/* ttologp.cc 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" #include "miscmaths/t2z.h" #include "miscmaths/volume.h" #include <string> #include "miscmaths/miscmaths.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" << " -logpout <outputvol> (default is " << 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; } }