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-rw-r--r--src/im-zmq.c354
-rw-r--r--src/im-zmq.h18
-rw-r--r--src/process_image.c12
3 files changed, 9 insertions, 375 deletions
diff --git a/src/im-zmq.c b/src/im-zmq.c
index 492b399e..7494e64b 100644
--- a/src/im-zmq.c
+++ b/src/im-zmq.c
@@ -7,9 +7,9 @@
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2018 Thomas White <taw@physics.org>
- * 2014 Valerio Mariani
- * 2017 Stijn de Graaf
+ * 2018-2020 Thomas White <taw@physics.org>
+ * 2014 Valerio Mariani
+ * 2017 Stijn de Graaf
*
* This file is part of CrystFEL.
*
@@ -137,351 +137,3 @@ void im_zmq_shutdown(struct im_zmq *z)
zmq_close(z->socket);
zmq_ctx_destroy(z->ctx);
}
-
-
-static msgpack_object *find_msgpack_kv(msgpack_object *obj, const char *key)
-{
- int i;
-
- if ( obj == NULL ) return NULL;
- if ( obj->type != MSGPACK_OBJECT_MAP ) return NULL;
-
- for ( i=0; i<obj->via.map.size; i++ ) {
- const char *kstr;
- size_t klen;
- assert(obj->via.map.ptr[i].key.type == MSGPACK_OBJECT_STR);
- kstr = obj->via.map.ptr[i].key.via.str.ptr;
- klen = obj->via.map.ptr[i].key.via.str.size;
- if ( strncmp(kstr, key, klen) == 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.
- *
- */
-ImageFeatureList *get_peaks_msgpack(msgpack_object *obj,
- const DataTemplate *dtempl,
- int half_pixel_shift)
-{
- ImageFeatureList *features;
- int num_peaks;
- int pk;
- msgpack_object *peak_list;
- msgpack_object *peak_x;
- msgpack_object *peak_y;
- msgpack_object *peak_i;
- double peak_offset = half_pixel_shift ? 0.5 : 0.0;
-
- if ( obj == NULL ) {
- ERROR("No MessagePack object to get peaks from.\n");
- return NULL;
- }
-
- /* Object has structure:
- * {
- * "peak_list": [[peak_x], [peak_y], [peak_i]]
- * "key2":val2,
- * ...
- * }
- */
- peak_list = find_msgpack_kv(obj, "peak_list");
- peak_x = &peak_list->via.array.ptr[0];
- peak_y = &peak_list->via.array.ptr[1];
- peak_i = &peak_list->via.array.ptr[2];
-
- /* Length of peak_x array gives number of peaks */
- num_peaks = peak_x->via.array.size;
-
- features = image_feature_list_new();
-
- for ( pk=0; pk<num_peaks; pk++ ) {
-
- float fs, ss, val;
- int pn;
-
- /* Retrieve data from peak_list and apply half_pixel_shift,
- * if appropriate */
- fs = peak_x->via.array.ptr[pk].via.f64 + peak_offset;
- ss = peak_y->via.array.ptr[pk].via.f64 + peak_offset;
- val = peak_i->via.array.ptr[pk].via.f64;
-
- /* Convert coordinates to panel-relative */
- if ( data_template_file_to_panel_coords(dtempl, &fs, &ss, &pn) ) {
- ERROR("Peak not in panel!\n");
- } else {
- image_add_feature(features, fs, ss, pn,
- NULL, val, NULL);
- }
- }
-
- return features;
-}
-
-
-static void im_zmq_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 over ZMQ yet.\n");
- }
- adjust_centering_for_rail(p);
- }
-}
-
-
-static void im_zmq_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 over ZMQ yet.\n");
- eV = 0.0;
- }
- image->lambda = ph_en_to_lambda(eV_to_J(eV))*beam->photon_energy_scale;
-}
-
-
-static int unpack_slab(struct image *image, double *data,
- int data_width, int data_height)
-{
- uint16_t *flags = NULL;
- float *sat = NULL;
- int pi;
-
- 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 ( isnan(data[idx]) || isinf(data[idx]) ) 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;
- }
- }
-
- }
-
- return 0;
-}
-
-
-static double *find_msgpack_data(msgpack_object *obj, int *width, int *height)
-{
- msgpack_object *corr_data_obj;
- msgpack_object *data_obj;
- msgpack_object *shape_obj;
- double *data;
-
- corr_data_obj = find_msgpack_kv(obj, "corr_data");
- if ( corr_data_obj == NULL ) {
- ERROR("No corr_data MessagePack object found.\n");
- return NULL;
- }
-
- data_obj = find_msgpack_kv(corr_data_obj, "data");
- if ( data_obj == NULL ) {
- ERROR("No data MessagePack object found inside corr_data.\n");
- return NULL;
- }
- if ( data_obj->type != MSGPACK_OBJECT_STR ) {
- ERROR("corr_data.data isn't a binary object.\n");
- return NULL;
- }
- data = (double *)data_obj->via.str.ptr;
-
- shape_obj = find_msgpack_kv(corr_data_obj, "shape");
- if ( shape_obj == NULL ) {
- ERROR("No shape MessagePack object found inside corr_data.\n");
- return NULL;
- }
- if ( shape_obj->type != MSGPACK_OBJECT_ARRAY ) {
- ERROR("corr_data.shape isn't an array object.\n");
- return NULL;
- }
- if ( shape_obj->via.array.size != 2 ) {
- ERROR("corr_data.shape is wrong size (%i, should be 2)\n",
- shape_obj->via.array.size);
- return NULL;
- }
- if ( shape_obj->via.array.ptr[0].type != MSGPACK_OBJECT_POSITIVE_INTEGER ) {
- ERROR("corr_data.shape contains wrong type of element.\n");
- return NULL;
- }
- *height = shape_obj->via.array.ptr[0].via.i64;
- *width = shape_obj->via.array.ptr[1].via.i64;
- return data;
-}
-
-
-static double *zero_array(const DataTemplate *dtempl, int *dw, int *dh)
-{
- int max_fs = 0;
- int max_ss = 0;
- int pi;
- double *data;
-
- for ( pi=0; pi<dtempl->n_panels; pi++ ) {
- if ( dtempl->panels[pi].orig_max_fs > max_fs ) {
- max_fs = dtempl->panels[pi].orig_max_fs;
- }
- if ( dtempl->panels[pi].orig_max_ss > max_ss ) {
- max_ss = dtempl->panels[pi].orig_max_ss;
- }
- }
-
- data = calloc((max_fs+1)*(max_ss+1), sizeof(double));
- *dw = max_fs+1;
- *dh = max_ss+1;
- return data;
-}
-
-
-/* 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,
- * ...
- * ...
- * }
- */
-struct image *unpack_msgpack_data(msgpack_object *obj,
- const DataTemplate *dtempl,
- int no_image_data)
-{
- struct image *image;
- int data_width, data_height;
- double *data;
-
- if ( obj == NULL ) {
- ERROR("No MessagePack object!\n");
- return NULL;
- }
-
- if ( !no_image_data ) {
- data = find_msgpack_data(obj, &data_width, &data_height);
- if ( data == NULL ) {
- ERROR("No image data in MessagePack object.\n");
- return NULL;
- }
- } else {
- data = zero_array(dtempl, &data_width, &data_height);
- }
-
- image = image_new();
- if ( image == NULL ) return NULL;
-
- if ( unpack_slab(image, data, data_width, data_height) ) {
- ERROR("Failed to unpack data slab.\n");
- return NULL;
- }
-
- im_zmq_fill_in_beam_parameters(image->beam, image);
- if ( image->lambda > 1000 ) {
- ERROR("Warning: Missing or nonsensical wavelength "
- "(%e m).\n", image->lambda);
- }
- im_zmq_fill_in_clen(image->det);
- fill_in_adu(image);
-
- return image;
-}
diff --git a/src/im-zmq.h b/src/im-zmq.h
index d47084fc..bbe5c6c8 100644
--- a/src/im-zmq.h
+++ b/src/im-zmq.h
@@ -50,14 +50,6 @@ extern void im_zmq_shutdown(struct im_zmq *z);
extern msgpack_object *im_zmq_fetch(struct im_zmq *z);
-extern ImageFeatureList *get_peaks_msgpack(msgpack_object *obj,
- const DataTemplate *dtempl,
- int half_pixel_shift);
-
-extern struct image *unpack_msgpack_data(msgpack_object *obj,
- const DataTemplate *dtempl,
- int no_image_data);
-
#else /* defined(HAVE_MSGPACK) && defined(HAVE_ZMQ) */
static UNUSED struct im_zmq *im_zmq_connect(const char *zmq_address) { return NULL; }
@@ -68,16 +60,6 @@ static UNUSED void im_zmq_shutdown(struct im_zmq *z) { return; }
static UNUSED void *im_zmq_fetch(struct im_zmq *z) { return NULL; }
-static UNUSED ImageFeatureList *get_peaks_msgpack(void *obj,
- const DataTemplate *dtempl,
- int half_pixel_shift)
-{ return NULL; }
-
-static UNUSED struct image *unpack_msgpack_data(void *obj,
- const DataTemplate *dtempl,
- int no_image_data)
-{ return NULL; }
-
#endif /* defined(HAVE_MSGPACK) && defined(HAVE_ZMQ) */
#endif /* CRYSTFEL_ZMQ_H */
diff --git a/src/process_image.c b/src/process_image.c
index 2c4ec61c..5cc89d1b 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -193,9 +193,9 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
if ( pargs->msgpack_obj != NULL ) {
set_last_task(last_task, "unpacking messagepack object");
- image = unpack_msgpack_data(pargs->msgpack_obj,
- iargs->dtempl,
- iargs->no_image_data);
+ image = image_msgpack_read(iargs->dtempl,
+ pargs->msgpack_obj,
+ iargs->no_image_data);
if ( image == NULL ) return;
} else {
image = file_wait_open_read(pargs->filename, pargs->event,
@@ -298,9 +298,9 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
break;
case PEAK_MSGPACK:
- image->features = get_peaks_msgpack(pargs->msgpack_obj,
- iargs->dtempl,
- iargs->half_pixel_shift);
+ image->features = image_msgpack_read_peaks(iargs->dtempl,
+ pargs->msgpack_obj,
+ iargs->half_pixel_shift);
break;
case PEAK_NONE:
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 01:38:31 +0000