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#include <rumba/baseManifold.h>
#include <rumba/manifoldFile.h>
#include <rumba/arghandler.h>
#include <rumba/util.hpp>
#include <rumba/parse.h>
#include <rumba/matrixio.h>
#include <iostream>
#include <cstdlib>
#include <algorithm>
using std::cout;
using std::endl;
using RUMBA::Argument;
Argument myArgs [] = {
Argument ( "lower", RUMBA::NUMERIC, 'l', 0 ),
Argument ("upper", RUMBA::NUMERIC, 'u', 0 ),
Argument()
};
void help_message()
{
std::cerr << "Usage: volume-normalize\n"
"[-i|--infile] infile [-o|--outfile] outfile\n"
"[[--lower|-l] lower] (default: 0)\n"
"[[--upper|-u] upper] (default: 100)\n" << std::endl;
}
int main(int argc, char** argv)
{
RUMBA::ArgHandler::setRequiredDefaultArg("infile");
RUMBA::ArgHandler::setRequiredDefaultArg("outfile");
bool help;
double tmp1,tmp2;
double lower = 0, upper = 100;
try
{
RUMBA::ArgHandler argh(argc,argv,myArgs);
std::string infile, outfile;
help = argh.arg ("help");
if ( help )
{
help_message();
exit(0);
}
argh.arg("infile", infile );
argh.arg("outfile", outfile );
argh.arg("lower",lower);
argh.arg("upper",upper );
// argh.arg("savestats",savestats);
RUMBA::ManifoldFile* inManifold;
RUMBA::BaseManifold* volume;
RUMBA::ManifoldFile* outManifold;
RUMBA::Manifold<double> stats;
inManifold= RUMBA::ManifoldFile::construct(infile.c_str());
if (!inManifold)
{
cout << "Fatal: can't identify file type" << endl;
exit (1);
}
outManifold = RUMBA::ManifoldFile::construct ( outfile, std::ios::out, inManifold );
for ( int i = 0; i < inManifold->timepoints(); ++i )
{
volume = inManifold->get
(
RUMBA::intPoint(0,0,0,i),
RUMBA::intPoint(
inManifold->width(),
inManifold->height(),
inManifold->depth(),
1
)
);
RUMBA::normalize ( lower, upper, volume );
outManifold->put ( volume, RUMBA::intPoint(0,0,0,i));
delete volume;
}
delete inManifold;
delete outManifold;
}
catch (RUMBA::MissingArgumentException& s)
{
cout << "Error, missing required argument: " << s.error() << endl;
help_message();
}
catch (RUMBA::DuplicateArgumentException& s)
{
cout << "Duplicate argument: " << s.error() << endl;
help_message();
}
catch (RUMBA::ArgHandlerException& s)
{
cout << "Error: " << s.error() << endl;
help_message();
}
catch ( RUMBA::Exception & e)
{
cout << "Fatal exception " << e.error() << endl;
}
return 0;
}
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