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Diffstat (limited to 'libcrystfel/src/image-seedee.c')
| -rw-r--r-- | libcrystfel/src/image-seedee.c | 195 |
1 files changed, 195 insertions, 0 deletions
diff --git a/libcrystfel/src/image-seedee.c b/libcrystfel/src/image-seedee.c new file mode 100644 index 00000000..1965aefa --- /dev/null +++ b/libcrystfel/src/image-seedee.c @@ -0,0 +1,195 @@ +/* + * image-seedee.c + * + * Image loading with Seedee + * + * Copyright © 2017-2022 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2018-2022 Thomas White <taw@physics.org> + * 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 <http://www.gnu.org/licenses/>. + * + */ + +#include <libcrystfel-config.h> + +#include <stdlib.h> +#include <stdio.h> +#include <stdint.h> +#include <assert.h> +#include <unistd.h> + +#include <image.h> +#include <utils.h> +#include <profile.h> + +#include "datatemplate_priv.h" + + +#if defined(HAVE_SEEDEE) + +#include <seedee/seedee.h> +#include <cjson/cJSON.h> + + +static int load_seedee_data(struct panel_template *p, + struct SeedeeNDArray *array, + float **pdata) +{ + int data_size_fs, data_size_ss; + float *data = NULL; + + data_size_ss = array->shape[0]; + data_size_fs = array->shape[1]; + + if ( (p->orig_min_fs + PANEL_WIDTH(p) > data_size_fs) + || (p->orig_min_ss + PANEL_HEIGHT(p) > data_size_ss) ) + { + ERROR("Data for panel %s (%i x %i + %i + %i) is outside data " + "array bounds (%i x %i)\n", + p->name, + PANEL_WIDTH(p), PANEL_HEIGHT(p), + p->orig_min_fs, p->orig_min_ss, + data_size_fs, data_size_ss); + return 1; + } + + if ( (array->datatype == 'u') + && (array->itemsize == 2) + && (array->byteorder == '<') ) + { + int fs, ss; + uint16_t *in_data = (uint16_t *)array->data; + + data = malloc(PANEL_WIDTH(p) * PANEL_HEIGHT(p) * sizeof(float)); + if ( data == NULL ) return 1; + + for ( ss=0; ss<PANEL_HEIGHT(p); ss++ ) { + for ( fs=0; fs<PANEL_WIDTH(p); fs++ ) { + size_t idx = fs+p->orig_min_fs + (ss+p->orig_min_ss)*data_size_fs; + data[fs+ss*PANEL_WIDTH(p)] = in_data[idx]; + } + } + *pdata = data; + + } else { + ERROR("Unrecognised data type %c%i%c\n", + array->datatype, array->itemsize, array->byteorder); + return 1; + } + + return 0; +} + + +/* Read the image data from 'data_block' into 'image', according to 'dtempl' */ +int image_seedee_read(struct image *image, + DataTemplate *dtempl, + void *data_block, + size_t data_block_size, + char *meta_data) +{ + struct SeedeeNDArray array; + int r; + bool zero_copy; + int i; + cJSON *json; + cJSON *data_format_str; + + json = cJSON_Parse(meta_data); + if ( json == NULL ) { + ERROR("Failed to parse JSON\n"); + return 1; + } + + data_format_str = cJSON_GetObjectItemCaseSensitive(json, "_data_format"); + if ( !cJSON_IsString(data_format_str) ) { + ERROR("_data_format isn't a string"); + cJSON_Delete(json); + return 1; + } + + profile_start("seedee-get-size"); + array.size = seedee_get_data_size(data_format_str->valuestring, + data_block, data_block_size, + &zero_copy, &array); + profile_end("seedee-get-size"); + array.data = malloc(array.size); + array.shape = malloc(array.ndims*sizeof(int)); + if ( (array.data == NULL) || (array.shape == NULL) ) { + cJSON_Delete(json); + return 1; + } + + if ( array.ndims != 2 ) { + ERROR("Seedee data has unexpected number of dimensions " + "(%i, expected 2)\n", array.ndims); + return 1; + } + + profile_start("seedee-deserialize"); + r = seedee_deserialize_ndarray(data_format_str->valuestring, + data_block, data_block_size, + 0, &array); + profile_end("seedee-deserialize"); + cJSON_Delete(json); + if ( r < 0 ) { + ERROR("Seedee deserialiation failed.\n"); + return 1; + } + + image->dp = malloc(dtempl->n_panels*sizeof(float *)); + if ( image->dp == NULL ) { + ERROR("Failed to allocate data array.\n"); + return 1; + } + + /* Set all pointers to NULL for easier clean-up */ + for ( i=0; i<dtempl->n_panels; i++ ) image->dp[i] = NULL; + + profile_start("seedee-panel"); + for ( i=0; i<dtempl->n_panels; i++ ) { + if ( load_seedee_data(&dtempl->panels[i], &array, &image->dp[i]) ) + { + ERROR("Failed to load data for panel '%s'\n", + dtempl->panels[i].name); + profile_end("seedee-panel"); + return 1; + } + } + profile_end("seedee-panel"); + + return 0; +} + + +#else /* defined(HAVE_SEEDEE) */ + +int image_seedee_read(struct image *image, + const DataTemplate *dtempl, + void *data, + size_t data_size, + char *meta_data) +{ + ERROR("Seedee is not supported in this installation (read).\n"); + return 1; +} + +#endif /* defined(HAVE_SEEDEE) */ |