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-rw-r--r--CMakeLists.txt2
-rw-r--r--src/zmq.c313
-rw-r--r--src/zmq.h48
3 files changed, 362 insertions, 1 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8888be0b..30b34d36 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -257,7 +257,7 @@ list(APPEND CRYSTFEL_EXECUTABLES list_events)
# indexamajig
set(INDEXAMAJIG_SOURCES src/indexamajig.c src/im-sandbox.c src/process_image.c
- src/time-accounts.c)
+ src/time-accounts.c src/zmq.c)
add_executable(indexamajig ${INDEXAMAJIG_SOURCES})
target_include_directories(indexamajig PRIVATE ${COMMON_INCLUDES})
diff --git a/src/zmq.c b/src/zmq.c
new file mode 100644
index 00000000..41bd2eec
--- /dev/null
+++ b/src/zmq.c
@@ -0,0 +1,313 @@
+/*
+ * zmq.c
+ *
+ * ZMQ data interface
+ *
+ * Copyright © 2017-2018 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2018 Thomas White <taw@physics.org>
+ * 2014 Valerio Mariani
+ * 2017 Stijna de Graaf
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <hdf5.h>
+#include <assert.h>
+#include <unistd.h>
+#include <msgpack.h>
+
+#include "events.h"
+#include "image.h"
+#include "hdf5-file.h"
+#include "utils.h"
+
+
+/**
+ * get_peaks_onda:
+ * @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_onda(msgpack_object *obj, struct image *image,
+ int half_pixel_shift)
+{
+
+ int num_peaks;
+ int pk;
+ double peak_offset = half_pixel_shift ? 0.5 : 0.0;
+
+ int entry;
+ char *key_str;
+ msgpack_object map_val, peak_list;
+
+ /* iterate over key-value pairs in msgpack_object
+ * object has structure:
+ * {"peak_list": [[peak_x], [peak_y], [peak_i]],"key2":val2,...}
+ */
+ for ( entry = 0; entry < obj->via.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; pk<num_peaks; pk++ ) {
+
+ float fs, ss, val;
+ struct panel *p;
+
+ /* retrieve data from peak_list and apply half_pixel_shift,
+ * if appropriate */
+ fs = peak_list.via.array.ptr[0].via.array.ptr[pk].via.f64 + peak_offset;
+ ss = peak_list.via.array.ptr[1].via.array.ptr[pk].via.f64 + peak_offset;
+ val = peak_list.via.array.ptr[2].via.array.ptr[pk].via.f64;
+
+ p = find_orig_panel(image->det, 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; i<det->n_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, appliespanel 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 obj_read(msgpack_object *obj, struct image *image)
+{
+
+ uint16_t *flags = NULL;
+ float *sat = NULL;
+ int pi;
+ int entry, sub_entry;
+ int data_width, data_height;
+ double *data;
+ char *key_str;
+ msgpack_object map_val;
+
+ // Iterate over key-value pairs in msgpack_object
+ for ( entry=0; entry<obj->via.map.size; entry++ ) {
+ key_str = (char *)obj->via.map.ptr[entry].key.via.str.ptr;
+ // Check for key is "corr_data"
+ if ( strncmp(key_str, "corr_data", 9) == 0 ) {
+ map_val = obj->via.map.ptr[entry].val;
+ // Iterate over key-value pairs in inner map
+ for ( sub_entry=0; sub_entry<map_val.via.map.size; sub_entry++ ) {
+ key_str = (char *)map_val.via.map.ptr[sub_entry].key.via.str.ptr;
+ // Check for key is "data"
+ if ( strncmp(key_str, "data", 4) == 0 ) {
+ data = (double *)map_val.via.map.ptr[sub_entry].val.via.bin.ptr;
+ // Check for key is "shape"
+ } else if ( strncmp(key_str, "shape", 5) == 0 ) {
+ data_height = map_val.via.map.ptr[sub_entry].val.via.array.ptr[0].via.i64;
+ data_width = map_val.via.map.ptr[sub_entry].val.via.array.ptr[1].via.i64;
+ }
+ }
+ }
+ }
+
+ if ( image->det == NULL ) {
+ ERROR("Geometry not available.\n");
+ return 1;
+ }
+
+ 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; pi<image->det->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; ss<p->h; ss++) {
+ for ( fs=0; fs<p->w; 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;
+ }
+ }
+
+ }
+
+ // might need to do some freeing of memory for msgpack object here
+
+ 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;
+}
diff --git a/src/zmq.h b/src/zmq.h
new file mode 100644
index 00000000..ee04f437
--- /dev/null
+++ b/src/zmq.h
@@ -0,0 +1,48 @@
+/*
+ * zmq.h
+ *
+ * ZMQ data interface
+ *
+ * Copyright © 2017-2018 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2018 Thomas White <taw@physics.org>
+ * 2014 Valerio Mariani
+ * 2017 Stijna de Graaf
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+
+#ifndef CRYSTFEL_ZMQ_H
+#define CRYSTFEL_ZMQ_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <msgpack.h>
+
+#include "image.h"
+
+extern int get_peaks_onda(msgpack_object *obj, struct image *image,
+ int half_pixel_shift);
+
+extern int obj_read(msgpack_object *obj, struct image *image);
+
+#endif /* CRYSTFEL_ZMQ_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-03 07:11:53 +0000