDF5 file */ - fs = fs - bx->p->min_fs + bx->p->orig_min_fs; - ss = ss - bx->p->min_ss + bx->p->orig_min_ss; + fs = fs + bx->p->orig_min_fs; + ss = ss + bx->p->orig_min_ss; printw("Indices %i %i %i\nPanel %s\nPosition fs = %.1f, ss = %.1f\n\n", h, k, l, bx->p->name, fs, ss); @@ -1280,6 +1280,12 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list) set_redundancy(refl, 0); get_detector_pos(refl, &pfs, &pss); + p = get_panel(refl); + pn = panel_number(ic->image->det, p); + if ( pn == ic->image->det->n_panels ) { + ERROR("Couldn't find panel %p\n", p); + continue; + } /* Explicit truncation of digits after the decimal point. * This is actually the correct thing to do here, not @@ -1289,12 +1295,11 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list) * belongs to pixel index 2. */ fid_fs = pfs; fid_ss = pss; - pn = find_panel_number(ic->image->det, fid_fs, fid_ss); - p = &ic->image->det->panels[pn]; - cfs = (fid_fs-p->min_fs) - ic->halfw; - css = (fid_ss-p->min_ss) - ic->halfw; + cfs = fid_fs - ic->halfw; + css = fid_ss - ic->halfw; + /* Add the box */ bx = add_box(ic); bx->refl = refl; bx->cfs = cfs; @@ -1414,6 +1419,12 @@ static void integrate_rings_once(Reflection *refl, struct image *image, set_redundancy(refl, 0); get_detector_pos(refl, &pfs, &pss); + p = get_panel(refl); + pn = panel_number(image->det, p); + if ( pn == image->det->n_panels ) { + ERROR("Couldn't find panel %p\n", p); + return; + } /* Explicit truncation of digits after the decimal point. * This is actually the correct thing to do here, not @@ -1423,11 +1434,9 @@ static void integrate_rings_once(Reflection *refl, struct image *image, * belongs to pixel index 2. */ fid_fs = pfs; fid_ss = pss; - pn = find_panel_number(image->det, fid_fs, fid_ss); - p = &image->det->panels[pn]; - cfs = (fid_fs-p->min_fs) - ic->halfw; - css = (fid_ss-p->min_ss) - ic->halfw; + cfs = fid_fs - ic->halfw; + css = fid_ss - ic->halfw; bx = add_box(ic); bx->refl = refl; diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c index 8a546630..f1a1e8ae 100644 --- a/libcrystfel/src/mosflm.c +++ b/libcrystfel/src/mosflm.c @@ -3,13 +3,13 @@ * * Invoke the DPS auto-indexing algorithm through MOSFLM * - * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * * Authors: * 2010 Richard Kirian - * 2010-2014 Thomas White + * 2010-2016 Thomas White * 2014 Takanori Nakane * * This file is part of CrystFEL. @@ -373,22 +373,18 @@ static void write_spt(struct image *image, const char *filename) for ( i=0; ifeatures, i); if ( f == NULL ) continue; - p = find_panel(image->det, f->fs, f->ss); - if ( p == NULL ) continue; + xs = f->fs*f->p->fsx + f->ss*f->p->ssx; + ys = f->fs*f->p->fsy + f->ss*f->p->ssy; + rx = (xs + f->p->cnx) / f->p->res; + ry = (ys + f->p->cny) / f->p->res; - xs = (f->fs-p->min_fs)*p->fsx + (f->ss-p->min_ss)*p->ssx; - ys = (f->fs-p->min_fs)*p->fsy + (f->ss-p->min_ss)*p->ssy; - rx = (xs + p->cnx) / p->res; - ry = (ys + p->cny) / p->res; - - x = -rx*fclen/p->clen; - y = ry*fclen/p->clen; /* Peak positions in m */ + x = -rx*fclen/f->p->clen; + y = ry*fclen/f->p->clen; /* Peak positions in m */ fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n", x*1e3, y*1e3, 0.0, 0.0, 1000.0, 10.0); diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c index 1b865bc8..7fc30ef7 100644 --- a/libcrystfel/src/peaks.c +++ b/libcrystfel/src/peaks.c @@ -3,12 +3,12 @@ * * Peak search and other image analysis * - * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * * Authors: - * 2010-2014 Thomas White + * 2010-2016 Thomas White * 2012 Kenneth Beyerlein * 2011 Andrew Martin * 2011 Richard Kirian @@ -69,10 +69,7 @@ static int cull_peaks_in_panel(struct image *image, struct panel *p) f = image_get_feature(image->features, i); if ( f == NULL ) continue; - if ( f->fs < p->min_fs ) continue; - if ( f->fs > p->max_fs ) continue; - if ( f->ss < p->min_ss ) continue; - if ( f->ss > p->max_ss ) continue; + if ( f->p != p ) continue; /* How many peaks are in the same column? */ ncol = 0; @@ -145,8 +142,7 @@ static int cull_peaks(struct image *image) static void add_crystal_to_mask(struct image *image, struct panel *p, - double ir_inn, int w, int h, - int *mask, Crystal *cr) + double ir_inn, int *mask, Crystal *cr) { Reflection *refl; RefListIterator *iter; @@ -156,19 +152,13 @@ static void add_crystal_to_mask(struct image *image, struct panel *p, refl != NULL; refl = next_refl(refl, iter) ) { - struct panel *p2; double pk2_fs, pk2_ss; signed int dfs, dss; - double pk2_cfs, pk2_css; get_detector_pos(refl, &pk2_fs, &pk2_ss); /* Determine if reflection is in the same panel */ - p2 = find_panel(image->det, pk2_fs, pk2_ss); - if ( p2 != p ) continue; - - pk2_cfs = pk2_fs - p->min_fs; - pk2_css = pk2_ss - p->min_ss; + if ( get_panel(refl) != p ) continue; for ( dfs=-ir_inn; dfs<=ir_inn; dfs++ ) { for ( dss=-ir_inn; dss<=ir_inn; dss++ ) { @@ -178,16 +168,16 @@ static void add_crystal_to_mask(struct image *image, struct panel *p, /* In peak region for this peak? */ if ( dfs*dfs + dss*dss > ir_inn*ir_inn ) continue; - fs = pk2_cfs + dfs; - ss = pk2_css + dss; + fs = pk2_fs + dfs; + ss = pk2_ss + dss; /* On panel? */ - if ( fs >= w ) continue; - if ( ss >= h ) continue; + if ( fs >= p->w ) continue; + if ( ss >= p->h ) continue; if ( fs < 0 ) continue; if ( ss < 0 ) continue; - mask[fs + ss*w]++; + mask[fs + ss*p->w]++; } } @@ -200,19 +190,16 @@ static void add_crystal_to_mask(struct image *image, struct panel *p, int *make_BgMask(struct image *image, struct panel *p, double ir_inn) { int *mask; - int w, h; int i; - w = p->max_fs - p->min_fs + 1; - h = p->max_ss - p->min_ss + 1; - mask = calloc(w*h, sizeof(int)); + mask = calloc(p->w*p->h, sizeof(int)); if ( mask == NULL ) return NULL; if ( image->crystals == NULL ) return mask; for ( i=0; in_crystals; i++ ) { add_crystal_to_mask(image, p, ir_inn, - w, h, mask, image->crystals[i]); + mask, image->crystals[i]); } return mask; @@ -221,7 +208,8 @@ int *make_BgMask(struct image *image, struct panel *p, double ir_inn) /* Returns non-zero if peak has been vetoed. * i.e. don't use result if return value is not zero. */ -static int integrate_peak(struct image *image, int cfs, int css, +static int integrate_peak(struct image *image, + int p_cfs, int p_css, struct panel *p, double *pfs, double *pss, double *intensity, double *sigma, double ir_inn, double ir_mid, double ir_out, @@ -234,30 +222,26 @@ static int integrate_peak(struct image *image, int cfs, int css, double fsct, ssct; double bg_tot = 0.0; int bg_counts = 0; - struct panel *p; double bg_mean, bg_var; double bg_tot_sq = 0.0; double var; double aduph; - int p_cfs, p_css; - signed int pn; - - pn = find_panel_number(image->det, cfs, css); - if ( pn == -1 ) return 2; - p = &image->det->panels[pn]; + int pn; if ( saturated != NULL ) *saturated = 0; - /* Determine regions where there is expected to be a peak */ - p_cfs = cfs - p->min_fs; - p_css = css - p->min_ss; /* Panel-relative coordinates */ - aduph = p->adu_per_photon; lim_sq = pow(ir_inn, 2.0); mid_lim_sq = pow(ir_mid, 2.0); out_lim_sq = pow(ir_out, 2.0); + pn = panel_number(image->det, p); + if ( pn == image->det->n_panels ) { + ERROR("Couldn't find panel %p\n", p); + return 20; + } + /* Estimate the background */ for ( dss=-ir_out; dss<=+ir_out; dss++ ) { for ( dfs=-ir_out; dfs<=+ir_out; dfs++ ) { @@ -328,8 +312,8 @@ static int integrate_peak(struct image *image, int cfs, int css, pk_counts++; pk_total += val; - fsct += val*(cfs+dfs); - ssct += val*(css+dss); + fsct += val*(p_cfs+dfs); + ssct += val*(p_css+dss); } } @@ -462,7 +446,7 @@ static void search_peaks_in_panel(struct image *image, float threshold, assert(mask_ss >= 0); /* Centroid peak and get better coordinates. */ - r = integrate_peak(image, mask_fs+p->min_fs, mask_ss+p->min_ss, + r = integrate_peak(image, mask_fs, mask_ss, p, &f_fs, &f_ss, &intensity, &sigma, ir_inn, ir_mid, ir_out, &saturated); @@ -473,8 +457,8 @@ static void search_peaks_in_panel(struct image *image, float threshold, } /* It is possible for the centroid to fall outside the image */ - if ( (f_fs < p->min_fs) || (f_fs > p->max_fs) - || (f_ss < p->min_ss) || (f_ss > p->max_ss) ) { + if ( (f_fs < 0) || (f_fs > p->w) + || (f_ss < 0) || (f_ss > p->h) ) { nrej_fra++; continue; } @@ -485,8 +469,7 @@ static void search_peaks_in_panel(struct image *image, float threshold, } /* Check for a nearby feature */ - image_feature_closest(image->features, f_fs, f_ss, &d, &idx, - image->det); + image_feature_closest(image->features, f_fs, f_ss, p, &d, &idx); if ( d < 2.0*ir_inn ) { nrej_pro++; continue; @@ -501,7 +484,7 @@ static void search_peaks_in_panel(struct image *image, float threshold, } /* Add using "better" coordinates */ - image_add_feature(image->features, f_fs, f_ss, + image_add_feature(image->features, f_fs, f_ss, p, image, intensity, NULL); nacc++; @@ -578,7 +561,8 @@ int peak_sanity_check(struct image *image, Crystal **crystals, int n_cryst) n_feat++; /* Reciprocal space position of found peak */ - q = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda); + q = get_q_for_panel(f->p, f->fs, f->ss, + NULL, 1.0/image->lambda); for ( j=0; jfeatures, i); @@ -651,13 +634,7 @@ void validate_peaks(struct image *image, double min_snr, continue; } - p = find_panel(image->det, f->fs, f->ss); - if ( p == NULL ) { - n_wtf++; - continue; - } - - r = integrate_peak(image, f->fs, f->ss, + r = integrate_peak(image, f->fs, f->ss, f->p, &f_fs, &f_ss, &intensity, &sigma, ir_inn, ir_mid, ir_out, &saturated); if ( r ) { @@ -673,8 +650,8 @@ void validate_peaks(struct image *image, double min_snr, } /* It is possible for the centroid to fall outside the image */ - if ( (f_fs < p->min_fs) || (f_fs > p->max_fs) - || (f_ss < p->min_ss) || (f_ss > p->max_ss) ) + if ( (f_fs < 0) || (f_fs > f->p->w) + || (f_ss < 0) || (f_ss > f->p->h) ) { n_dft++; continue; @@ -686,14 +663,15 @@ void validate_peaks(struct image *image, double min_snr, } /* Check for a nearby feature */ - image_feature_closest(flist, f_fs, f_ss, &d, &idx, image->det); + image_feature_closest(flist, f_fs, f_ss, f->p, &d, &idx); if ( d < 2.0*ir_inn ) { n_prx++; continue; } /* Add using "better" coordinates */ - image_add_feature(flist, f_fs, f_ss, image, intensity, NULL); + image_add_feature(flist, f_fs, f_ss, f->p, image, intensity, + NULL); } diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c index 70345803..743b4d04 100644 --- a/libcrystfel/src/predict-refine.c +++ b/libcrystfel/src/predict-refine.c @@ -3,11 +3,11 @@ * * Prediction refinement * - * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2010-2015 Thomas White + * 2010-2016 Thomas White * * This file is part of CrystFEL. * @@ -140,10 +140,10 @@ static void UNUSED write_pairs(const char *filename, struct reflpeak *rps, fs = rps[i].peak->fs; ss = rps[i].peak->ss; + p = rps[i].panel; - p = find_panel(det, fs, ss); - write_fs = fs - p->min_fs + p->orig_min_fs; - write_ss = ss - p->min_ss + p->orig_min_ss; + write_fs = fs + p->orig_min_fs; + write_ss = ss + p->orig_min_ss; fprintf(fh, "%7.2f %7.2f dev r,x,y: %9f %9f %9f %9f\n", write_fs, write_ss, @@ -229,7 +229,6 @@ static int pair_peaks(struct image *image, Crystal *cr, struct imagefeature *f; double h, k, l, hd, kd, ld; Reflection *refl; - struct panel *p; /* Assume all image "features" are genuine peaks */ f = image_get_feature(image->features, i); @@ -258,12 +257,11 @@ static int pair_peaks(struct image *image, Crystal *cr, * in how far away it is from the peak location. * The predicted position and excitation errors will be * filled in by update_partialities(). */ - p = find_panel(image->det, f->fs, f->ss); - set_panel(refl, p); + set_panel(refl, f->p); rps[n].refl = refl; rps[n].peak = f; - rps[n].panel = p; + rps[n].panel = f->p; n++; } diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c index dffce8f6..0d67bf8c 100644 --- a/libcrystfel/src/stream.c +++ b/libcrystfel/src/stream.c @@ -3,12 +3,12 @@ * * Stream tools * - * Copyright © 2013-2015 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2013-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * * Authors: - * 2010-2015 Thomas White + * 2010-2016 Thomas White * 2014 Valerio Mariani * 2011 Richard Kirian * 2011 Andrew Aquila @@ -106,16 +106,16 @@ static int read_peaks(FILE *fh, struct image *image) return 1; } - add_x = x-p->orig_min_fs+p->min_fs; - add_y = y-p->orig_min_ss+p->min_ss; + add_x = x-p->orig_min_fs; + add_y = y-p->orig_min_ss; image_add_feature(image->features, add_x, add_y, - image, intensity, NULL); + p, image, intensity, NULL); } else { image_add_feature(image->features, x, y, - image, intensity, NULL); + p, image, intensity, NULL); } } @@ -165,10 +165,10 @@ static int read_peaks_2_3(FILE *fh, struct image *image) return 1; } - add_x = x-p->orig_min_fs+p->min_fs; - add_y = y-p->orig_min_ss+p->min_ss; + add_x = x-p->orig_min_fs; + add_y = y-p->orig_min_ss; - image_add_feature(image->features, add_x, add_y, + image_add_feature(image->features, add_x, add_y, p, image, intensity, NULL); } @@ -196,7 +196,8 @@ static int write_peaks(struct image *image, FILE *ofh) f = image_get_feature(image->features, i); if ( f == NULL ) continue; - r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda); + r = get_q_for_panel(f->p, f->fs, f->ss, + NULL, 1.0/image->lambda); q = modulus(r.u, r.v, r.w); if ( image->det != NULL ) { @@ -212,8 +213,8 @@ static int write_peaks(struct image *image, FILE *ofh) /* Convert coordinates to match arrangement of panels in * HDF5 file */ - write_fs = f->fs - p->min_fs + p->orig_min_fs; - write_ss = f->ss - p->min_ss + p->orig_min_ss; + write_fs = f->fs + p->orig_min_fs; + write_ss = f->ss + p->orig_min_ss; fprintf(ofh, "%7.2f %7.2f %10.2f %10.2f\n", write_fs, write_ss, q/1.0e9, f->intensity); @@ -244,28 +245,22 @@ static int write_peaks_2_3(struct image *image, FILE *ofh) struct imagefeature *f; struct rvec r; double q; - struct panel *p; double write_fs, write_ss; f = image_get_feature(image->features, i); if ( f == NULL ) continue; - r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda); + r = get_q_for_panel(f->p, f->fs, f->ss, + NULL, 1.0/image->lambda); q = modulus(r.u, r.v, r.w); - p = find_panel(image->det, f->fs, f->ss); - if ( p == NULL ) { - ERROR("Panel not found\n"); - return 1; - } - /* Convert coordinates to match arrangement of panels in HDF5 * file */ - write_fs = f->fs - p->min_fs + p->orig_min_fs; - write_ss = f->ss - p->min_ss + p->orig_min_ss; + write_fs = f->fs + f->p->orig_min_fs; + write_ss = f->ss + f->p->orig_min_ss; fprintf(ofh, "%7.2f %7.2f %10.2f %10.2f %s\n", - write_fs, write_ss, q/1.0e9, f->intensity, p->name); + write_fs, write_ss, q/1.0e9, f->intensity, f->p->name); } @@ -328,8 +323,8 @@ static RefList *read_stream_reflections_2_3(FILE *fh, struct detector *det) if ( p == NULL ) { ERROR("Couldn't find panel '%s'\n", pn); } else { - write_fs = fs - p->orig_min_fs + p->min_fs; - write_ss = ss - p->orig_min_ss + p->min_ss; + write_fs = fs - p->orig_min_fs; + write_ss = ss - p->orig_min_ss; set_detector_pos(refl, write_fs, write_ss); set_panel(refl, p); } @@ -406,8 +401,8 @@ static RefList *read_stream_reflections_2_1(FILE *fh, struct detector *det) ERROR("No panel at %.2f,%.2f\n", fs, ss); } else { - write_fs = fs - p->orig_min_fs + p->min_fs; - write_ss = ss - p->orig_min_ss + p->min_ss; + write_fs = fs - p->orig_min_fs; + write_ss = ss - p->orig_min_ss; set_detector_pos(refl, write_fs, write_ss); } @@ -480,8 +475,8 @@ static RefList *read_stream_reflections_2_2(FILE *fh, struct detector *det) ERROR("No panel at %.2f,%.2f\n", fs, ss); } else { - write_fs = fs - p->orig_min_fs + p->min_fs; - write_ss = ss - p->orig_min_ss + p->min_ss; + write_fs = fs - p->orig_min_fs; + write_ss = ss - p->orig_min_ss; set_detector_pos(refl, write_fs, write_ss); } @@ -555,8 +550,8 @@ static int write_stream_reflections_2_1(FILE *fh, RefList *list, /* Convert coordinates to match arrangement of panels * in HDF5 file */ - write_fs = fs - p->min_fs + p->orig_min_fs; - write_ss = ss - p->min_ss + p->orig_min_ss; + write_fs = fs + p->orig_min_fs; + write_ss = ss + p->orig_min_ss; fprintf(fh, "%3i %3i %3i %10.2f %s %10.2f %7i " "%6.1f %6.1f\n", @@ -617,8 +612,8 @@ static int write_stream_reflections_2_2(FILE *fh, RefList *list, /* Convert coordinates to match arrangement of panels in HDF5 * file */ - write_fs = fs - p->min_fs + p->orig_min_fs; - write_ss = ss - p->min_ss + p->orig_min_ss; + write_fs = fs + p->orig_min_fs; + write_ss = ss + p->orig_min_ss; fprintf(fh, "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f" " %6.1f %6.1f\n", @@ -654,10 +649,11 @@ static int write_stream_reflections_2_3(FILE *fh, RefList *list, double intensity, esd_i, pk, bg; double fs, ss; double write_fs, write_ss; - struct panel *p = NULL; + struct panel *p; get_indices(refl, &h, &k, &l); get_detector_pos(refl, &fs, &ss); + p = get_panel(refl); intensity = get_intensity(refl); esd_i = get_esd_intensity(refl); pk = get_peak(refl); @@ -666,14 +662,8 @@ static int write_stream_reflections_2_3(FILE *fh, RefList *list, /* Reflections with redundancy = 0 are not written */ if ( get_redundancy(refl) == 0 ) continue; - p = find_panel(image->det,fs,ss); - if ( p == NULL ) { - ERROR("Panel not found\n"); - return 1; - } - - write_fs = fs-p->min_fs+p->orig_min_fs; - write_ss = ss-p->min_ss+p->orig_min_ss; + write_fs = fs+p->orig_min_fs; + write_ss = ss+p->orig_min_ss; fprintf(fh, "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f " diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c index bda60d89..7add6904 100644 --- a/libcrystfel/src/xds.c +++ b/libcrystfel/src/xds.c @@ -3,12 +3,12 @@ * * Invoke xds for crystal autoindexing * - * Copyright © 2013-2015 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2013-2016 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2013 Cornelius Gati * * Authors: - * 2010-2015 Thomas White + * 2010-2016 Thomas White * 2013 Cornelius Gati * * This file is part of CrystFEL. @@ -321,27 +321,19 @@ static void write_spot(struct image *image) { struct imagefeature *f; - struct panel *p; double xs, ys, rx, ry, x, y; f = image_get_feature(image->features, i); if ( f == NULL ) continue; - p = find_panel(image->det, f->fs, f->ss); - if ( p == NULL ) continue; - - xs = (f->fs-p->min_fs)*p->fsx + (f->ss-p->min_ss)*p->ssx; - ys = (f->fs-p->min_fs)*p->fsy + (f->ss-p->min_ss)*p->ssy; - rx = ((xs + p->cnx) / p->res); - ry = ((ys + p->cny) / p->res); - - //printf("xs=%f ys=%f ----> rx=%f ry=%f\n", xs, ys, rx, ry); + xs = f->fs*f->p->fsx + f->ss*f->p->ssx; + ys = f->fs*f->p->fsy + f->ss*f->p->ssy; + rx = (xs + f->p->cnx) / f->p->res; + ry = (ys + f->p->cny) / f->p->res; x = rx; y = ry; /* Peak positions in m */ - //printf("x=%f y=%f\n", x, y); - x = (rx / 70e-6) + 1500; y = (ry / 70e-6) + 1500; -- cgit v1.2.3