From 20c476104e67a9b98caeefd857cab84320fc916a Mon Sep 17 00:00:00 2001 From: Thomas White Date: Thu, 6 Dec 2018 16:29:43 +0100 Subject: Add make_pixelmap to core CrystFEL --- src/make_pixelmap.c | 338 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 338 insertions(+) create mode 100644 src/make_pixelmap.c (limited to 'src/make_pixelmap.c') diff --git a/src/make_pixelmap.c b/src/make_pixelmap.c new file mode 100644 index 00000000..dfd91907 --- /dev/null +++ b/src/make_pixelmap.c @@ -0,0 +1,338 @@ +/* + * make_pixelmap.c + * + * Create a pixel map file from a CrystFEL geometry description + * + * Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2012-2018 Thomas White + * 2016-2016 Omri Mor + * + * 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 . + * + */ + + +#ifdef HAVE_CONFIG_H +#include +#endif + +#define _ISOC99_SOURCE +#include +#include +#include +#include +#include +#include +#include +#include + +#include "crystfel/detector.h" + + +static void show_help(const char *s) +{ + printf("Syntax: %s [options] \n\n", s); + printf( +"Create a pixel map file.\n" +"\n" +" -h, --help Display this help message.\n" +"\n" +" -o, --output= Output filename. Default: pixelmap.h5.\n" +" --badmap Generate bad pixel map instead of geometry\n" +" --good-pixel= Value for good pixels in bad map. Default 1.\n" +" --bad-pixel= Value for bad pixels in bad map. Default 0.\n" +); +} + + +static void create_array(hid_t gh, const char *name, void *vals, + hid_t type, int width, int height) +{ + hid_t dh, sh; + herr_t r; + hsize_t size[2]; + hsize_t max_size[2]; + + /* Note the "swap" here, according to section 3.2.5, + * "C versus Fortran Dataspaces", of the HDF5 user's guide. */ + size[0] = height; + size[1] = width; + max_size[0] = height; + max_size[1] = width; + sh = H5Screate_simple(2, size, max_size); + + dh = H5Dcreate2(gh, name, type, sh, + H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if ( dh < 0 ) { + ERROR("Couldn't create dataset\n"); + return; + } + + r = H5Dwrite(dh, type, H5S_ALL, H5S_ALL, H5P_DEFAULT, vals); + if ( r < 0 ) { + ERROR("Couldn't write data\n"); + H5Dclose(dh); + return; + } + + H5Sclose(sh); + H5Dclose(dh); +} + + +static void create_scalar(hid_t gh, const char *name, float val) +{ + hid_t dh, sh; + herr_t r; + + sh = H5Screate(H5S_SCALAR); + + STATUS("%s: %e\n", name, val); + + dh = H5Dcreate2(gh, name, H5T_NATIVE_FLOAT, sh, + H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if ( dh < 0 ) { + ERROR("Couldn't create dataset\n"); + return; + } + + r = H5Dwrite(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &val); + if ( r < 0 ) { + ERROR("Couldn't write data\n"); + H5Dclose(dh); + return; + } + + H5Sclose(sh); + H5Dclose(dh); +} + + +static void write_pixelmap_hdf5(const char *filename, + float *x, float *y, float *z, + int width, int height, float res, float coffset) +{ + hid_t fh; + + fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + if ( fh < 0 ) { + ERROR("Couldn't create file: %s\n", filename); + return; + } + + create_array(fh, "x", x, H5T_NATIVE_FLOAT, width, height); + create_array(fh, "y", y, H5T_NATIVE_FLOAT, width, height); + create_array(fh, "z", z, H5T_NATIVE_FLOAT, width, height); + + create_scalar(fh, "res", res); + create_scalar(fh, "coffset", coffset); + + H5Fclose(fh); +} + + +static void write_badmap_hdf5(const char *filename, uint16_t *b, + int width, int height) +{ + hid_t fh, gh; + + fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + if ( fh < 0 ) { + ERROR("Couldn't create file: %s\n", filename); + return; + } + + gh = H5Gcreate(fh, "data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + + create_array(gh, "/data/data", b, H5T_STD_U16LE, width, height); + + H5Fclose(fh); +} + + +int main(int argc, char *argv[]) +{ + int c; + char *input_file = NULL; + char *output_file = NULL; + struct detector *det = NULL; + int fs, ss, w, h; + float *x, *y, *z; + uint16_t *b; + int i; + float res, coffset; + int badmap = 0; + int good_pixel_val = 1; + int bad_pixel_val = 0; + + /* Long options */ + const struct option longopts[] = { + {"help", 0, NULL, 'h'}, + {"output", 1, NULL, 'o'}, + {"badmap", 0, &badmap, 1}, + {"good-pixel", 1, NULL, 301}, + {"bad-pixel", 1, NULL, 302}, + {0, 0, NULL, 0} + }; + + /* Short options */ + while ((c = getopt_long(argc, argv, "ho:", + longopts, NULL)) != -1) { + + switch (c) { + + case 'h' : + show_help(argv[0]); + return 0; + + case 'o' : + output_file = strdup(optarg); + break; + + case 301: + if (sscanf(optarg, "%d", &good_pixel_val) != 1) + { + ERROR("Invalid value for --good-pixel\n"); + return 1; + } + break; + + case 302: + if (sscanf(optarg, "%d", &bad_pixel_val) != 1) + { + ERROR("Invalid value for --bad-pixel\n"); + return 1; + } + break; + + case 0 : + break; + + default : + ERROR("Unhandled option '%c'\n", c); + break; + + } + + } + + if ( argc != (optind+1) ) { + ERROR("Please provide exactly one geometry file name.\n"); + return 1; + } + + input_file = strdup(argv[optind++]); + + if ( output_file == NULL ) { + output_file = strdup("pixelmap.h5"); + } + + /* Load geometry */ + det = get_detector_geometry(input_file, NULL); + if ( det == NULL ) { + ERROR("Failed to read geometry from '%s'\n", input_file); + return 1; + } + free(input_file); + + /* Determine max orig fs and ss */ + w = 0; h = 0; + for ( i=0; in_panels; i++ ) { + if ( det->panels[i].orig_max_fs > w ) { + w = det->panels[i].orig_max_fs; + } + if ( det->panels[i].orig_max_ss > h ) { + h = det->panels[i].orig_max_ss; + } + } + w += 1; h += 1; /* Inclusive -> Exclusive */ + STATUS("Data slab size: %i x %i\n", w, h); + + x = malloc(w*h*sizeof(float)); + y = malloc(w*h*sizeof(float)); + z = malloc(w*h*sizeof(float)); + b = malloc(w*h*sizeof(uint16_t)); + if ( (x==NULL) || (y==NULL) || (z==NULL) || (b==NULL) ) { + ERROR("Failed to allocate memory.\n"); + return 1; + } + + for ( ss=0; ssorig_min_fs)*p->fsx + + (css - p->orig_min_ss)*p->ssx; + ys = (cfs - p->orig_min_fs)*p->fsy + + (css - p->orig_min_ss)*p->ssy; + + rx = (xs + p->cnx) / p->res; + ry = (ys + p->cny) / p->res; + + x[fs + w*ss] = rx; + y[fs + w*ss] = ry; + z[fs + w*ss] = 0.0; /* FIXME */ + + nfs = fs - p->orig_min_fs; + nss = ss - p->orig_min_ss; + if ( in_bad_region(det, p, nfs, nss) ) { + b[fs + w*ss] = bad_pixel_val; + } else { + b[fs + w*ss] = good_pixel_val; + } + + } + + progress_bar(ss, h, "Converting"); + } + STATUS("\n"); + + res = det->defaults.res; + /* use the res of the first panel if not in global definitions + * assumes one of these exist */ + if ( res == -1.0 ) { + res = det->panels[0].res; + } + + coffset = det->defaults.coffset; + /* use the coffset of the first panel if not in global definitions + * assumes one of these exist*/ + if ( coffset == 0.0 ) { + coffset = det->panels[0].coffset; + } + + if ( badmap ) { + write_badmap_hdf5(output_file, b, w, h); + } else { + write_pixelmap_hdf5(output_file, x, y, z, w, h, res, coffset); + } + + return 0; +} -- cgit v1.2.3