1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
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
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
|
/*
* hdfsee.c
*
* Quick yet non-crappy HDF viewer
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <gtk/gtk.h>
#include <glib/gthread.h>
#include <getopt.h>
#include "displaywindow.h"
#include "utils.h"
#include "render.h"
/* Global program state */
DisplayWindow *main_window_list[64];
size_t main_n_windows = 0;
static void show_help(const char *s)
{
printf("Syntax: %s [options] image.h5\n\n", s);
printf(
"Quick HDF5 image viewer.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -p, --peak-overlay=<filename> Draw circles in positions listed in file.\n"
" -i, --int-boost=<n> Multiply intensity by <n>.\n"
" -b, --binning=<n> Set display binning to <n>.\n"
" --filter-cm Perform common-mode noise subtraction.\n"
" --filter-noise Apply an aggressive noise filter which\n"
" sets all pixels in each 3x3 region to\n"
" zero if any of them have negative\n"
" values.\n"
" -c, --colscale=<scale> Use the given colour scale. Choose from:\n"
" mono : Greyscale, black is zero.\n"
" invmono : Greyscale, white is zero.\n"
" colour : Colour scale:\n"
" black-blue-pink-red-orange-\n"
" -yellow-white.\n"
"\n");
}
/* Called to notify that an image display window has been closed */
void hdfsee_window_closed(DisplayWindow *dw)
{
size_t i;
for ( i=0; i<main_n_windows; i++ ) {
if ( main_window_list[i] == dw ) {
size_t j;
for ( j=i+1; j<main_n_windows; j++ ) {
main_window_list[j] = main_window_list[j+1];
}
}
}
main_n_windows--;
if ( main_n_windows == 0 ) gtk_exit(0);
}
int main(int argc, char *argv[])
{
int c;
size_t i;
int nfiles;
char *peaks = NULL;
int boost = 1;
int binning = 2;
int config_cmfilter = 0;
int config_noisefilter = 0;
int colscale = SCALE_COLOUR;
char *cscale = NULL;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"peak-overlay", 1, NULL, 'p'},
{"int-boost", 1, NULL, 'i'},
{"binning", 1, NULL, 'b'},
{"filter-cm", 0, &config_cmfilter, 1},
{"filter-noise", 0, &config_noisefilter, 1},
{"colscale", 1, NULL, 'c'},
{0, 0, NULL, 0}
};
gtk_init(&argc, &argv);
/* Short options */
while ((c = getopt_long(argc, argv, "hp:b:i:c:",
longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'p' :
peaks = strdup(optarg);
break;
case 'i' :
boost = atoi(optarg);
if ( boost < 1 ) {
ERROR("Intensity boost must be a positive"
" integer.\n");
}
break;
case 'b' :
binning = atoi(optarg);
if ( boost < 1 ) {
ERROR("Binning must be a positive integer.\n");
}
break;
case 'c' :
cscale = strdup(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
nfiles = argc-optind;
if ( nfiles < 1 ) {
ERROR("You need to give me a file to open!\n");
return -1;
}
if ( cscale == NULL ) cscale = strdup("colour");
if ( strcmp(cscale, "mono") == 0 ) {
colscale = SCALE_MONO;
} else if ( strcmp(cscale, "invmono") == 0 ) {
colscale = SCALE_INVMONO;
} else if ( strcmp(cscale, "colour") == 0 ) {
colscale = SCALE_COLOUR;
} else if ( strcmp(cscale, "color") == 0 ) {
colscale = SCALE_COLOUR;
} else {
ERROR("Unrecognised colour scale '%s'\n", cscale);
return 1;
}
free(cscale);
for ( i=0; i<nfiles; i++ ) {
main_window_list[i] = displaywindow_open(argv[optind+i], peaks,
boost, binning,
config_cmfilter,
config_noisefilter,
colscale);
if ( main_window_list[i] == NULL ) {
ERROR("Couldn't open display window\n");
} else {
main_n_windows++;
}
}
gtk_main();
return 0;
}
|
