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ConvertImageND.cxx
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ConvertImageND.cxx
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/*=========================================================================
Program: C3D: Command-line companion tool to ITK-SNAP
Module: ConvertImageND.cxx
Language: C++
Website: itksnap.org/c3d
Copyright (c) 2014 Paul A. Yushkevich
This file is part of C3D, a command-line companion tool to ITK-SNAP
C3D is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
=========================================================================*/
#include "ConvertImageND.h"
#include "AddImages.h"
#include "AlignByLandmarks.h"
#include "AntiAliasImage.h"
#include "ApplyMetric.h"
#include "ApplyNoise.h"
#include "BiasFieldCorrectionN4.h"
#include "BinaryHoleFill.h"
#include "BinaryImageCentroid.h"
#include "BinaryMathOperation.h"
#include "Canny.h"
#include "ClipImageIntensity.h"
#include "CompositeImages.h"
#include "ComputeFFT.h"
#include "ComputeMoments.h"
#include "ComputeOverlaps.h"
#include "ConnectedComponents.h"
#include "Convolution.h"
#include "CoordinateMap.h"
#include "CopyTransform.h"
#include "CreateImage.h"
#include "CreateInterpolator.h"
#include "DicomSeriesList.h"
#include "ExportPatches.h"
#include "ExtractRegion.h"
#include "ExtractSlice.h"
#include "ExtrudeSegmentation.h"
#include "FastMarching.h"
#include "FastMarchingMorphology.h"
#include "FlipImage.h"
#include "FillBackgroundWithNeighborhoodNoise.h"
#include "GeneralLinearModel.h"
#include "HessianEigenValues.h"
#include "HessianObjectness.h"
#include "HistogramMatch.h"
#include "ImageERF.h"
#include "ImageGradient.h"
#include "ImageLaplacian.h"
#include "LabelOverlapMeasures.h"
#include "LabelStatistics.h"
#include "LabelVoting.h"
#include "LandmarksToSpheres.h"
#include "LaplacianSharpening.h"
#include "LevelSetSegmentation.h"
#include "MatchBoundingBoxes.h"
#include "MathematicalMorphology.h"
#include "MeanFilter.h"
#include "MedianFilter.h"
#include "MixtureModel.h"
#include "MomentsFeatures.h"
#include "MRFVote.h"
#include "MultiplyImages.h"
#include "NonLocalMeansDenoise.h"
#include "NonLocalMeansUpsample.h"
#include "NormalizedCrossCorrelation.h"
#include "NormalizeLocalWindow.h"
#include "OtsuThreshold.h"
#include "OverlayLabelImage.h"
#include "PadImage.h"
#include "PeronaMalik.h"
#include "PrintImageInfo.h"
#include "Rank.h"
#include "ReadImage.h"
#include "ReciprocalImage.h"
#include "ReorderStack.h"
#include "ReplaceIntensities.h"
#include "ResampleImage.h"
#include "ResliceImage.h"
#include "RetainLabels.h"
#include "RFApply.h"
#include "RFTrain.h"
#include "SampleImage.h"
#include "ScalarToRGB.h"
#include "ScaleShiftImage.h"
#include "SetOrientation.h"
#include "SetSform.h"
#include "SignedDistanceTransform.h"
#include "SLICSuperVoxel.h"
#include "SmoothImage.h"
#include "SmoothMultiLabelImage.h"
#include "SplitMultilabelImage.h"
#include "StapleAlgorithm.h"
#include "StructureTensorEigenValues.h"
#include "SwapDimensions.h"
#include "TestImage.h"
#include "ThresholdImage.h"
#include "TileImages.h"
#include "TrimImage.h"
#include "TustisonWellComposedness.h"
#include "UnaryMathOperation.h"
#include "UpdateMetadataKey.h"
#include "Vote.h"
#include "VoxelwiseComponentFunction.h"
#include "VoxelwiseRegression.h"
#include "WarpImage.h"
#include "WarpLabelImage.h"
#include "WriteImage.h"
#include "WeightedSum.h"
#include "WeightedSumVoxelwise.h"
#include "WrapDimension.h"
// Optional commands that depend on ITK5 modules
#ifdef CONVERT3D_USE_ITK_REMOTE_MODULES
#include "MorphologicalContourInterpolation.h"
#endif
#include <cstring>
#include <algorithm>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <regex>
// Support for regular expressions via KWSYS in ITK
#include <itksys/RegularExpression.hxx>
// Image to image filter - for some global tolerance code
#include <itkImageToImageFilter.h>
// Documentation manual
#include "Documentation.h"
// Markdown documentation string generated at compile-time
// this looks a little odd, but works - the include file contains raw bytes
unsigned char c3d_md[] = {
#include "markdown_docs.h"
0x00
};
using namespace itksys;
extern const char *Convert3DVersionInfo;
// Helper function: read a double, throw exception if unreadable
double myatof(const char *str)
{
char *end = 0;
double d = strtod(str, &end);
if (*end != 0)
throw "strtod conversion failed";
return d;
};
long myatol(const char *str)
{
char *end = 0;
double d = strtol(str, &end, 10);
if (*end != 0)
throw "strtol conversion failed";
return d;
};
unsigned long myatoul(const char *cstr)
{
char *end = 0;
unsigned long ul = strtoul(cstr, &end, 10);
if (*end != 0)
throw "strtoul conversion failed";
return ul;
}
std::string str_to_lower(const char *input)
{
std::string s(input);
std::transform(s.begin(), s.end(), s.begin(), (int(*)(int)) tolower);
return s;
}
// Check whether value is a valid float (no leading spaces allowed)
bool is_double(const char *input)
{
std::istringstream iss(input);
double f;
iss >> std::noskipws >> f; // noskipws considers leading whitespace invalid
// Check the entire string was consumed and if either failbit or badbit is set
return iss.eof() && !iss.fail();
}
// Check wheter value is a valid unsigned short (no leading spaces allowed)
bool is_unsigned_short(const char *input)
{
std::istringstream iss0(input);
int s;
iss0 >> std::noskipws >> s;
if (s < 0)
return false;
std::istringstream iss(input);
unsigned short us;
iss >> std::noskipws >> us; // noskipws considers leading whitespace invalid
// Check the entire string was consumed and if either failbit or badbit is set
return iss.eof() && !iss.fail();
}
// split string into tokens based on delimiter
std::vector<std::string> split_string(std::string s, std::string delimiter)
{
std::vector<std::string> ret;
size_t pos = 0;
std::string token;
while ((pos = s.find(delimiter)) != std::string::npos)
{
token = s.substr(0, pos);
ret.push_back(token);
s.erase(0, pos + delimiter.length());
}
if (s.length() > 0)
ret.push_back(s);
return ret;
}
std::vector<int> ReadIntegerArgs(char* argv[], int argc)
{
std::vector<int> cmd_args;
for(unsigned int i = 1; i < argc; i++) {
try { // try to convert to int
int value = std::stoi(argv[i]);
cmd_args.push_back(value);
} catch(const std::logic_error &e) { break; }
}
return cmd_args;
}
/*
out << "Command Listing: " << endl;
out << " -accum" << endl;
out << " -add" << endl;
out << " -align-landmarks, -alm" << endl;
out << " -anisotropic-diffusion, -ad" << endl;
out << " -antialias, -alias" << endl;
out << " -as, -set" << endl;
out << " -atan2" << endl;
out << " -background" << endl;
out << " -biascorr" << endl;
out << " -binarize" << endl;
*** out << " -canny" << endl;
out << " -centroid" << endl;
out << " -clear" << endl;
out << " -clip" << endl;
out << " -colormap, -color-map" << endl;
out << " -connected-components, -connected, -comp" << endl;
out << " -coordinate-map-voxel, -cmv" << endl;
out << " -coordinate-map-physical, -cmp" << endl;
out << " -copy-transform, -ct" << endl;
out << " -cos" << endl;
out << " -create" << endl;
out << " -dilate" << endl;
out << " -divide" << endl;
out << " -dup" << endl;
out << " -endaccum" << endl;
out << " -endfor" << endl;
out << " -erode" << endl;
out << " -erf" << endl;
out << " -exp" << endl;
*** out << " -fft" << endl;
out << " -flip" << endl;
out << " -foreach" << endl;
out << " -glm" << endl;
*** out << " -hessobj, -hessian-objectness" << endl;
*** out << " -histmatch, -histogram-match" << endl;
out << " -holefill, -hf" << endl;
out << " -info" << endl;
out << " -info-full" << endl;
out << " -insert, -ins" << endl;
out << " -interpolation, -interp, -int" << endl;
out << " -iterations" << endl;
*** out << " -label-overlap" << std::endl;
out << " -label-statistics, -lstat" << endl;
out << " -landmarks-to-spheres, -lts" << endl;
out << " -laplacian, -laplace" << endl;
out << " -levelset" << endl;
out << " -levelset-curvature" << endl;
out << " -levelset-advection" << endl;
out << " -ln, -log" << endl;
out << " -log10" << endl;
out << " -max, -maximum" << endl;
out << " -mcs, -multicomponent-split" << endl;
out << " -mean" << endl;
out << " -merge" << endl;
*** out << " -mf, -mean-filter" << endl;
out << " -mi, -mutual-info" << endl;
out << " -min, -minimum" << endl;
out << " -mixture, -mixture-model" << endl;
out << " -multiply, -times" << endl;
out << " -n4, -n4-bias-correction" << endl;
out << " -ncc, -normalized-cross-correlation" << endl;
out << " -nmi, -normalized-mutual-info" << endl;
*** out << " -nlw, -normwin, -normalize-local-window" << endl;
*** out << " -normpdf" << endl;
out << " -noround" << endl;
out << " -nospm" << endl;
out << " -o" << endl;
out << " -omc, -output-multicomponent" << endl;
out << " -oo, -output-multiple" << endl;
out << " -orient" << endl;
out << " -origin" << endl;
out << " -origin-voxel" << endl;
out << " -overlap" << endl;
out << " -overlay-label-image, -oli" << endl;
out << " -pad" << endl;
out << " -percent-intensity-mode, -pim" << endl;
*** out << " -pixel" << endl;
out << " -pop" << endl;
out << " -popas" << endl;
out << " -probe" << endl;
out << " -push, -get" << endl;
out << " -rank" << endl;
out << " -reciprocal" << endl;
out << " -region" << endl;
out << " -reorder" << endl;
out << " -replace" << endl;
out << " -resample" << endl;
out << " -resample-mm" << endl;
out << " -reslice-itk" << endl;
out << " -reslice-matrix" << endl;
out << " -reslice-identity" << endl;
*** out << " -rf-train" << endl;
*** out << " -rf-apply" << endl;
out << " -rms" << endl;
out << " -round" << endl;
out << " -scale" << endl;
out << " -set-sform" << endl;
out << " -shift" << endl;
out << " -signed-distance-transform, -sdt" << endl;
out << " -sin" << endl;
out << " -slice" << endl;
out << " -smooth" << endl;
out << " -spacing" << endl;
out << " -split" << endl;
out << " -sqrt" << endl;
out << " -staple" << endl;
out << " -spm" << endl;
out << " -stretch" << endl;
*** out << " -subtract" << endl;
*** out << " -supervoxel, -sv" << endl;
out << " -test-image" << endl;
out << " -test-probe" << endl;
out << " -threshold, -thresh" << endl;
out << " -tile" << endl;
out << " -trim" << endl;
out << " -trim-to-size" << endl;
out << " -type" << endl;
out << " -verbose" << endl;
*** out << " -version" << endl;
out << " -vote" << endl;
out << " -vote-label" << endl;
out << " -voxel-sum" << endl;
out << " -voxel-integral, -voxel-int" << endl;
out << " -voxelwise-regression, -voxreg" << endl;
out << " -warp" << endl;
out << " -wrap" << endl;
out << " -weighted-sum, -wsum" << endl;
out << " -weighted-sum-voxelwise, -wsv" << endl;
*/
/**
* Parameters for the various algorithms. Stored in a separate structure
* in order to reduce number of variables declared in the header
*/
template <class TPixel, unsigned int VDim>
struct ConvertAlgorithmParameters
{
// Root mean square error for anti-aliasing algorithm
double m_AntiAliasRMS;
// Level set algorithm parameters
LevelSetParameters m_LevelSet;
// Random forest parameters
RFParameters<TPixel, VDim> m_RandomForest;
ConvertAlgorithmParameters()
{
m_AntiAliasRMS = 0.07;
}
};
template<class TPixel, unsigned int VDim>
ImageConverter<TPixel,VDim>
::ImageConverter()
: os_out(&std::cout), os_err(&std::cerr), verbose(&devnull)
{
// Disable multithreading
m_SystemNumberOfThreads = itk::MultiThreaderBase::GetGlobalMaximumNumberOfThreads();
itk::MultiThreaderBase::SetGlobalMaximumNumberOfThreads(1);
itk::MultiThreaderBase::SetGlobalDefaultNumberOfThreads(1);
// Initialize to defaults
m_TypeId = "float";
m_Background = 0.0;
m_RoundFactor = 0.5;
m_FlagSPM = false;
m_UseCompression = false;
m_MultiComponentSplit = false;
m_Iterations = 0;
m_LoopType = LOOP_NONE;
m_PercentIntensityMode = PIM_QUANTILE;
// Create the parameters
m_Param = new ParameterType();
// Documentation initially NULL to not waste time parsing it
m_Documentation = NULL;
// Create an interpolator
m_Interpolation = "linear";
CreateInterpolator<TPixel, VDim>(this).CreateLinear();
// Set orientation and coordinate tolerances to something more
// reasonable than the ITK defaults
m_Tolerance = 1.0e-4;
itk::ImageToImageFilterCommon::SetGlobalDefaultCoordinateTolerance(m_Tolerance);
itk::ImageToImageFilterCommon::SetGlobalDefaultDirectionTolerance(m_Tolerance);
}
template<class TPixel, unsigned int VDim>
ImageConverter<TPixel,VDim>
::~ImageConverter()
{
delete m_Param;
if(m_Documentation)
delete m_Documentation;
}
template<class TPixel, unsigned int VDim>
void
ImageConverter<TPixel, VDim>
::PrintCommandListing(std::ostream &out)
{
if(!m_Documentation)
m_Documentation = new Documentation(c3d_md);
// Print the automatically generated command listing
m_Documentation->PrintCommandListing(out);
// Print additional information on getting help
out << "Getting help:" << std::endl;
out << " "
<< std::setw(32) << std::left
<< "-h"
<< ": List commands" << std::endl;
out << " "
<< std::setw(32) << std::left
<< "-h command"
<< ": Print help on command (e.g. -h add)" << std::endl;
out << " "
<< std::setw(32) << std::left
<< "-manual"
<< ": Print complete reference manual" << std::endl;
}
template<class TPixel, unsigned int VDim>
void
ImageConverter<TPixel, VDim>
::PrintCommandHelp(std::ostream &out, const char *command)
{
if(!m_Documentation)
m_Documentation = new Documentation(c3d_md);
if(!m_Documentation->PrintCommandHelp(out, command))
{
out << "No help available for command " << command << std::endl;
}
}
template<class TPixel, unsigned int VDim>
void
ImageConverter<TPixel, VDim>
::PrintManual(std::ostream &out)
{
if(!m_Documentation)
m_Documentation = new Documentation(c3d_md);
m_Documentation->PrintManual(out);
}
template<class TPixel, unsigned int VDim>
int
ImageConverter<TPixel, VDim>
::ProcessCommand(int argc, char *argv[])
{
// Get the first command
string cmd = argv[0];
// this->sout() << "COMMAND: " << cmd << endl;
// Commands in alphabetical order
if (cmd == "-accum")
{
if (this->m_LoopType != LOOP_NONE)
throw ConvertException("Nested -foreach and -accum loops are not allowed");
this->m_LoopType = LOOP_ACCUM;
return this->AccumulateLoop(argc, argv);
}
else if (cmd == "-abs" || cmd == "-fabs")
{
UnaryMathOperation<TPixel, VDim> adapter(this);
adapter(&std::fabs);
return 0;
}
else if (cmd == "-acos")
{
UnaryMathOperation<TPixel, VDim> adapter(this);
adapter(&std::acos);
return 0;
}
else if (cmd == "-add")
{
BinaryMathOperation<TPixel, VDim> adapter(this);
adapter(BinaryMathOperation<TPixel, VDim>::ADD);
return 0;
}
else if (cmd == "-align-landmarks" || cmd == "-alm")
{
int dof = atoi(argv[1]);
std::string fnout = argv[2];
AlignByLandmarks<TPixel,VDim> adapter(this);
adapter(dof, fnout);
return 2;
}
else if (cmd == "-anisotropic-diffusion" || cmd == "-ad")
{
double cond = atof(argv[1]);
int niter = atoi(argv[2]);
PeronaMalik<TPixel, VDim> adapter(this);
adapter(cond, (size_t) niter);
return 2;
}
// Anti-alias a binary image, turning it into a smoother floating point image;
// the argument is the iso-surface value
// This command is affected by -iterations and -rms flags
else if (cmd == "-antialias" || cmd == "-alias")
{
AntiAliasImage<TPixel, VDim> adapter(this);
adapter(atof(argv[1]), m_Param->m_AntiAliasRMS);
return 1;
}
// Associate variable name with image currently at the top of
// the stack
else if (cmd == "-as" || cmd == "-set")
{
string var(argv[1]);
if (m_ImageStack.size() == 0)
throw ConvertException("No image to assign to variable %s", var.c_str());
m_ImageVars[var] = m_ImageStack.back();
return 1;
}
else if (cmd == "-asin")
{
UnaryMathOperation<TPixel, VDim> adapter(this);
adapter(&std::asin);
return 0;
}
else if (cmd == "-atan2")
{
BinaryMathOperation<TPixel, VDim> adapter(this);
adapter(BinaryMathOperation<TPixel, VDim>::ATAN2);
return 0;
}
else if (cmd == "-background")
{
m_Background = atof(argv[1]);
*verbose << "Background value set to " << m_Background << endl;
return 1;
}
else if (cmd == "-biascorr" || cmd == "-n4" || cmd == "-n4-bias-correction" )
{
BiasFieldCorrectionN4<TPixel, VDim> adapter(this);
adapter();
return 0;
}
// f(x) = (x == xBackground) ? 0 : 1
else if (cmd == "-binarize")
{
ThresholdImage<TPixel, VDim> adapter(this);
adapter(m_Background, m_Background, 0.0, 1.0);
return 0;
}
else if (cmd == "-canny")
{
Canny<TPixel, VDim> adapter(this);
RealVector sigma = ReadRealSize(argv[1]);
double tLower = ReadIntensityValue(argv[2]);
double tUpper = ReadIntensityValue(argv[3]);
adapter(sigma, tLower, tUpper);
return 3;
}
else if (cmd == "-ceil")
{
UnaryMathOperation<TPixel, VDim> adapter(this);
adapter(&std::ceil);
return 0;
}
else if (cmd == "-centroid")
{
BinaryImageCentroid<TPixel, VDim> adapter(this);
adapter();
return 0;
}
else if (cmd == "-centroid-mark")
{
double mark_value = atof(argv[1]);
BinaryImageCentroid<TPixel, VDim> adapter(this);
adapter(mark_value);
return 1;
}
else if (cmd == "-connected-components" || cmd == "-connected" || cmd == "-comp")
{
ConnectedComponents<TPixel, VDim> adapter(this);
adapter();
return 0;
}
else if (cmd == "-clear")
{
*verbose << "Clearing the stack" << endl;
m_ImageStack.clear();
return 0;
}
else if (cmd == "-clip")
{
double iMin = ReadIntensityValue(argv[1]);
double iMax = ReadIntensityValue(argv[2]);
ClipImageIntensity<TPixel, VDim>(this)(iMin, iMax);
return 2;
}
else if (cmd == "-colormap" || cmd == "-color-map")
{
// Read the name of the color map
std::string cmname = argv[1];
// Optionally, read the range of the color map (instead of using image min/max)
int np = 1;
double int_min = 0.0, int_max = 0.0;
// Try readin
if (argc > 3)
{
try
{
int_min = ReadIntensityValue(argv[2]);
int_max = ReadIntensityValue(argv[3]);
np = 3;
}
catch(ConvertException &exc) {}
}
ScalarToRGB<TPixel, VDim>(this)(cmname, int_min, int_max);
return np;
}
else if (cmd == "-composite")
{
CompositeImages<TPixel, VDim>(this)();
return 0;
}
else if (cmd == "-compress")
{
m_UseCompression = true;
return 0;
}
else if (cmd == "-no-compress")
{
m_UseCompression = false;
return 0;
}
else if (cmd == "-conv")
{
Convolution<TPixel,VDim>(this)();
return 0;
}
else if (cmd == "-coordinate-map-voxel" || cmd == "-cmv")
{
CoordinateMap<TPixel,VDim>(this)(false);
return 0;
}
else if (cmd == "-coordinate-map-physical" || cmd == "-cmp")
{
CoordinateMap<TPixel,VDim>(this)(true);
return 0;
}
else if (cmd == "-copy-transform" || cmd == "-ct")
{
CopyTransform<TPixel, VDim> adapter(this);
adapter();
return 0;
}
else if (cmd == "-cos")
{
UnaryMathOperation<TPixel, VDim> adapter(this);
adapter(&std::cos);
return 0;
}
// Create a new image with given size and voxel size
else if (cmd == "-create")
{
SizeType dims = ReadSizeVector(argv[1]);
RealVector voxel = ReadRealSize(argv[2]);
CreateImage<TPixel, VDim> adapter(this);
adapter(dims, voxel);
return 2;
}
else if (cmd == "-dicom-series-list")
{
DicomSeriesList<TPixel, VDim> adapter(this);
adapter(argv[1]);
return 1;
}
else if (cmd == "-dicom-series-read")
{
typedef ReadImage<TPixel, VDim> Adapter;
typename Adapter::ImageInfo info;
info.dicom_series_id = argv[2];
Adapter adapter(this);
adapter(argv[1], info);
return 2;
}
else if (cmd == "-dilate")
{
MathematicalMorphology<TPixel,VDim> adapter(this);
adapter(MathematicalMorphology<TPixel,VDim>::DILATION, atof(argv[1]), ReadSizeVector(argv[2]));
return 2;
}
else if (cmd == "-divide")
{
BinaryMathOperation<TPixel, VDim> adapter(this);
adapter(BinaryMathOperation<TPixel, VDim>::DIVIDE);
return 0;
}
else if (cmd == "-dup" || cmd == "-duplicate")
{
m_ImageStack.push_back(m_ImageStack.back());
return 0;
}
else if (cmd == "-endaccum")
{
// This command ends the accum loop
if (this->m_LoopType != LOOP_ACCUM)
throw ConvertException("Out of place -endaccum command");
this->m_LoopType = LOOP_NONE;
return 0;
}
else if (cmd == "-endfor")
{
// This command ends the for loop
if (this->m_LoopType != LOOP_FOREACH)
throw ConvertException("Out of place -endfor command");
this->m_LoopType = LOOP_NONE;
return 0;
}
else if (cmd == "-erode")
{
MathematicalMorphology<TPixel,VDim> adapter(this);
adapter(MathematicalMorphology<TPixel,VDim>::EROSION, atof(argv[1]), ReadSizeVector(argv[2]));
return 2;
}
else if (cmd == "-erf")
{
double thresh = atof(argv[1]);
double scale = atof(argv[2]);
ImageERF<TPixel, VDim> adapter(this);
adapter(thresh, scale);
return 2;
}
else if (cmd == "-exp")
{
UnaryMathOperation<TPixel, VDim> adapter(this);
adapter(&std::exp);
return 0;
}
else if (cmd == "-export-patches" || cmd == "-xp")
{
ExportPatches<TPixel,VDim> adapter(this);
std::string fn = argv[1];
SizeType radius = this->ReadSizeVector(argv[2]);
double freq = atof(argv[3]);
adapter(fn.c_str(), radius, freq);
return 3;
}
else if (cmd == "-export-patches-aug" || cmd == "-xpa")
{
int n_aug = atoi(argv[1]);
double sigma_angle = atof(argv[2]);
ExportPatches<TPixel,VDim>::SetAugmentationParameters(n_aug, sigma_angle);
return 2;
}
else if (cmd == "-extrude-seg")
{
ExtrudeSegmentation<TPixel, VDim> adapter(this);
adapter();
return 0;
}
else if (cmd == "-fill-background-with-noise" || cmd == "-fbn")
{
FillBackgroundWithNeighborhoodNoise<TPixel, VDim> adapter(this);
SizeType radius = ReadSizeVector(argv[1]);
int steps = atoi(argv[2]);
adapter(radius, steps);
return 2;
}
else if (cmd == "-fft")
{
ComputeFFT<TPixel, VDim> adapter(this);
adapter();
return 0;
}
else if (cmd == "-flip")
{
string flipax = argv[1];
FlipImage<TPixel, VDim> adapter(this);
adapter(flipax);
return 1;
}
else if (cmd == "-floor")
{
UnaryMathOperation<TPixel, VDim> adapter(this);
adapter(&std::floor);
return 0;
}
else if (cmd == "-fm" || cmd == "-fast-marching")
{
FastMarching<TPixel, VDim> adapter(this);
double stop_value = atof(argv[1]);
adapter(stop_value);
return 1;
}
else if (cmd == "-fm-dilate" || cmd == "-fmd")
{
LabelSet active = ReadLabelSet(argv[1]);
LabelSet target = ReadLabelSet(argv[2]);
long newlabel = myatol(argv[3]);
double radius = myatof(argv[4]);
FastMarchingMorphology<TPixel, VDim> adapter(this);
adapter(active, target, newlabel, radius);
return 4;
}
else if (cmd == "-foreach")
{
if (this->m_LoopType != LOOP_NONE)
throw ConvertException("Nested loops are not allowed");
this->m_LoopType = LOOP_FOREACH;
return this->ForEachLoop(argc, argv);
}
else if (cmd == "-foreach-comp")
{
if (this->m_LoopType != LOOP_NONE)
throw ConvertException("Nested loops are not allowed");
this->m_LoopType = LOOP_FOREACH;
int ncomp = atoi(argv[1]);
return this->ForEachComponentLoop(ncomp, argc - 1, argv + 1) + 1;
}
else if (cmd == "-glm")
{
string mat(argv[1]);
string con(argv[2]);
GeneralLinearModel<TPixel, VDim> adapter(this);
adapter(mat, con);
return 2;
}
else if (cmd == "-grad" || cmd == "-gradient")
{
ImageGradient<TPixel,VDim> adapter(this);
adapter();
return 0;
}
else if (cmd == "-h" || cmd == "-help" || cmd == "--help")
{
if(argc > 1 && argv[1][0] != '-')
{
PrintCommandHelp(this->sout(), argv[1]);
return 1;
}
else
{
PrintCommandListing(this->sout());
return 0;
}
}
else if(cmd == "-hf" || cmd == "-holefill")
{
double foreground = atof(argv[1]);
bool full_conn = atoi(argv[2]);
BinaryHoleFill<TPixel, VDim> adapter(this);
adapter(foreground, full_conn);
return 2;
}
else if (cmd == "-hesseig" || cmd == "-hessian-eigenvalues")
{
double scale = atof(argv[1]);
HessianEigenValues<TPixel,VDim> adapter(this);
adapter(scale);
return 1;
}