/* * zmq.c * * ZMQ data interface * * Copyright © 2017-2018 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: * 2018 Thomas White * 2014 Valerio Mariani * 2017 Stijn de Graaf * * This file is part of CrystFEL. * * CrystFEL is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * CrystFEL is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with CrystFEL. If not, see . * */ #ifdef HAVE_CONFIG_H #include #endif #include #include #include #include #include #include #include #include #include "events.h" #include "image.h" #include "hdf5-file.h" #include "utils.h" struct im_zmq { void *ctx; void *socket; zmq_msg_t msg; msgpack_unpacked unpacked; int unpacked_set; }; struct im_zmq *im_zmq_connect(const char *zmq_address) { struct im_zmq *z; z = malloc(sizeof(struct im_zmq)); if ( z == NULL ) return NULL; z->unpacked_set = 0; z->ctx = zmq_ctx_new(); if ( z->ctx == NULL ) return NULL; z->socket = zmq_socket(z->ctx, ZMQ_REQ); if ( z->socket == NULL ) return NULL; STATUS("Connecting to ZMQ at '%s'\n", zmq_address); if ( zmq_connect(z->socket, zmq_address) == -1 ) { ERROR("ZMQ connection failed: %s\n", zmq_strerror(errno)); return NULL; } STATUS("ZMQ connected.\n"); return z; } msgpack_object *im_zmq_fetch(struct im_zmq *z) { int msg_size; int r; if ( zmq_send(z->socket, "m", 1, 0) == -1 ) { ERROR("ZMQ message send failed: %s\n", zmq_strerror(errno)); return NULL; } zmq_msg_init(&z->msg); msg_size = zmq_msg_recv(&z->msg, z->socket, 0); if ( msg_size == -1 ) { ERROR("ZMQ recieve failed: %s\n", zmq_strerror(errno)); zmq_msg_close(&z->msg); return NULL; } msgpack_unpacked_init(&z->unpacked); r = msgpack_unpack_next(&z->unpacked, zmq_msg_data(&z->msg), msg_size, NULL); if ( r != MSGPACK_UNPACK_SUCCESS ) { ERROR("Msgpack unpack failed: %i\n", r); zmq_msg_close(&z->msg); return NULL; } z->unpacked_set = 1; return &z->unpacked.data; } /* Clean structures ready for next frame */ void im_zmq_clean(struct im_zmq *z) { if ( z->unpacked_set ) { msgpack_unpacked_destroy(&z->unpacked); zmq_msg_close(&z->msg); z->unpacked_set = 0; } } void im_zmq_shutdown(struct im_zmq *z) { if ( z == NULL ) return; zmq_msg_close(&z->msg); zmq_close(z->socket); zmq_ctx_destroy(z->ctx); } static msgpack_object *find_msgpack_kv(msgpack_object *obj, const char *key) { int i; for ( i=0; ivia.map.size; i++ ) { const char *kstr; kstr = obj->via.map.ptr[i].key.via.str.ptr; if ( strcmp(kstr, key) == 0 ) { return &obj->via.map.ptr[i].val; } } return NULL; } /** * get_peaks_msgpack: * @obj: A %msgpack_object containing data in OnDA format * @image: An %image structure * @half_pixel_shift: Non-zero if 0.5 should be added to all peak coordinates * * Get peaks from msgpack_object. The data should be in a map, with the value * given by "peak_list" as an array of arrays. The first of these should contain * the list of fs positions of the peaks, the second the ss positions, and the * third the intensities of the peaks. * * http://c.msgpack.org/c/ provides documentation on msgpack objects * * CrystFEL considers all peak locations to be distances from the corner of the * detector panel, in pixel units, consistent with its description of detector * geometry (see 'man crystfel_geometry'). The software which generates the * CXI files, including Cheetah, may instead consider the peak locations to be * pixel indices in the data array. In this case, the peak coordinates should * have 0.5 added to them. This will be done if @half_pixel_shift is non-zero. * * Returns: non-zero on error, zero otherwise. * */ int get_peaks_msgpack(msgpack_object *obj, struct image *image, int half_pixel_shift) { int num_peaks; int pk; int entry; char *key_str; msgpack_object map_val, peak_list; double peak_offset = half_pixel_shift ? 0.5 : 0.0; if ( obj == NULL ) { ERROR("No MessagePack object to get peaks from.\n"); return 1; } /* Iterate over key-value pairs in msgpack_object * Object has structure: * {"peak_list": [[peak_x], [peak_y], [peak_i]],"key2":val2,...} */ for ( entry=0; entryvia.map.size; entry++ ) { key_str = (char *)obj->via.map.ptr[entry].key.via.str.ptr; /* Check if key matches "peak_list" */ if ( strncmp(key_str, "peak_list", 9) == 0 ) { map_val = obj->via.map.ptr[entry].val; /* Length of peak_x array gives number of peaks */ num_peaks = map_val.via.array.ptr[0].via.array.size; peak_list = map_val; } } if ( image->features != NULL ) { image_feature_list_free(image->features); } image->features = image_feature_list_new(); image->num_peaks = num_peaks; for ( pk=0; pkdet, fs, ss); if ( p == NULL ) continue; if ( p->no_index ) continue; /* Convert coordinates to panel-relative */ fs = fs - p->orig_min_fs; ss = ss - p->orig_min_ss; image_add_feature(image->features, fs, ss, p, image, val, NULL); } return 0; } static void onda_fill_in_clen(struct detector *det) { int i = 0; for ( i=0; in_panels; i++) { struct panel *p = &det->panels[i]; if ( p->clen_from != NULL ) { ERROR("Can't get clen from OnDA yet.\n"); } adjust_centering_for_rail(p); } } /* Equivalent to fill_in_beam_parameters but without reference to imagefiles */ static void onda_fill_in_beam_parameters(struct beam_params *beam, struct image *image) { double eV; if (beam->photon_energy_from == NULL ) { /* Explicit value given */ eV = beam->photon_energy; } else { ERROR("Can't get photon energy from OnDA yet.\n"); eV = 0.0; } image->lambda = ph_en_to_lambda(eV_to_J(eV))*beam->photon_energy_scale; } /* Unpacks the raw panel data from a msgpack_object, applies panel geometry, * and stores the resulting data in an image struct. Object has structure * { * "corr_data": * { * "data": binary_data, * "shape": [data_height, data_width], * ... * ... * }, * "key2": val2, * ... * ... * } */ int unpack_msgpack_data(msgpack_object *obj, struct image *image) { uint16_t *flags = NULL; float *sat = NULL; int pi; int data_width, data_height; double *data; msgpack_object *corr_data_obj; msgpack_object *shape; if ( image->det == NULL ) { ERROR("Geometry not available.\n"); return 1; } corr_data_obj = find_msgpack_kv(obj, "corr_data"); data = (double *)find_msgpack_kv(corr_data_obj, "data")->via.bin.ptr; shape = find_msgpack_kv(corr_data_obj, "shape"); data_height = shape->via.array.ptr[0].via.i64; data_width = shape->via.array.ptr[1].via.i64; 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 ( pi=0; pidet->n_panels; pi++ ) { struct panel *p; int fs, ss; p = &image->det->panels[pi]; image->dp[pi] = malloc(p->w*p->h*sizeof(float)); image->bad[pi] = malloc(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; } if ( (p->orig_min_fs + p->w > data_width) || (p->orig_min_ss + p->h > data_height) ) { ERROR("Panel %s is outside range of data provided\n", p->name); return 1; } for ( ss=0; ssh; ss++) { for ( fs=0; fsw; fs++) { int idx; int cfs, css; int bad = 0; cfs = fs+p->orig_min_fs; css = ss+p->orig_min_ss; idx = cfs + css*data_width; image->dp[pi][fs+p->w*ss] = data[idx]; if ( sat != NULL ) { image->sat[pi][fs+p->w*ss] = sat[idx]; } else { image->sat[pi][fs+p->w*ss] = INFINITY; } if ( p->no_index ) bad = 1; if ( in_bad_region(image->det, p, cfs, css) ) { bad = 1; } if ( flags != NULL ) { int f; f = flags[idx]; if ( (f & image->det->mask_good) != image->det->mask_good ) bad = 1; if ( f & image->det->mask_bad ) bad = 1; } image->bad[pi][fs+p->w*ss] = bad; } } } if ( image->beam != NULL ) { onda_fill_in_beam_parameters(image->beam, image); if ( image->lambda > 1000 ) { ERROR("Warning: Missing or nonsensical wavelength " "(%e m).\n", image->lambda); } } onda_fill_in_clen(image->det); fill_in_adu(image); return 0; }