shell command for SmoothImage.cxx from ANTs library - c++

Question

I have the code below which I would like to run it from a bash script in ubuntu. Inside my bash script, I wrote the command below.
$DOANTS/SmoothImage $216*512*512 $RESULTS/Registration/NiftyReg/StructureGuided/Pat28_MLAF0113_pv_Aff_BSpline_Iso_ArgMax.nii.gz $1 $RESULTS/Registration/NiftyReg/StructureGuided/Pat28_${CASES[$i]}\_Prostate_Aff_BSpline_Iso_ArgMax_smoothed.nii.gz
but I get the following error:
Unsupported dimension
I am not sure why the dimension is not passed. would be thankful if you could let me know the reason. The true size of image is. 216*512*512
The code is as below:
#include "antsUtilities.h"
#include <algorithm>
#include "itkMedianImageFilter.h"
#include "itkDiscreteGaussianImageFilter.h"
#include "ReadWriteData.h"
namespace ants
{
template <unsigned int ImageDimension>
int SmoothImage(int argc, char *`1 [])
{
typedef float PixelType;
typedef itk::Image<PixelType, ImageDimension> ImageType;
std::vector<float> sigmaVector = ConvertVector<float>( argv[3] );
typename ImageType::Pointer image1 = ITK_NULLPTR;
typename ImageType::Pointer varimage = ITK_NULLPTR;
ReadImage<ImageType>(image1, argv[2]);
typedef itk::DiscreteGaussianImageFilter<ImageType, ImageType> dgf;
typedef itk::MedianImageFilter<ImageType, ImageType> medf;
typename dgf::Pointer filter = dgf::New();
typename medf::Pointer filter2 = medf::New();
bool usespacing = false;
if( argc > 5 )
{
usespacing = atoi(argv[5]);
}
bool usemedian = false;
if( argc > 6 )
{
usemedian = atoi(argv[6]);
}
if( !usespacing )
{
filter->SetUseImageSpacingOff();
}
else
{
filter->SetUseImageSpacingOn();
}
if( !usemedian )
{
if( sigmaVector.size() == 1 )
{
filter->SetVariance( vnl_math_sqr( sigmaVector[0] ) );
}
else if( sigmaVector.size() == ImageDimension )
{
typename dgf::ArrayType varianceArray;
for( unsigned int d = 0; d < ImageDimension; d++ )
{
varianceArray[d] = vnl_math_sqr( sigmaVector[d] );
}
filter->SetVariance( varianceArray );
}
else
{
std::cerr << "Incorrect sigma vector size. Must either be of size 1 or ImageDimension." << std::endl;
}
filter->SetMaximumError( 0.01f );
filter->SetInput( image1 );
filter->Update();
varimage = filter->GetOutput();
}
else
{
typename ImageType::SizeType rad;
if( sigmaVector.size() == 1 )
{
rad.Fill( static_cast<unsigned long>( sigmaVector[0] ) );
}
else if( sigmaVector.size() == ImageDimension )
{
for( unsigned int d = 0; d < ImageDimension; d++ )
{
rad[d] = sigmaVector[d];
}
}
else
{
std::cerr << "Incorrect sigma vector size. Must either be of size 1 or ImageDimension." << std::endl;
}
filter2->SetRadius(rad);
filter2->SetInput( image1 );
filter2->Update();
varimage = filter2->GetOutput();
}
WriteImage<ImageType>( varimage, argv[4] );
return EXIT_SUCCESS;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int SmoothImage( std::vector<std::string> args, std::ostream* /*out_stream = NULL */ )
{
// put the arguments coming in as 'args' into standard (argc,argv) format;
// 'args' doesn't have the command name as first, argument, so add it manually;
// 'args' may have adjacent arguments concatenated into one argument,
// which the parser should handle
args.insert( args.begin(), "SmoothImage" );
int argc = args.size();
char* * argv = new char *[args.size() + 1];
for( unsigned int i = 0; i < args.size(); ++i )
{
// allocate space for the string plus a null character
argv[i] = new char[args[i].length() + 1];
std::strncpy( argv[i], args[i].c_str(), args[i].length() );
// place the null character in the end
argv[i][args[i].length()] = '\0';
}
argv[argc] = ITK_NULLPTR;
// class to automatically cleanup argv upon destruction
class Cleanup_argv
{
public:
Cleanup_argv( char* * argv_, int argc_plus_one_ ) : argv( argv_ ), argc_plus_one( argc_plus_one_ )
{
}
~Cleanup_argv()
{
for( unsigned int i = 0; i < argc_plus_one; ++i )
{
delete[] argv[i];
}
delete[] argv;
}
private:
char* * argv;
unsigned int argc_plus_one;
};
Cleanup_argv cleanup_argv( argv, argc + 1 );
// antscout->set_stream( out_stream );
if( argc < 4 )
{
std::cout << "Usage: " << std::endl;
std::cout << argv[0]
<<
" ImageDimension image.ext smoothingsigma outimage.ext {sigma-is-in-spacing-coordinates-0/1} {medianfilter-0/1}"
<< std::endl;
std::cout << " if median, then sigma means radius of filtering " << std::endl;
std::cout << " A separate sigma can be specified for each dimension, e.g., 1.5x1x2 " << std::endl;
if( argc >= 2 &&
( std::string( argv[1] ) == std::string("--help") || std::string( argv[1] ) == std::string("-h") ) )
{
return EXIT_SUCCESS;
}
return EXIT_FAILURE;
}
switch( atoi(argv[1]) )
{
case 2:
{
return SmoothImage<2>(argc, argv);
}
break;
case 3:
{
return SmoothImage<3>(argc, argv);
}
break;
case 4:
{
return SmoothImage<4>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
enter code here

Answer 1

I think maybe you're making an assumption that bash does inline math on the command line. It doesn't. Try for example -
$ echo $216*512*512
$ 16*512*512
In fact, unless I'm missing some syntactic magic of which I'm unaware, the $2 is simply being interpreted as the second parameter to the parent script, as in -
$ function check() { echo $216*512*512; }
$ check fragile rock
$ rock16*512*512
See? However, I think what you've got here is a typo. The $2 was probably meant to be by itself, because the first parameter to your program is a selector that you use near the end to instantiate the templated version of your smoothing function. So, the second parameter to the calling script becomes the first parameter of SmoothImage, as in -
$DOANTS/SmoothImage $2 16*512*512 $RESULTS/Registration/NiftyReg/StructureGuided/Pat28_MLAF0113_pv_Aff_BSpline_Iso_ArgMax.nii.gz $1 $RESULTS/Registration/NiftyReg/StructureGuided/Pat28_${CASES[$i]}\_Prostate_Aff_BSpline_Iso_ArgMax_smoothed.nii.gz
If however, as you say, the size parameter is 16*512*512 or 216*512*512 as the case may be, you're still running into the problem that bash doesn't do math in that way on the command line. What you want is something like -
declare -ri size=16*512*512
# or just "let size=16*512*512", the "declare -ri" just makes it a read-only integer
$DOANTS/SmoothImage $2 $size $RESULTS/Registration/NiftyReg/StructureGuided/Pat28_MLAF0113_pv_Aff_BSpline_Iso_ArgMax.nii.gz $1 $RESULTS/Registration/NiftyReg/StructureGuided/Pat28_${CASES[$i]}\_Prostate_Aff_BSpline_Iso_ArgMax_smoothed.nii.gz
I think that's where you're headed. If you want some evidence that this works, on your bash command line, try -
$ let size=16*512*512
$ echo $size
$ 4194304
Your C++ is probably fine (though I haven't gone through it in detail, but at a glance it looks OK). The problem is your bash. If you want features like inline math, you might consider looking at Python to drive your C++ programs. Just a thought.