Move MessagePack stuff to separate file

Note the nicer separation: ZMQ is in indexamajig only, whereas
MessagePack becomes something generally accessible through libcrystfel.

1 files changed, 3 insertions, 351 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;
-}