indexamajig.c 3.33 KB
Newer Older
Thomas White's avatar
Thomas White committed
1
/*
2
 * indexamajig.c
Thomas White's avatar
Thomas White committed
3
4
5
 *
 * Find hits, index patterns, output hkl+intensity etc.
 *
Thomas White's avatar
Thomas White committed
6
 * (c) 2006-2010 Thomas White <taw@physics.org>
Thomas White's avatar
Thomas White committed
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
 *
 * Part of CrystFEL - crystallography with a FEL
 *
 */


#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>

#include "utils.h"
#include "hdf5-file.h"
Thomas White's avatar
Thomas White committed
26
#include "index.h"
Thomas White's avatar
Thomas White committed
27
28
#include "intensities.h"
#include "ewald.h"
29
#include "peaks.h"
Thomas White's avatar
Thomas White committed
30
31
32
33
34
35
36
37
38
39
40
41


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Process and index FEL diffraction images.\n"
"\n"
"  -h, --help              Display this help message.\n"
"\n"
"  -i, --input=<filename>  Specify file containing list of images to process.\n"
"                           '-' means stdin, which is the default.\n"
Thomas White's avatar
Thomas White committed
42
43
44
45
"      --no-index          Do everything else (including fine peak search and\n"
"                           writing 'xfel.drx' if DirAx is being used), but\n"
"                           don't actually index.\n"
"      --dirax             Use DirAx for indexing.\n"
Thomas White's avatar
Thomas White committed
46
"      --dump-peaks        Write the results of the peak search to stdout.\n"
Thomas White's avatar
Thomas White committed
47
48
49
50
51
52
53
54
55
56
57
58
"\n");
}


int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
	FILE *fh;
	char *rval;
	int n_images;
	int n_hits;
59
	int config_noindex = 0;
Thomas White's avatar
Thomas White committed
60
	int config_dumpfound = 0;
Thomas White's avatar
Thomas White committed
61
	int config_dirax = 0;
Thomas White's avatar
Thomas White committed
62
63
64
65
66

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
67
		{"no-index",           0, &config_noindex,     1},
Thomas White's avatar
Thomas White committed
68
		{"dump-peaks",         0, &config_dumpfound,   1},
Thomas White's avatar
Thomas White committed
69
		{"dirax",              0, &config_dirax,       1},
Thomas White's avatar
Thomas White committed
70
71
72
73
		{0, 0, NULL, 0}
	};

	/* Short options */
74
	while ((c = getopt_long(argc, argv, "hi:w", longopts, NULL)) != -1) {
Thomas White's avatar
Thomas White committed
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118

		switch (c) {
		case 'h' : {
			show_help(argv[0]);
			return 0;
		}

		case 'i' : {
			filename = strdup(optarg);
			break;
		}

		case 0 : {
			break;
		}

		default : {
			return 1;
		}
		}

	}

	if ( filename == NULL ) {
		filename = strdup("-");
	}
	if ( strcmp(filename, "-") == 0 ) {
		fh = stdin;
	} else {
		fh = fopen(filename, "r");
	}
	free(filename);
	if ( fh == NULL ) {
		ERROR("Failed to open input file\n");
		return 1;
	}

	n_images = 0;
	n_hits = 0;
	do {

		char line[1024];
		struct hdfile *hdfile;
		struct image image;
Thomas White's avatar
Thomas White committed
119
		int fom;
Thomas White's avatar
Thomas White committed
120
121

		rval = fgets(line, 1023, fh);
Thomas White's avatar
Thomas White committed
122
		if ( rval == NULL ) continue;
Thomas White's avatar
Thomas White committed
123
124
		chomp(line);

Thomas White's avatar
Thomas White committed
125
		image.features = NULL;
Thomas White's avatar
Thomas White committed
126
		image.molecule = NULL;
Thomas White's avatar
Thomas White committed
127

Thomas White's avatar
Thomas White committed
128
129
		STATUS("Processing '%s'\n", line);

130
131
		n_images++;

Thomas White's avatar
Thomas White committed
132
133
		hdfile = hdfile_open(line);
		if ( hdfile == NULL ) {
134
			continue;
Thomas White's avatar
Thomas White committed
135
136
		} else if ( hdfile_set_first_image(hdfile, "/") ) {
			ERROR("Couldn't select path\n");
137
			continue;
Thomas White's avatar
Thomas White committed
138
139
140
141
		}

		hdf5_read(hdfile, &image);

Thomas White's avatar
Thomas White committed
142
143
		fom = image_fom(&image);
		if ( fom > 0 ) {
Thomas White's avatar
Thomas White committed
144

Thomas White's avatar
Thomas White committed
145
			/* Calculate orientation matrix (by magic) */
Thomas White's avatar
Thomas White committed
146
147
148
149
			index_pattern(&image, config_noindex, config_dumpfound,
			              config_dirax);

			if ( image.molecule == NULL ) continue;
Thomas White's avatar
Thomas White committed
150
151

			/* View head-on (unit cell is tilted) */
Thomas White's avatar
Thomas White committed
152
			image.orientation.w = 1.0;
Thomas White's avatar
Thomas White committed
153
154
155
156
157
158
159
			image.orientation.x = 0.0;
			image.orientation.y = 0.0;
			image.orientation.z = 0.0;
			get_ewald(&image);

			/* Read h,k,l,I */
			output_intensities(&image);
Thomas White's avatar
Thomas White committed
160
161
162
163
164
165
166
167
168
169
170
171
172
173

			n_hits++;

		}

	} while ( rval != NULL );

	fclose(fh);

	STATUS("There were %i images.\n", n_images);
	STATUS("%i hits were found.\n", n_hits);

	return 0;
}