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ENH: Changes to the command line parser to permit multiple metrics pe…
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…r stage in antsRegistration.
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@ntustison @hjmjohnson
ntustison authored and hjmjohnson committed Jan 18, 2013
1 parent 26dd8f3 commit a07c2f3
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Showing 20 changed files with 1,134 additions and 1,091 deletions.
40 changes: 20 additions & 20 deletions Examples/ANTSConformalMapping.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,7 @@ void InitializeCommandLineOptions( itk::ants::CommandLineParser *parser )
OptionType::Pointer option = OptionType::New();
option->SetShortName( 'h' );
option->SetDescription( description );
option->AddValue( std::string( "0" ) );
option->AddFunction( std::string( "0" ) );
parser->AddOption( option );
}

Expand All @@ -155,7 +155,7 @@ void InitializeCommandLineOptions( itk::ants::CommandLineParser *parser )
OptionType::Pointer option = OptionType::New();
option->SetLongName( "help" );
option->SetDescription( description );
option->AddValue( std::string( "0" ) );
option->AddFunction( std::string( "0" ) );
parser->AddOption( option );
}

Expand Down Expand Up @@ -220,9 +220,9 @@ int ANTSConformalMapping( itk::ants::CommandLineParser *parser )
float inflate_param = 0;
typename itk::ants::CommandLineParser::OptionType::Pointer infOption =
parser->GetOption( "inflate" );
if( infOption && infOption->GetNumberOfValues() > 0 )
if( infOption && infOption->GetNumberOfFunctions() )
{
if( infOption->GetNumberOfParameters() == 2 )
if( infOption->GetFunction( 0 )->GetNumberOfParameters() == 2 )
{
inflate_param = parser->Convert<float>(infOption->GetParameter( 0 ) );
inflate_iterations = parser->Convert<unsigned int>(infOption->GetParameter( 1 ) );
Expand All @@ -240,9 +240,9 @@ int ANTSConformalMapping( itk::ants::CommandLineParser *parser )
float maxCost = 40, distCostW = 1, labelCostW = 0;
typename itk::ants::CommandLineParser::OptionType::Pointer costOption =
parser->GetOption( "segmentation-cost" );
if( costOption && costOption->GetNumberOfValues() > 0 )
if( costOption && costOption->GetNumberOfFunctions() )
{
if( costOption->GetNumberOfParameters() == 3 )
if( costOption->GetFunction( 0 )->GetNumberOfParameters() == 3 )
{
maxCost = parser->Convert<float>(costOption->GetParameter( 0 ) );
distCostW = parser->Convert<float>(costOption->GetParameter( 1 ) );
Expand All @@ -257,9 +257,9 @@ int ANTSConformalMapping( itk::ants::CommandLineParser *parser )
}

typename itk::ants::CommandLineParser::OptionType::Pointer displayOption = parser->GetOption( "display-mesh" );
if( displayOption && displayOption->GetNumberOfValues() > 0 )
if( displayOption && displayOption->GetNumberOfFunctions() )
{
if( displayOption->GetNumberOfParameters() > 0 )
if( displayOption->GetFunction( 0 )->GetNumberOfParameters() > 0 )
{
std::string dispm = displayOption->GetParameter( 0 );
antscout << " render " << dispm << std::endl;
Expand Down Expand Up @@ -309,7 +309,7 @@ int ANTSConformalMapping( itk::ants::CommandLineParser *parser )
*/
typename itk::ants::CommandLineParser::OptionType::Pointer inOption =
parser->GetOption( "input-mesh" );
if( inOption && inOption->GetNumberOfParameters() == 2 )
if( inOption && inOption->GetFunction( 0 )->GetNumberOfParameters() == 2 )
{
std::string innm = inOption->GetParameter( 0 );
vtkSmartPointer<vtkPolyDataReader> labReader = vtkSmartPointer<vtkPolyDataReader>::New();
Expand Down Expand Up @@ -355,9 +355,9 @@ int ANTSConformalMapping( itk::ants::CommandLineParser *parser )
inflatedmesh = vtkSmartPointer<vtkPolyData>(smoother->GetOutput() );
antscout << " done smoothing " << std::endl;
flattener->SetSurfaceMesh(inflatedmesh);
if( outputOption->GetNumberOfParameters() > 0 )
if( outputOption->GetFunction( 0 )->GetNumberOfParameters() > 0 )
{
for( unsigned int p = 0; p < outputOption->GetNumberOfParameters(); p++ )
for( unsigned int p = 0; p < outputOption->GetFunction( 0 )->GetNumberOfParameters(); p++ )
{
if( p == 2 && inflatedmesh )
{
Expand All @@ -379,13 +379,13 @@ int ANTSConformalMapping( itk::ants::CommandLineParser *parser )
flattener->SetSurfaceFeatureMesh(featuremesh);
}

bool paramws = parser->template Convert<bool>( parser->GetOption( "param-while-searching" )->GetValue() );
bool paramws = parser->template Convert<bool>( parser->GetOption( "param-while-searching" )->GetFunction() );
flattener->SetParamWhileSearching(paramws);

unsigned int labeltoflatten = parser->template Convert<unsigned int>(
parser->GetOption( "label-to-flatten" )->GetValue() );
parser->GetOption( "label-to-flatten" )->GetFunction() );
flattener->SetLabelToFlatten(labeltoflatten);
std::string canonicaldomain = parser->GetOption( "canonical-domain" )->GetValue();
std::string canonicaldomain = parser->GetOption( "canonical-domain" )->GetFunction();
// canonicaldomain=ConvertToLowerCase( canonicaldomain );
antscout << " you will map label " << labeltoflatten << " to a " << canonicaldomain << std::endl;
if( canonicaldomain == std::string("circle") )
Expand All @@ -402,7 +402,7 @@ int ANTSConformalMapping( itk::ants::CommandLineParser *parser )
return EXIT_FAILURE;
}

std::string boundaryparam = parser->GetOption( "boundary-param" )->GetValue();
std::string boundaryparam = parser->GetOption( "boundary-param" )->GetFunction();
// do stuff -- but not implemented yet
// flattener->SetDiscBoundaryList(NULL);

Expand All @@ -420,11 +420,11 @@ int ANTSConformalMapping( itk::ants::CommandLineParser *parser )
/**
* output
*/
if( outputOption && outputOption->GetNumberOfValues() > 0 )
if( outputOption && outputOption->GetNumberOfFunctions() )
{
if( outputOption->GetNumberOfParameters() > 0 )
if( outputOption->GetFunction( 0 )->GetNumberOfParameters() > 0 )
{
for( unsigned int p = 0; p < outputOption->GetNumberOfParameters(); p++ )
for( unsigned int p = 0; p < outputOption->GetFunction( 0 )->GetNumberOfParameters(); p++ )
{
if( p == 0 )
{
Expand Down Expand Up @@ -531,7 +531,7 @@ int ANTSConformalMapping( std::vector<std::string> args, std::ostream* out_strea
parser->Parse( argc, argv );

if( argc < 2 || parser->Convert<bool>(
parser->GetOption( "help" )->GetValue() ) )
parser->GetOption( "help" )->GetFunction() ) )
{
parser->PrintMenu( antscout, 5, false );
if( argc < 2 )
Expand All @@ -541,7 +541,7 @@ int ANTSConformalMapping( std::vector<std::string> args, std::ostream* out_strea
return EXIT_SUCCESS;
}
else if( parser->Convert<bool>(
parser->GetOption( 'h' )->GetValue() ) )
parser->GetOption( 'h' )->GetFunction() ) )
{
parser->PrintMenu( antscout, 5, true );
return EXIT_SUCCESS;
Expand Down
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