OpenTissue::image_analysis Namespace Reference

Namespaces
namespace	detail
Functions
template<typename image_type >
void	compute_default_labels (image_type &U)
template<typename image_type , typename feature_grid_type >
void	compute_feature_space (image_type const &U, feature_grid_type &feature_grid)
template<typename feature_grid_type , typename histogram_type >
void	compute_feature_space_histogram (feature_grid_type const &feature_grid, size_t const &I, size_t const &J, size_t const &K, histogram_type &histogram)
template<typename histogram_type , typename log_histogram_type >
void	compute_feature_space_log_histogram (histogram_type const &histogram, log_histogram_type &log_histogram)
template<typename feature_grid_type , typename matrix3x3_type , typename vector3_type >
void	compute_feature_space_whitening (feature_grid_type &feature_grid, matrix3x3_type &R, vector3_type &d)
template<typename grid_type_in , typename equalized_histogram_type >
void	compute_histogram_equalization (grid_type_in const &image, equalized_histogram_type &equal_histogram)
template<typename image_type , typename histogram_type >
void	compute_intensity_gradient_histogram (image_type const &U, unsigned short const &cnt_intensity_buckets, unsigned short const &cnt_grad_mag_buckets, histogram_type &histogram, OpenTissue::grid::Grid< size_t, OpenTissue::math::default_math_types > &index_grid)
template<typename image_type , typename histogram_type >
void	compute_intensity_histogram (image_type const &U, histogram_type &histogram, size_t buckets=256)
template<typename feature_grid_type , typename vector3_type , typename matrix3x3_type >
void	feature_space_pca (feature_grid_type const &feature_grid, vector3_type &mean, matrix3x3_type &C)

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Function Documentation

template<typename image_type >

void OpenTissue::image_analysis::compute_default_labels

(

image_type &

U

)

Default Labelling. A simple default labelling based on a 2D intensity-gradient magnitude histogram. It serves mainly as an example.

Parameters:

U

The image that should be labelled. Note that upon return values of the image are changed. Each voxel are assigned a label.

template<typename image_type , typename feature_grid_type >

void OpenTissue::image_analysis::compute_feature_space	(	image_type const &	U,
		feature_grid_type &	feature_grid
	)

Compute Histogram Space Grid.

Parameters:

	U	The image to compute a histogram of.
	feature_grid	Each voxel contains a triplet correspond to intensity, gradient magnitude and second derivatives of the corresponding voxel in U.

template<typename feature_grid_type , typename histogram_type >

void OpenTissue::image_analysis::compute_feature_space_histogram	(	feature_grid_type const &	feature_grid,
		size_t const &	I,
		size_t const &	J,
		size_t const &	K,
		histogram_type &	histogram
	)

Create Feature Space Histogram.

Parameters:

	feature_grid	The feature space grid.
	I	Number of intensity buckets in histogram.
	J	Number of gradient magnitude buckets in histogram.
	K	Number of second derivative buckets in histogram.
	histogram	Upon return holds a histogram of the feature space.

template<typename histogram_type , typename log_histogram_type >

void OpenTissue::image_analysis::compute_feature_space_log_histogram	(	histogram_type const &	histogram,
		log_histogram_type &	log_histogram
	)

Compute Feature Space Log Histogram.

Parameters:

	histogram	A feature space histogram.
	log_histogram	Upon return contains the log histogram of the feature space histogram.

template<typename feature_grid_type , typename matrix3x3_type , typename vector3_type >

void OpenTissue::image_analysis::compute_feature_space_whitening	(	feature_grid_type &	feature_grid,
		matrix3x3_type &	R,
		vector3_type &	d
	)

Feature Space Whitening. This function rotates and scales feature space according to a PCA analysis.

Parameters:

	feature_grid	The feature space grid.
	R	Upon return this argument holds the rotational warp applied to the feature space.
	d	Upon return this argument holds a 3D vector containing the scaling along the x,y and z axes.

template<typename grid_type_in , typename equalized_histogram_type >

void OpenTissue::image_analysis::compute_histogram_equalization	(	grid_type_in const &	image,
		equalized_histogram_type &	equal_histogram
	)

Histogram Equalization.

template<typename image_type , typename histogram_type >

void OpenTissue::image_analysis::compute_intensity_gradient_histogram	(	image_type const &	U,
		unsigned short const &	cnt_intensity_buckets,
		unsigned short const &	cnt_grad_mag_buckets,
		histogram_type &	histogram,
		OpenTissue::grid::Grid< size_t, OpenTissue::math::default_math_types > &	index_grid
	)

Compute Intensity-Gradient magnitude 2D histogram.

Parameters:

	U	The image to compute a histogram of.
	cnt_intensity_buckets	The number of intensity buckets in the histogram (first axis).
	cnt_grad_mag_buckets	The number of gradient magnitude buckets in the histogram (second axis).
	histogram	Upon return holds the computed histogram.
	index_grid	Upon return holds histogram indices of each voxel.

template<typename image_type , typename histogram_type >

void OpenTissue::image_analysis::compute_intensity_histogram	(	image_type const &	U,
		histogram_type &	histogram,
		size_t	buckets = 256
	)

Compute Intensity histogram.

Parameters:

	U	The image to compute a histogram of.
	histogram	Upon return holds the computed histogram. This could be declared as std::vector<size_t> histogram;

template<typename feature_grid_type , typename vector3_type , typename matrix3x3_type >

void OpenTissue::image_analysis::feature_space_pca	(	feature_grid_type const &	feature_grid,
		vector3_type &	mean,
		matrix3x3_type &	C
	)

Feature space PCA. Performs a principal component analysis on a feature space grid.

Parameters:

	feature_grid	A feature space grid (itensity, gradient magnitude, second derivative).
	mean	Upon return this argument holds the mean value of the feature space grid.
	C	Upon return this arguments holds the covariance of the feature space grid.