image_processing.h File Reference

Image processing functions. More...

#include <IMP/em2d/em2d_config.h>
#include "IMP/em2d/PolarResamplingParameters.h"
#include "IMP/em2d/Matrix.h"
#include "IMP/base_types.h"
#include <algorithm>
#include <cmath>
#include <cereal/access.hpp>

Include dependency graph for image_processing.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes
class	IMP::em2d::MatchTemplateResult
class	IMP::em2d::SegmentationParameters
	Class to provide all the parameters to the segmentation function. More...

Namespaces
	IMP
	Base functionality and abstract base classes for representation, scoring and sampling.
	IMP::em2d
	Restraints using electron microscopy 2D images (class averages).

Typedefs
typedef IMP::Vector < MatchTemplateResult >	IMP::em2d::MatchTemplateResults
typedef IMP::Vector < SegmentationParameters >	IMP::em2d::SegmentationParametersList

Functions
void	IMP::em2d::add_noise (DoubleMatrix &v, double op1, double op2, const String &mode="uniform", double df=3)
	Add noise to the values of a matrix. More...
void	IMP::em2d::apply_circular_mask (const DoubleMatrix &mat, DoubleMatrix &result, int radius, double value=0.0)
void	IMP::em2d::apply_diffusion_filter (const DoubleMatrix &m, DoubleMatrix &result, double beta, double pixelsize, unsigned int time_steps)
void	IMP::em2d::apply_mask (const DoubleMatrix &m, DoubleMatrix &result, const IntMatrix &mask, double val)
	Applies a binary mask to an image. More...
void	IMP::em2d::apply_threshold (DoubleMatrix &m, DoubleMatrix &result, double threshold=0.0)
void	IMP::em2d::apply_variance_filter (const DoubleMatrix &input, DoubleMatrix &filtered, int kernelsize)
IntMatrix	IMP::em2d::create_circular_mask (int rows, int cols, int radius)
DoubleMatrix	IMP::em2d::crop (const DoubleMatrix &m, const IntPair &center, int size)
void	IMP::em2d::do_combined_fill_holes_and_threshold (DoubleMatrix &m, DoubleMatrix &result, double n_stddevs, double threshold=0.0)
	Combines the fill holes and thresholding operations together with normalize. More...
void	IMP::em2d::do_dilate_and_shrink_warp (DoubleMatrix &m, const DoubleMatrix &grayscale, DoubleMatrix &kernel)
	(U. Adiga, 2005) More...
void	IMP::em2d::do_extend_borders (const DoubleMatrix &orig, DoubleMatrix &dst, unsigned int pix)
void	IMP::em2d::do_fill_holes (const DoubleMatrix &m, DoubleMatrix &result, double h)
	Fills the holes in the matrix m of height h. More...
void	IMP::em2d::do_histogram_stretching (DoubleMatrix &m, int boxes, int offset)
int	IMP::em2d::do_labeling (const IntMatrix &m, IntMatrix &mat_to_label)
	Labeling function for a matrix. More...
void	IMP::em2d::do_morphologic_contrast_enhancement (const DoubleMatrix &m, DoubleMatrix &result, const DoubleMatrix &kernel, unsigned int iterations)
void	IMP::em2d::do_morphologic_reconstruction (const DoubleMatrix &mask, DoubleMatrix &marker, int neighbors_mode=4)
	morphologic grayscale reconstruction (L Vincent, 1993) More...
void	IMP::em2d::do_normalize (DoubleMatrix &m)
	Normalize a matrix to mean 0 and stddev 1. It is done in place. More...
void	IMP::em2d::do_remove_small_objects (IntMatrix &m, double percentage, int background=0, int foreground=1)
	Removes small objects from a matrix of integers. More...
void	IMP::em2d::do_resample_polar (const DoubleMatrix &input, DoubleMatrix &resampled, const PolarResamplingParameters &polar_params)
	Resamples a matrix to polar coordinates. More...
void	IMP::em2d::do_segmentation (const DoubleMatrix &m, DoubleMatrix &result, const SegmentationParameters &params)
	Segmentation of images. More...
MatchTemplateResults	IMP::em2d::get_best_template_matches (const DoubleMatrix &m, const DoubleMatrix &templ, unsigned int n)
void	IMP::em2d::get_diffusion_filtering_partial_derivative (const DoubleMatrix &m, DoubleMatrix &der, double dx, double dy, double ang)
void	IMP::em2d::get_domes (DoubleMatrix &m, DoubleMatrix &result, double h)
	Gets the domes of m with height h. More...
Floats	IMP::em2d::get_histogram (const DoubleMatrix &m, int bins)
	Computes the histogram of a matrix. More...
double	IMP::em2d::get_mean (const DoubleMatrix &mat, const IntMatrix &mask)
void	IMP::em2d::get_morphologic_gradient (const DoubleMatrix &m, DoubleMatrix &result, const DoubleMatrix &kernel)
double	IMP::em2d::get_overlap_percentage (DoubleMatrix &m1, DoubleMatrix &m2, const IntPair &center)
void	IMP::em2d::get_transformed (const DoubleMatrix &input, DoubleMatrix &transformed, const algebra::Transformation2D &T)

Detailed Description

Image processing functions.

Copyright 2007-2026 IMP Inventors. All rights reserved.

Definition in file image_processing.h.