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/*
* 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 *data, int *bad)
{
int data_size_fs, data_size_ss;
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;
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];
}
}
} else if ( (array->datatype == 'u')
&& (array->itemsize == 4)
&& (array->byteorder == '<') )
{
int fs, ss;
uint32_t *in_data = (uint32_t *)array->data;
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];
}
}
} else if ( (array->datatype == 'i')
&& (array->itemsize == 4)
&& (array->byteorder == '<') )
{
int fs, ss;
int32_t *in_data = (int32_t *)array->data;
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];
}
}
} else if ( (array->datatype == 'f')
&& (array->itemsize == 8)
&& (array->byteorder == '<') )
{
int fs, ss;
double *in_data = (double *)array->data;
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];
}
}
} else {
ERROR("Unrecognised data type %c%i%c\n",
array->datatype, array->itemsize, array->byteorder);
return 1;
}
/* Note: when adding a new data type, don't forget that you are
* responsible for marking NaN/inf pixels as bad. */
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);
free(array.data);
free(array.shape);
return 1;
}
if ( array.ndims != 2 ) {
ERROR("Seedee data has unexpected number of dimensions "
"(%i, expected 2)\n", array.ndims);
free(array.data);
free(array.shape);
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");
free(array.data);
free(array.shape);
return 1;
}
profile_start("seedee-panel");
for ( i=0; i<dtempl->n_panels; i++ ) {
if ( load_seedee_data(&dtempl->panels[i], &array,
image->dp[i], image->bad[i]) )
{
ERROR("Failed to load data for panel '%s'\n",
dtempl->panels[i].name);
profile_end("seedee-panel");
free(array.data);
free(array.shape);
return 1;
}
}
profile_end("seedee-panel");
free(array.data);
free(array.shape);
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) */
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