Newer
Older
Mark Woolrich, FMRIB Image Analysis Group
Copyright (C) 1999-2000 University of Oxford */
/* CCOPYRIGHT */
#include <iostream>
#include <fstream>
#define WANT_STREAM
#define WANT_MATH
#include "newmatap.h"
#include "newmatio.h"
using namespace NEWMAT;
using namespace MISCMATHS;
// the real defaults are provided in the function parse_command_line
class globaloptions {
public:
string varsfname;
string cbsfname;
int dof;
string logpfname;
public:
globaloptions();
~globaloptions() {};
};
globaloptions globalopts;
globaloptions::globaloptions()
{
// set up defaults
logpfname = "logps";
}
void print_usage(int argc, char *argv[])
{
cout << "Usage: " << argv[0] << " [options] <varsfile> <cbsfile> <dof> \n"
<< " Available options are:\n"
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
<< globalopts.logpfname << ")\n"
<< " -help\n\n";
}
void parse_command_line(int argc, char* argv[])
{
if(argc<2){
print_usage(argc,argv);
exit(1);
}
int inp = 1;
int n=1;
string arg;
char first;
while (n<argc) {
arg=argv[n];
if (arg.size()<1) { n++; continue; }
first = arg[0];
if (first!='-') {
if(inp == 1)
globalopts.varsfname = arg;
else if(inp == 2)
globalopts.cbsfname = arg;
else if(inp == 3)
globalopts.dof = 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);
}
if (n+1>=argc)
{
cerr << "Lacking argument to option " << arg << endl;
break;
}
// put options with 1 argument here
if ( arg == "-logpout") {
globalopts.logpfname = argv[n+1];
n+=2;
} else {
cerr << "Unrecognised option " << arg << endl;
n++;
}
} // while (n<argc)
if (globalopts.varsfname.size()<1) {
cerr << "Vars filename not found\n\n";
print_usage(argc,argv);
exit(2);
}
}
int main(int argc,char *argv[])
{
try{
cerr << log(10) << endl;
parse_command_line(argc, argv);
Volume vars, cbs;
vars.read(globalopts.varsfname.c_str());
cbs.read(globalopts.cbsfname.c_str());
int numTS = vars.Nrows();
cerr << numTS << endl;
Volume ps(numTS);
T2z::ComputePs(vars, cbs, globalopts.dof, ps);
VolumeInfo volinfo = vars.getInfo();
volinfo.intent_code = NIFTI_INTENT_LOGPVAL;
ps.setInfo(volinfo);
ps.writeAsFloat(globalopts.logpfname.c_str());
}
catch(Exception p_excp)
{
cerr << p_excp.what() << endl;
throw;
}
catch(...)
{
cerr << "Image error" << endl;
throw;
}
}