Add make_pixelmap to core CrystFEL

1 files changed, 338 insertions, 0 deletions

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 <taw@physics.org>
+ *   2016-2016 Omri Mor <omor1@asu.edu>
+ *
+ * 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/>.
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#define _ISOC99_SOURCE
+#include <math.h>
+#include <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+
+#include "crystfel/detector.h"
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s [options] <input.geom>\n\n", s);
+	printf(
+"Create a pixel map file.\n"
+"\n"
+" -h, --help                Display this help message.\n"
+"\n"
+" -o, --output=<filename>   Output filename.  Default: pixelmap.h5.\n"
+"     --badmap              Generate bad pixel map instead of geometry\n"
+"     --good-pixel=<n>      Value for good pixels in bad map.  Default 1.\n"
+"     --bad-pixel=<n>       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; i<det->n_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; ss<h; ss++ ) {
+		for ( fs=0; fs<w; fs++ ) {
+
+			double rx, ry;
+			struct panel *p;
+			double xs, ys;
+			double cfs, css;
+			int nfs, nss;
+
+			p = find_orig_panel(det, fs, ss);
+
+			/* Add half a pixel to fs and ss to get the fs,ss
+			 * coordinates of the CENTRE of the pixel */
+			cfs = fs + 0.5;
+			css = ss + 0.5;
+			xs = (cfs - p->orig_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;
+}