MR::Filter Namespace Reference

Classes
class	Base
class	ConnectedComponents
class	Connector
class	CopyKernel4D
class	Dilate
	a filter to dilate a mask More...
class	DWIBrainMask
	a filter to compute a whole brain mask from a DWI image. More...
class	Erode
	a filter to erode a mask More...
class	FFT
	a filter to perform an FFT on an image More...
class	Gradient
class	ImageCorrelationCostFunction
class	MaskClean
	a filter to clean up masks typically output by DWIBrainMask filter More...
class	Median
class	Normalise
class	OptimalThreshold
	a filter to compute the optimal threshold to mask a DataSet. More...
class	Resize
class	Smooth
class	ZClean

Functions
template<class ImageType >
void	fft (ImageType &&vox, const size_t axis, const bool inverse=false)
template<class ImageType , class MaskType >
ImageType::value_type	estimate_optimal_threshold (ImageType &input, MaskType &mask)
template<class ImageType >
ImageType::value_type	estimate_optimal_threshold (ImageType &input)
template<template< class ImageType > class Interpolator, class ImageTypeDestination , class ImageTypeSource >
void	reslice (ImageTypeSource &source, ImageTypeDestination &destination, const transform_type &transform=Adapter::NoTransform, const vector< uint32_t > &oversampling=Adapter::AutoOverSample, const typename ImageTypeDestination::value_type value_when_out_of_bounds=Interp::Base< ImageTypeDestination >::default_out_of_bounds_value())
	convenience function to regrid one Image onto another More...
template<template< class VoxelType > class Interpolator, class ImageTypeDestination , class ImageTypeSource , class WarpType >
void	warp (ImageTypeSource &source, ImageTypeDestination &destination, WarpType &warp, const typename ImageTypeDestination::value_type value_when_out_of_bounds=Interpolator< ImageTypeSource >::default_out_of_bounds_value(), const vector< uint32_t > oversample=Adapter::AutoOverSample, const bool jacobian_modulate=false)
	convenience function to warp one image onto another More...

Function Documentation

estimate_optimal_threshold() [1/2]

template<class ImageType >

ImageType::value_type MR::Filter::estimate_optimal_threshold ( ImageType &  input )

inline

Definition at line 210 of file optimal_threshold.h.

estimate_optimal_threshold() [2/2]

template<class ImageType , class MaskType >

ImageType::value_type MR::Filter::estimate_optimal_threshold	(	ImageType &	input,
		MaskType &	mask
	)

Definition at line 186 of file optimal_threshold.h.

reslice()

template<template< class ImageType > class Interpolator, class ImageTypeDestination , class ImageTypeSource >

void MR::Filter::reslice	(	ImageTypeSource &	source,
		ImageTypeDestination &	destination,
		const transform_type &	transform = Adapter::NoTransform,
		const vector< uint32_t > &	oversampling = Adapter::AutoOverSample,
		const typename ImageTypeDestination::value_type	value_when_out_of_bounds = Interp::Base<ImageTypeDestination>::default_out_of_bounds_value()
	)

convenience function to regrid one Image onto another

This function resamples (regrids) the Image source onto the Image& destination, using the templated interpolator class.

A linear transformation can be optionally applied (that maps from the destination to the source)

For example:

// source and destination data:
auto source = Image<float>::create (argument[0]);
 
auto template_header = Image::header (argument[1]);
auto destination = Image<float>::create (argument[2], template_header);
 
// regrid source onto destination using linear interpolation:
Image::Filter::reslice<Interp::Linear> (source, destination);

Definition at line 48 of file reslice.h.

warp()

template<template< class VoxelType > class Interpolator, class ImageTypeDestination , class ImageTypeSource , class WarpType >

void MR::Filter::warp	(	ImageTypeSource &	source,
		ImageTypeDestination &	destination,
		WarpType &	warp,
		const typename ImageTypeDestination::value_type	value_when_out_of_bounds = Interpolator<ImageTypeSource>::default_out_of_bounds_value(),
		const vector< uint32_t >	oversample = Adapter::AutoOverSample,
		const bool	jacobian_modulate = false
	)

convenience function to warp one image onto another

This function resamples (regrids) the Image source onto the Image& destination, using the templated interpolator class and a supplied deformation field.

For example:

// source and destination data:
auto source = Image<float>::open(argument[0]);
 
auto warp = Image<float>::open(argument[1]);
 
auto template = Header::open(argument[2]);
 
auto destination = Image<float>::create (argument[3], template)
 
// regrid source onto destination using linear interpolation:
Filter::warp<Image::Interp::Linear> (source, destination, warp);

Definition at line 65 of file warp.h.