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#include <rumba/baseManifold.h>
#include <rumba/manifold.h>
#include <rumba/manifoldFile.h>
#include <rumba/arghandler.h>
#include <rumba/parse.h>
// #include <rumba/util.hpp>
#include <iostream>
#include <cstdlib>
#include <vector>
#include "../matrixutils/normalize.h"
using std::cerr;
using std::endl;
using RUMBA::stream_cast;
using RUMBA::Argument;
void help_message()
{
std::cerr << "Usage: normalize-transform\n"
"[-i|--infile] infile [-o|--outfile] outfile\n"
"[-r|--range] (global|volume|pixel)\n (default: global)\n"
"[-t|--type] (z|r|m)\n"
"[[--lower|-l] lower] (default: 0. Only applicable for range scaling)\n"
"[[--upper|-u] upper] (default: 100. Only applicable for range scaling)\n" << std::endl;
}
int main(int argc, char** argv)
{
Argument myArgs [5];
myArgs[0]=Argument ( "type", RUMBA::ALPHA, 't', "r" );
myArgs[1]=Argument ( "range", RUMBA::ALPHA, 'r', "global" );
myArgs[2]=Argument ( "lower", RUMBA::NUMERIC, 'l', 0 );
myArgs[3]=Argument ("upper", RUMBA::NUMERIC, 'u', 0 );
myArgs[4]=Argument();
std::string infile, outfile;
std::string type,range;
double upper,lower;
RUMBA::intPoint origin,dims;
bool verbose;
bool debug = true;
int normalize_type = 0;
RUMBA::ArgHandler::setRequiredDefaultArg("infile");
RUMBA::ArgHandler::setRequiredDefaultArg("outfile");
try
{
RUMBA::ArgHandler argh(argc,argv,myArgs);
if (argh.arg("help"))
{
help_message();
exit(0);
}
verbose = argh.arg("verbose");
argh.arg("infile", infile );
argh.arg("outfile", outfile );
argh.arg("type",type);
argh.arg("range",range);
if ( argh.arg("upper"))
argh.arg("upper",upper);
if ( argh.arg("lower"))
argh.arg("lower",lower);
std::vector<string> v = argh.loose();
if ( type == "z" )
normalize_type = RUMBA::Z_NORMALIZE;
else if ( type == "r" )
normalize_type = RUMBA::RANGE_NORMALIZE;
else if ( type == "m" )
normalize_type = RUMBA::MEAN_NORMALIZE;
else
throw RUMBA::Exception(
std::string("bad normalize method ")+type);
if ( range != "pixel" && range != "volume" && range != "global" )
throw RUMBA::Exception (std::string("Invalid range: "+range));
RUMBA::Manifold<double> M(infile.c_str());
if ( range == "pixel" )
RUMBA::pixel_normalize ( &M, normalize_type );
else if ( range == "volume" )
RUMBA::volume_normalize ( &M, normalize_type );
else if ( range == "global" )
RUMBA::global_normalize ( &M, normalize_type );
M.save ( outfile.c_str() );
if (verbose)
M.print(std::cerr);
}
catch (RUMBA::MissingArgumentException& s)
{
cerr << "Error, missing required argument: " << s.error() << endl;
help_message();
}
catch (RUMBA::DuplicateArgumentException& s)
{
cerr << "Duplicate argument: " << s.error() << endl;
help_message();
}
catch (RUMBA::ArgHandlerException& s)
{
cerr << "Error: " << s.error() << endl;
help_message();
}
catch ( RUMBA::Exception & e)
{
cerr << "Fatal exception " << e.error() << endl;
}
return 0;
}
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