Newer
Older
/* FilmOlsOptions.cc
Mark Woolrich, FMRIB Image Analysis Group
Copyright (C) 1999-2000 University of Oxford */
/* CCOPYRIGHT */
#define WANT_STREAM
#define WANT_MATH
#include <iostream.h>
#include <fstream.h>
#include <stdlib.h>
#include <stdio.h>
#include "newmatap.h"
#include "newmatio.h"
#include "FilmOlsOptions.h"
#ifndef NO_NAMESPACE
using namespace NEWMAT;
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
#endif
FilmOlsOptions* FilmOlsOptions::gopt = NULL;
void FilmOlsOptions::parse_command_line(int argc, char** argv, ofstream& logfile)
{
if(argc<2){
print_usage(argc,argv);
exit(1);
}
int inp = 1;
int n=1;
string arg;
char first;
logfile << "Arguments: " << endl;
while (n<argc) {
arg=argv[n];
// output argument to logfile:
logfile << arg << " ";
if (arg.size()<1) { n++; continue; }
first = arg[0];
if (first!='-') {
if(inp == 1)
gopt->inputfname = arg;
else if(inp == 2)
gopt->paradigmfname = arg;
else if(inp == 3)
gopt->thresh = atoi(argv[n]);
else
{
cerr << "Mismatched argument " << arg << endl;
break;
}
n++;
inp++;
continue;
}
// put options without arguments here
if ( arg == "-help" ) {
print_usage(argc,argv);
exit(0);
} else if ( arg == "-v" ) {
gopt->verbose = true;
n++;
continue;
} else if ( arg == "-ar" ) {
gopt->fitAutoRegressiveModel = true;
n++;
continue;
} else if ( arg == "-gl" ) {
gopt->globalEst = true;
n++;
continue;
} else if ( arg == "-sa" ) {
gopt->smoothACEst = true;
n++;
continue;
} else if ( arg == "-det" ) {
gopt->detrend = true;
n++;
continue;
} else if ( arg == "-noest" ) {
gopt->noest = true;
n++;
continue;
}
if (n+1>=argc)
{
cerr << "Lacking argument to option " << arg << endl;
break;
}
// put options with 1 argument here
if ( arg == "-ms") {
gopt->ms = atoi(argv[n+1]);
logfile << argv[n+1] << " ";
n+=2;
} else if ( arg == "-sp" ) {
gopt->susanpath = argv[n+1];
logfile << argv[n+1] << " ";
n+=2;
} else if ( arg == "-rn" ) {
gopt->datadir = argv[n+1];
logfile << argv[n+1] << " ";
n+=2;
} else {
cerr << "Unrecognised option " << arg << endl;
n++;
}
} // while (n<argc)
logfile << endl << "---------------------------------------------" << endl << endl;
if (gopt->inputfname.size()<1) {
print_usage(argc,argv);
throw Exception("Input filename not found");
}
if (gopt->paradigmfname.size()<1) {
print_usage(argc,argv);
throw Exception("Paradigm filename not found");
}
if (gopt->thresh < 0) {
print_usage(argc,argv);
throw Exception("Invalid thresh");
}
}
void FilmOlsOptions::print_usage(int argc, char *argv[])
{
cout << "Usage: " << argv[0] << " [options] <groupfile> <paradigmfile> <thresh>\n\n"
<< " Available options are:\n"
<< " -sa (smooths auto corr estimates)\n"
<< " -ms <num> (susan mask size)\n"
<< " -v (outputs full data)\n"
<< " -ar (fits autoregressive model - default "
<< "is to estimate direct from raw autocorr estimate)\n"
<< " -gl (use global estimate only)\n"
<< " -pw (prewhiten)\n"
<< " -noest (do not estimate auto corrs)\n"
<< " -det (detrend data as preprocessing step)\n"
<< " -rn <dir> (directory name to store results in, default is "
<< gopt->datadir << ")\n"
<< " -sp <path> (path for SUSAN executable, default is "
<< gopt->susanpath << ")\n"
<< " -help\n\n";
}
#ifndef NO_NAMESPACE
}
#endif