IMP::em2d Namespace Reference

See IMP.em2d Overview for more information.

Classes
class	CenteredMat
class	ChiSquaredScore
	Score based on Chi^2 = ((pixels_iamge - pixels_projection)/stddev_image)^2. More...
class	DistanceFilterTable
class	DummyRestraint
	Dummy restraint between two particles. More...
class	Em2DRestraint
class	EM2DScore
class	Fine2DRegistrationRestraint
class	GridStates
class	HasHigherCCC
	Comparison by value of the ccc. More...
class	HasLowerScore
	Compare two classes that return a score. More...
class	Image
	2D Electron Microscopy images in IMP More...
class	JPGImageReaderWriter
	Class to read and write EM images in JPG format. More...
class	LessPairBySecond
	Comparison of pairs by checking the second element. More...
class	MasksManager
	Manage of projection masks. More...
class	MatchTemplateResult
class	ParticlesDummyRestraint
	Dummy restraint for a set of particles. Same use as DummyRestraint. More...
class	PolarResamplingParameters
class	ProjectionFinder
	class to perform registration of model projections to images images More...
class	ProjectionMask
class	ProjectionParameters
class	ProjectionParametersScoreState
class	ProjectionStates
class	RegistrationResult
	Class to manage registration results. More...
class	ScoreFunction
	Base class for all scoring functions related to em2d. More...
class	SegmentationParameters
	Class to provide all the parameters to the segmentation function. More...
class	SpiderImageReaderWriter

Typedefs
typedef IMP::base::Vector < AverageDistanceLinkage >	AverageDistanceLinkages
typedef IMP::base::Vector < IMP::base::Pointer < ChiSquaredScore > >	ChiSquaredScores
typedef IMP::base::Vector < ClusterSet >	ClusterSets
typedef IMP::base::Vector < IMP::base::Pointer < CollisionCrossSection > >	CollisionCrossSections
typedef IMP::base::Vector < CompleteLinkage >	CompleteLinkages
typedef cv::MatConstIterator_ < double >	cvDoubleConstMatIterator
typedef cv::Mat_< double >	cvDoubleMat
typedef cv::MatIterator_< double >	cvDoubleMatIterator
typedef cv::Mat_< int >	cvIntMat
typedef cv::MatIterator_< int >	cvIntMatIterator
typedef cv::Point_< int >	cvPixel
typedef std::vector< cvPixel >	cvPixels
typedef IMP::base::Vector < IMP::base::Pointer < DistanceFilter > >	DistanceFilters
typedef IMP::base::Vector < IMP::base::Pointer < DistanceFilterTable > >	DistanceFilterTables
typedef IMP::base::Vector < IMP::base::Pointer < DummyRestraint > >	DummyRestraints
typedef IMP::base::Vector < Em2DRestraintParameters >	Em2DRestraintParametersList
typedef IMP::base::Vector < IMP::base::Pointer < Em2DRestraint > >	Em2DRestraints
typedef IMP::base::Vector < IMP::base::Pointer < EM2DScore > >	EM2DScores
typedef IMP::base::Vector < IMP::base::Pointer < Fine2DRegistrationRestraint > >	Fine2DRegistrationRestraints
typedef IMP::base::Vector < IMP::base::Pointer < GridStates > >	GridStatesList
typedef IMP::base::Vector < IMP::base::Pointer< Image > >	Images
	A vector of reference counted pointers to EM images of type double. More...
typedef std::map< Ints, unsigned int, IntsOrder >	KeyIndexMap
typedef std::vector< KeyIndexMap >	KeyIndexMaps
typedef std::pair< Ints, unsigned int >	KeyIndexPair
typedef std::list < pair_cluster_id_distance >	list_cluster_id_distance
typedef boost::shared_ptr < MasksManager >	MasksManagerPtr
typedef IMP::base::Vector < MasksManager >	MasksManagers
typedef IMP::base::Vector < MatchTemplateResult >	MatchTemplateResults
typedef IMP::base::Vector < IMP::base::Pointer < MeanAbsoluteDifference > >	MeanAbsoluteDifferences
typedef std::pair< unsigned int,double >	pair_cluster_id_distance
typedef IMP::base::Vector < IMP::base::Pointer < ParticlesDummyRestraint > >	ParticlesDummyRestraints
typedef IMP::base::Vector < PolarResamplingParameters >	PolarResamplingParametersList
typedef IMP::base::Vector < ProjectingOptions >	ProjectingOptionsList
typedef IMP::base::Vector < ProjectingParameters >	ProjectingParametersList
typedef IMP::base::Vector < IMP::base::Pointer < ProjectionFinder > >	ProjectionFinders
typedef boost::shared_ptr < ProjectionMask >	ProjectionMaskPtr
typedef IMP::base::Vector < ProjectionMask >	ProjectionMasks
typedef IMP::base::Vector < IMP::base::Pointer < ProjectionStates > >	ProjectionStatesList
typedef IMP::base::Vector < RegistrationResult >	RegistrationResults
typedef std::pair < algebra::Transformation2D, double >	ResultAlign2D
typedef IMP::base::Vector < IMP::base::Pointer < RigidBodiesImageFitRestraint > >	RigidBodiesImageFitRestraints
typedef IMP::base::Vector < IMP::base::Pointer < ScoreFunction > >	ScoreFunctions
typedef IMP::base::Vector < SegmentationParameters >	SegmentationParametersList
typedef IMP::base::Vector < SingleLinkage >	SingleLinkages
typedef std::vector < algebra::Transformation3Ds >	Transformation3DsList
typedef FloatsList	VectorOfFloats
typedef IntsList	VectorOfInts

Functions
void	add_noise (cv::Mat &v, double op1, double op2, const String &mode="uniform", double df=3)
	Add noise to the values of a matrix. More...
void	add_noise (Image *im1, double op1, double op2, const String &mode="uniform", double df=3)
void	apply_circular_mask (const cv::Mat &mat, cv::Mat &result, int radius, double value=0.0)
void	apply_diffusion_filter (const cv::Mat &m, cv::Mat &result, double beta, double pixelsize, unsigned int time_steps)
void	apply_diffusion_filter (Image *input, Image *filtered, double beta, double pixelsize, int time_steps)
void	apply_mask (const cv::Mat &m, cv::Mat &result, const cvIntMat &mask, double val)
	Applies a binary mask to an image. More...
void	apply_mean_outside_mask (Image *img, double radius)
void	apply_threshold (cv::Mat &m, cv::Mat &result, double threshold=0.0)
void	apply_variance_filter (const cv::Mat &input, cv::Mat &filtered, int kernelsize)
void	apply_variance_filter (Image *input, Image *filtered, int kernelsize)
cvIntMat	create_circular_mask (int rows, int cols, int radius)
Images	create_evenly_distributed_projections (const ParticlesTemp &ps, unsigned int n, const ProjectingOptions &options)
void	crop (Image *img, const IntPair &center, int size)
cv::Mat	crop (const cv::Mat &m, const IntPair &center, int size)
void	do_combined_fill_holes_and_threshold (cv::Mat &m, cv::Mat &result, double n_stddevs, double threshold=0.0)
	Combines the fill holes and tresholding operations together with normalize. More...
void	do_combined_fill_holes_and_threshold (Image *input, Image *result, double n_stddevs)
void	do_dilate_and_shrink_warp (cv::Mat &m, const cv::Mat &greyscale, cv::Mat &kernel)
	(U. Adiga, 2005) More...
void	do_extend_borders (Image *im1, Image *im2, unsigned int pix)
void	do_extend_borders (cv::Mat &orig, cv::Mat &dst, unsigned int pix)
void	do_fill_holes (const cv::Mat &m, cv::Mat &result, double h)
	Fills the holes in the matrix m of height h. More...
void	do_fill_holes (Image *input, Image *result, double n_stddevs)
template<class LinkageFunction >
ClusterSet	do_hierarchical_agglomerative_clustering (const FloatsList &distances)
void	do_histogram_stretching (cv::Mat &m, int boxes, int offset)
int	do_labeling (const cvIntMat &m, cvIntMat &mat_to_label)
	Labeling function for a matrix. More...
void	do_matrix_to_image_flip (cv::Mat &m)
void	do_morphologic_contrast_enhancement (const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel, unsigned int iterations)
void	do_morphologic_reconstruction (const cv::Mat &mask, cv::Mat &marker, int neighbors_mode=4)
	morphologic grayscale reconstruction (L Vincent, 1993) More...
void	do_normalize (Image *im, bool force=false)
void	do_normalize (cv::Mat &m)
	Normalize a openCV matrix to mean 0 and stddev 1. It is done in place.
void	do_place (cv::Mat &mask, cv::Mat &m, const algebra::Vector2D &v)
void	do_project_particles (const ParticlesTemp &ps, cv::Mat &m2, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const ProjectingOptions &options, MasksManagerPtr masks)
	Projects a set of particles. This is the core function that others call. More...
algebra::Vector2Ds	do_project_vectors (const algebra::Vector3Ds &ps, const algebra::Rotation3D &R, const algebra::Vector3D &translation)
	Project the points contained in Vector3Ds to gen vectors in 2D. More...
algebra::Vector2Ds	do_project_vectors (const algebra::Vector3Ds &ps, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const algebra::Vector3D &center)
	Project the points contained in Vector3Ds. More...
void	do_remove_small_objects (cvIntMat &m, double percentage, int background=0, int foreground=1)
	Removes small objects from a matrix of integers. More...
void	do_remove_small_objects (Image *input, double percentage, int background=0, int foreground=1)
void	do_resample_polar (const cv::Mat &input, cv::Mat &resampled, const PolarResamplingParameters &polar_params)
	Resamples a matrix to polar coordinates. More...
void	do_resample_polar (Image *im1, Image *im2, const PolarResamplingParameters &polar_params)
void	do_segmentation (const cv::Mat &m, cv::Mat &result, const SegmentationParameters &params)
	Segmentation of images. More...
void	do_segmentation (Image *input, Image *result, const SegmentationParameters &params)
void	do_subtract_images (Image *first, Image *second, Image *result)
void	get_autocorrelation2d (const cv::Mat &m, cv::Mat &corr)
void	get_autocorrelation2d (Image *im1, Image *im2)
void	get_autocorrelation2d_no_preprocessing (const cv::Mat &M, cv::Mat &corr)
	Autocorrelation without preprocessing. More...
double	get_average_rotation_error (const RegistrationResults &correct_RRs, const RegistrationResults &computed_RRs)
double	get_average_shift_error (const RegistrationResults &correct_RRs, const RegistrationResults &computed_RRs)
MatchTemplateResults	get_best_template_matches (const cv::Mat &m, const cv::Mat &templ, unsigned int n)
ResultAlign2D	get_complete_alignment (const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
em2d::ResultAlign2D	get_complete_alignment_no_preprocessing (const cv::Mat &input, const cv::Mat &INPUT, const cv::Mat &POLAR1, cv::Mat &m_to_align, const cv::Mat &POLAR2, bool apply=false)
ResultAlign2D	get_complete_alignment_with_centers_no_preprocessing (const algebra::Vector2D &center1, const algebra::Vector2D &center2, const cv::Mat &AUTOC_POLAR1, const cv::Mat &AUTOC_POLAR2)
void	get_correlation2d (const cv::Mat &A, const cv::Mat &B, cv::Mat &corr)
	Correlation matrix between two 2D matrices using FFT. More...
void	get_correlation2d (Image *im1, Image *im2, Image *corr)
void	get_correlation2d_no_preprocessing (const cv::Mat &M1, const cv::Mat &M2, cv::Mat &corr)
double	get_cross_correlation_coefficient (const cv::Mat &m1, const cv::Mat &m2)
	Computes the cross-correlation coefficient between to matrices.
double	get_cross_correlation_coefficient (Image *im1, Image *im2)
	Cross correlation between two images. More...
std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...
void	get_diffusion_filtering_partial_derivative (const cv::Mat &m, cv::Mat &der, double dx, double dy, double ang)
void	get_domes (cv::Mat &m, cv::Mat &result, double h)
	Gets the domes of m with height h. More...
unsigned int	get_enclosing_image_size (const ParticlesTemp &ps, double pixel_size, unsigned int slack)
RegistrationResults	get_evenly_distributed_registration_results (unsigned int n_projections)
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...
void	get_fft_using_optimal_size (const cv::Mat &m, cv::Mat &M)
double	get_global_score (const RegistrationResults &RRs)
Floats	get_histogram (const cv::Mat &m, int bins)
	Computes the histogram of a matrix. More...
Floats	get_histogram (Image *img, int bins)
double	get_mean (const cv::Mat &mat, const cvIntMat &mask)
void	get_morphologic_gradient (const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel)
double	get_overlap_percentage (cv::Mat &m1, cv::Mat &m2, const IntPair &center)
void	get_projection (em2d::Image *img, const ParticlesTemp &ps, const RegistrationResult &reg, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="")
	Generates a projection from particles. More...
em2d::Images	get_projections (const ParticlesTemp &ps, const algebra::SphericalVector3Ds &vs, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
	Generates projectios from particles. More...
em2d::Images	get_projections (const ParticlesTemp &ps, const RegistrationResults &registration_values, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
	Generates projectios from particles. More...
double	get_random_between_zero_and_one ()
RegistrationResults	get_random_registration_results (unsigned int n, double maximum_shift=5.0)
	Provides a set of random registration results (or parameters) More...
double	get_rotation_error (const RegistrationResult &rr1, const RegistrationResult &rr2)
em2d::ResultAlign2D	get_rotational_alignment (const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
ResultAlign2D	get_rotational_alignment_no_preprocessing (const cv::Mat &POLAR1, const cv::Mat &POLAR2)
double	get_shift_error (const RegistrationResult &rr1, const RegistrationResult &rr2)
	Distance between the two in-plane translations.
void	get_spectrum (const cv::Mat &m, cv::Mat &real, cv::Mat &imag)
void	get_transformed (const cv::Mat &input, cv::Mat &transformed, const algebra::Transformation2D &T)
ResultAlign2D	get_translational_alignment (const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
	Aligns two matrices translationally. More...
ResultAlign2D	get_translational_alignment_no_preprocessing (const cv::Mat &M1, const cv::Mat &M2)
Ints	get_unique_index (const algebra::Rotation3D &rot)
void	my_meanStdDev (const cv::Mat &m, cv::Scalar &mean, cv::Scalar &stddev)
template<class T >
void	print_vector (const std::vector< T > &v)
Images	read_images (const Strings &names, const ImageReaderWriter *rw)
RegistrationResults	read_registration_results (const String &filename)
	Reads a set of registration results.
void	save_images (Images images, const Strings &names, const ImageReaderWriter *rw)
void	show (const cv::Mat &m, std::ostream &out=std::cout)
	Prints a OpenCV matrix.
template<typename T >
void	show (const cv::Mat_< T > &m, std::ostream &out=std::cout)
	Show a Mat_.
void	write_matrix (cv::Mat &m, std::string name)
	Quick and dirty way of writing a OpenCV matrix to a Spider image.
void	write_registration_results (String filename, const RegistrationResults &results)
	Writes a set of registration results.
void	write_vectors_as_pdb (const algebra::Vector2Ds vs, const String filename)
void	write_vectors_as_pdb (const algebra::Vector3Ds vs, const String filename)

Variables
const unsigned int	ALIGN2D_NO_PREPROCESSING = 0
	Methods for registration used by the finder.
const unsigned int	ALIGN2D_PREPROCESSING = 1
const unsigned int	ALIGN2D_WITH_CENTERS = 2

Standard module methods
All IMP modules have a set of standard methods to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()

Typedef Documentation

typedef IMP::base::Vector< AverageDistanceLinkage > IMP::em2d::AverageDistanceLinkages

Pass or store a set of AverageDistanceLinkage .

Definition at line 201 of file hierarchical_clustering.h.

typedef IMP::base::Vector<IMP::base::Pointer< ChiSquaredScore > > IMP::em2d::ChiSquaredScores

Store a set of objects.

Definition at line 96 of file scores2D.h.

typedef IMP::base::Vector< ClusterSet > IMP::em2d::ClusterSets

Pass or store a set of ClusterSet .

Definition at line 126 of file hierarchical_clustering.h.

typedef IMP::base::Vector<IMP::base::Pointer< CollisionCrossSection > > IMP::em2d::CollisionCrossSections

Store a set of objects.

Definition at line 81 of file CollisionCrossSection.h.

typedef IMP::base::Vector< CompleteLinkage > IMP::em2d::CompleteLinkages

Pass or store a set of CompleteLinkage .

Definition at line 178 of file hierarchical_clustering.h.

typedef IMP::base::Vector<IMP::base::Pointer< DistanceFilter > > IMP::em2d::DistanceFilters

Store a set of objects.

Definition at line 59 of file domino_filters.h.

typedef IMP::base::Vector<IMP::base::Pointer< DistanceFilterTable > > IMP::em2d::DistanceFilterTables

Store a set of objects.

Definition at line 44 of file domino_filter_tables.h.

typedef IMP::base::Vector<IMP::base::Pointer< DummyRestraint > > IMP::em2d::DummyRestraints

Store a set of objects.

Definition at line 64 of file DummyRestraint.h.

typedef IMP::base::Vector< Em2DRestraintParameters > IMP::em2d::Em2DRestraintParametersList

Pass or store a set of Em2DRestraintParameters .

Definition at line 72 of file ProjectionFinder.h.

typedef IMP::base::Vector<IMP::base::Pointer< Em2DRestraint > > IMP::em2d::Em2DRestraints

Store a set of objects.

Definition at line 139 of file Em2DRestraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< EM2DScore > > IMP::em2d::EM2DScores

Store a set of objects.

Definition at line 110 of file scores2D.h.

typedef IMP::base::Vector<IMP::base::Pointer< Fine2DRegistrationRestraint > > IMP::em2d::Fine2DRegistrationRestraints

Store a set of objects.

Definition at line 103 of file Fine2DRegistrationRestraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< GridStates > > IMP::em2d::GridStatesList

Store a set of objects.

Definition at line 71 of file domino_particle_states.h.

typedef IMP::base::Vector<IMP::base::Pointer< Image > > IMP::em2d::Images

Store a set of objects.

Definition at line 216 of file Image.h.

typedef IMP::base::Vector< MasksManager > IMP::em2d::MasksManagers

Pass or store a set of MasksManager .

Definition at line 210 of file ProjectionMask.h.

typedef IMP::base::Vector< MatchTemplateResult > IMP::em2d::MatchTemplateResults

Pass or store a set of MatchTemplateResult .

Definition at line 91 of file image_processing.h.

typedef IMP::base::Vector<IMP::base::Pointer< MeanAbsoluteDifference > > IMP::em2d::MeanAbsoluteDifferences

Store a set of objects.

Definition at line 118 of file scores2D.h.

typedef IMP::base::Vector<IMP::base::Pointer< ParticlesDummyRestraint > > IMP::em2d::ParticlesDummyRestraints

Store a set of objects.

Definition at line 93 of file DummyRestraint.h.

typedef IMP::base::Vector< PolarResamplingParameters > IMP::em2d::PolarResamplingParametersList

Pass or store a set of PolarResamplingParameters .

Definition at line 195 of file PolarResamplingParameters.h.

typedef IMP::base::Vector< ProjectingOptions > IMP::em2d::ProjectingOptionsList

Pass or store a set of ProjectingOptions .

Definition at line 106 of file project.h.

typedef IMP::base::Vector< ProjectingParameters > IMP::em2d::ProjectingParametersList

Pass or store a set of ProjectingParameters .

Definition at line 53 of file project.h.

typedef IMP::base::Vector<IMP::base::Pointer< ProjectionFinder > > IMP::em2d::ProjectionFinders

Store a set of objects.

Definition at line 243 of file ProjectionFinder.h.

typedef IMP::base::Vector< ProjectionMask > IMP::em2d::ProjectionMasks

Pass or store a set of ProjectionMask .

Definition at line 78 of file ProjectionMask.h.

typedef IMP::base::Vector<IMP::base::Pointer< ProjectionStates > > IMP::em2d::ProjectionStatesList

Store a set of objects.

Definition at line 115 of file domino_particle_states.h.

typedef IMP::base::Vector< RegistrationResult > IMP::em2d::RegistrationResults

Pass or store a set of RegistrationResult .

Definition at line 163 of file RegistrationResult.h.

typedef std::pair<algebra::Transformation2D,double> IMP::em2d::ResultAlign2D

Definition of the result of an alignment. Contains the transformation to apply to the matrix to align and the cross correlation of the solution

Definition at line 22 of file align2D.h.

typedef IMP::base::Vector<IMP::base::Pointer< RigidBodiesImageFitRestraint > > IMP::em2d::RigidBodiesImageFitRestraints

Store a set of objects.

Definition at line 89 of file RigidBodiesImageFitRestraint.h.

typedef IMP::base::Vector<IMP::base::Pointer< ScoreFunction > > IMP::em2d::ScoreFunctions

Store a set of objects.

Definition at line 84 of file scores2D.h.

typedef IMP::base::Vector< SegmentationParameters > IMP::em2d::SegmentationParametersList

Pass or store a set of SegmentationParameters .

Definition at line 73 of file image_processing.h.

typedef IMP::base::Vector< SingleLinkage > IMP::em2d::SingleLinkages

Pass or store a set of SingleLinkage .

Definition at line 154 of file hierarchical_clustering.h.

typedef std::vector<algebra::Transformation3Ds > IMP::em2d::Transformation3DsList

Class for the movement of rigid bodies respect to each other. The class is initiated with the rigid body that is going to move (let's call it A). Afterwards, one of more rigid bodies can be added as references. Each reference rigid body needs to specify the set of the internal (relative) transformations that A can have respect to it.

Parameters

[in]

Definition at line 34 of file RelativePositionMover.h.

Function Documentation

void IMP::em2d::add_noise	(	cv::Mat &	v,
		double	op1,
		double	op2,
		const String &	mode = "uniform",
		double	df = 3
	)

Supported distributions:

• uniform distribution, giving the range (lower, upper). DEFAULT
• gaussian distribution, giving the mean and the standard deviation

   add_noise(v1,0, 1);
   // uniform distribution between 0 and 1
  
   v1.add_noise(0, 1, "uniform");
   // the same
  
   v1.add_noise(0, 1, "gaussian");
  // gaussian distribution with 0 mean and stddev=1

void IMP::em2d::apply_circular_mask	(	const cv::Mat &	mat,
		cv::Mat &	result,
		int	radius,
		double	value = 0.0
	)

Applies a circular to a matrix. The center of the mask is the center of the matrx.

Parameters

[in]

Radius

of the mask

void IMP::em2d::apply_diffusion_filter	(	const cv::Mat &	m,
		cv::Mat &	result,
		double	beta,
		double	pixelsize,
		unsigned int	time_steps
	)

Smoothing filter by application of the reaction-diffusion equation of Beltrami flow. Adiga, JSB, 2005

Parameters

[in]

beta

contribution of diffusion versus edge enhancement. 0 - pure reaction, 90 - pure diffusion

Note

The function only works for matrices containing doubles

void IMP::em2d::apply_diffusion_filter	(	Image *	input,
		Image *	filtered,
		double	beta,
		double	pixelsize,
		int	time_steps
	)

Apply the diffusion filter

Parameters

input	Input image
filtered	The image containing the result
beta	The beta parameter of the difussion filter
pixelsize	The pixel size of the image
time_steps	The number of time steps used for the diffusion

Definition at line 309 of file Image.h.

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void IMP::em2d::apply_mask	(	const cv::Mat &	m,
		cv::Mat &	result,
		const cvIntMat &	mask,
		double	val
	)

Parameters

[in]	m	Input matrix
[in]	result	matrix with the result
[in]	mask	If the mask is 0, the result has the value of val. Otherwise is the value of m.
[in]	value	value to apply when the mask is 0

void IMP::em2d::apply_mean_outside_mask	(	Image *	img,
		double	radius
	)

Fills the values that are outside a circle centered at the center of the image with the mean of the values inside the circle the matrix center

Parameters

[in]	img	Image. It is modified in situ
[in]	radius	of the circle

void IMP::em2d::apply_threshold	(	cv::Mat &	m,
		cv::Mat &	result,
		double	threshold = 0.0
	)

Applys a threshold to an image

Parameters

[in]

threshold.

all pixels below this value are set to zero

void IMP::em2d::apply_variance_filter	(	const cv::Mat &	input,
		cv::Mat &	filtered,
		int	kernelsize
	)

Variance filter for an image. Computes the variance for each pixel using the surrounding ones.

Parameters

[in]	input	image with the data
[out]	filtered	matrix result of the filtering with the variances
[in]	kernelsize	The variance is computed using kernelsize x kernelsize pixels around each one. Kernelsize can only be odd.

void IMP::em2d::apply_variance_filter	(	Image *	input,
		Image *	filtered,
		int	kernelsize
	)

Apply a variance filter to an image

Parameters

input	Input image
filtered	The image containing the result
kernelsize	The size of the kernel to use. The matrix used as kernel will have the same number of rows and columns

Definition at line 296 of file Image.h.

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cvIntMat IMP::em2d::create_circular_mask	(	int	rows,
		int	cols,
		int	radius
	)

Creates a circular matrix that is a mask

Parameters

[in]	rows
[in]	cols
[in]	radius	The radius of the mask. The center of the mask is the center of the matrix

Returns

A binary matrix (0/1) with value 1 inside the radius

Images IMP::em2d::create_evenly_distributed_projections	(	const ParticlesTemp &	ps,
		unsigned int	n,
		const ProjectingOptions &	options
	)

This function is slightly different than the other ones. Only generates evenly distributed projections and determines the size of the images that encloses the particles. Should not be used unless this is exactly what you want.

void IMP::em2d::crop	(	Image *	img,
		const IntPair &	center,
		int	size
	)

Crops an image.

Parameters

[in]	img	Image to crop. It is modified in place
[in]	center	The pixel used as the center for cropping
[in]	size	The size of the new image

cv::Mat IMP::em2d::crop	(	const cv::Mat &	m,
		const IntPair &	center,
		int	size
	)

Crop an image

Parameters

[in]	m	Matrix to crop
[in]	center	The pixel used as the center for cropping
[in]	size	The size of the new image

Returns

A matrix with the cropped region

void IMP::em2d::do_combined_fill_holes_and_threshold	(	cv::Mat &	m,
		cv::Mat &	result,
		double	n_stddevs,
		double	threshold = 0.0
	)

Parameters

[in]	m	Input matrix
[out]	result	the result matrix
[in]	n_stddevs	Number of standard deviations used to compute the holes
[in]	threshold	Removes values below the threshold value

Note

The function does normalize -> fill_holes -> normalize -> threshold -> normalize

void IMP::em2d::do_dilate_and_shrink_warp	(	cv::Mat &	m,
		const cv::Mat &	greyscale,
		cv::Mat &	kernel
	)

Parameters

[in]	m	binary matrix to dilate and shrink
[in]	greyscale	greyscale matrix that controls the shrinking
[in]	kernel	dilation kernel

Note

Only tested with binary matrices m with background =0 and foreground = 1

void IMP::em2d::do_extend_borders	(	cv::Mat &	orig,
		cv::Mat &	dst,
		unsigned int	pix
	)

Extends the bordes of an image

Parameters

[in]	orig	The image to extend
[in]	dst	The image destination
[in]	pix	number of pixels to extend the borders

void IMP::em2d::do_fill_holes	(	const cv::Mat &	m,
		cv::Mat &	result,
		double	h
	)

Parameters

[in]	m	the input matrix
[in]	result	the result matrix
[in]	h	the height

Note

The function does not work in-place

template<class LinkageFunction >

ClusterSet IMP::em2d::do_hierarchical_agglomerative_clustering

(

const FloatsList &

distances

)

Parameters

[in]	distances	Vector of Floats containing all the possible distances(i,j) between elements to cluster. Given N elements to cluster, there are N vectors of size N
[in]	Function	to calculate distance between clusters.
[out]	a	ClusterSet class containing all the clustering steps.

Definition at line 216 of file hierarchical_clustering.h.

int IMP::em2d::do_labeling	(	const cvIntMat &	m,
		cvIntMat &	mat_to_label
	)

Parameters

[in]	m	binary matrix to scan. The matrix needs to contain zeros and ones but they can be stored as doubles, floats or ints
[out]	result	matrix it is returned as a matrix of ints
[out]	labels	The number of labels in the image

void IMP::em2d::do_matrix_to_image_flip

(

cv::Mat &

m

)

Transforms a matrix as is given by FFT functions, into a image interpretation. Works the opposite way too.

Parameters

m	The matrix to flip. The it is changed in situ

void IMP::em2d::do_morphologic_contrast_enhancement	(	const cv::Mat &	m,
		cv::Mat &	result,
		const cv::Mat &	kernel,
		unsigned int	iterations
	)

morphologic enhancement of the contrast This function detects areas in the images and enhances the contrast between them

Parameters

[in]	m	Imput matrix
[out]	result
[in]	kernel	morphologic kernel to use
[in]	iterations	Higher number, more contrast

void IMP::em2d::do_morphologic_reconstruction	(	const cv::Mat &	mask,
		cv::Mat &	marker,
		int	neighbors_mode = 4
	)

Parameters

[in]	mask	image to reconstruct
[out]	marker	this image contains the initial marker points and will contain the final result
[in]	neighbors_mode	number of neighbors for a pixel to consider when doing the morphologic reconstruction (values: 4, 8).

void IMP::em2d::do_normalize	(	Image *	im,
		bool	force = false
	)

Normalize an image subtracting the mean and dividing by the standard deviation

Parameters

im	Image
force	If true, the image is normalized even if the header says that it is already normalized

void IMP::em2d::do_place	(	cv::Mat &	mask,
		cv::Mat &	m,
		const algebra::Vector2D &	v
	)

Parameters

[in]	mask	matrix to place in m
[in]	m	matrix
[in]	v	Pixel of the matrix dest where the center of m is put.

Definition at line 92 of file ProjectionMask.h.

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void IMP::em2d::do_project_particles	(	const ParticlesTemp &	ps,
		cv::Mat &	m2,
		const algebra::Rotation3D &	R,
		const algebra::Vector3D &	translation,
		const ProjectingOptions &	options,
		MasksManagerPtr	masks
	)

Parameters

[in]	ps	particles to project
[in]	R	rotation to apply to the particles (respect to the centroid)
[in]	translation	Translation to apply after rotation
[in]	clear_matrix_before	If true the matrix is set to zero before projecting the particles. You want this 99% of the time, as setting to false will add one projection on top of the other

Note

See the function get_projection() for the rest of the parameters

algebra::Vector2Ds IMP::em2d::do_project_vectors	(	const algebra::Vector3Ds &	ps,
		const algebra::Rotation3D &	R,
		const algebra::Vector3D &	translation
	)

Parameters

[in]	ps	the points
[in]	R	Rotation to apply to the points to project them in the Z axis
[in]	translation	translation to apply to the points

Returns

A set of Vector2D with the projected points

algebra::Vector2Ds IMP::em2d::do_project_vectors	(	const algebra::Vector3Ds &	ps,
		const algebra::Rotation3D &	R,
		const algebra::Vector3D &	translation,
		const algebra::Vector3D &	center
	)

Parameters

[in]	ps	the points
[in]	R	Rotation to apply to the points to project them in the Z axis
[in]	translation	translation to apply to the points
[in]	center	Center point used for the rotation around it

Returns

A set of Vector2D with the projected points

void IMP::em2d::do_remove_small_objects	(	cvIntMat &	m,
		double	percentage,
		int	background = 0,
		int	foreground = 1
	)

Parameters

[in]	m	the matrix
[in]	percentage	The percentage respect to the largest object that other objects have to be in order to survive the removal.
[in]	background	value for the background after removed
[in]	background	value for the foreground after removed

void IMP::em2d::do_resample_polar	(	const cv::Mat &	input,
		cv::Mat &	resampled,
		const PolarResamplingParameters &	polar_params
	)

Parameters

[in]	m	matrix to resample
[out]	result	matrix to contain the resampling
[in]	polar	params Parameters used for the resampling. Extremely useful for speeding up the procedure if they are given with the transformation maps, that can be built in the PolarResamplingParameters class

void IMP::em2d::do_resample_polar	(	Image *	im1,
		Image *	im2,
		const PolarResamplingParameters &	polar_params
	)

Resample an image to polar coordinates

Parameters

im1	The input image
im2	The output image
polar_params	The parameters used for the sampling

void IMP::em2d::do_segmentation	(	const cv::Mat &	m,
		cv::Mat &	result,
		const SegmentationParameters &	params
	)

Parameters

[in]	m	The EM image to segment
[in]	result	The segmented image, with the shape of the molecule

void IMP::em2d::do_subtract_images	(	Image *	first,
		Image *	second,
		Image *	result
	)

Subtract two images

Parameters

first	First image
second	The second image is subtracted from the second
result	Result image

void IMP::em2d::get_autocorrelation2d	(	const cv::Mat &	m,
		cv::Mat &	corr
	)

Computes the autocorrelation matrix

Parameters

m	The input matrix
corr	The result matrix containing the autocorrelation

void IMP::em2d::get_autocorrelation2d	(	Image *	im1,
		Image *	im2
	)

Compute the autocorrelation for an image

Parameters

im1	The input image
im2	The output image

Definition at line 254 of file Image.h.

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void IMP::em2d::get_autocorrelation2d_no_preprocessing	(	const cv::Mat &	M,
		cv::Mat &	corr
	)

Parameters

[in]	M	matrix containing the dft
[out]	corr	the matrix to store the autocorrelation. Must have the proper dimensions when passed Autocorrelation without preprocessing.
	M	matrix containing the dft
	corr	The matrix to store the autocorrelation. Must have the proper dimensions when passed.

MatchTemplateResults IMP::em2d::get_best_template_matches	(	const cv::Mat &	m,
		const cv::Mat &	templ,
		unsigned int	n
	)

Gets the n first matches between an image and a template

Parameters

[in]	m	Matrix
[in]	templ	Matrix with a template to be found in m
[in]	n	Number of positions to recover

ResultAlign2D IMP::em2d::get_complete_alignment	(	const cv::Mat &	input,
		cv::Mat &	m_to_align,
		bool	apply = false
	)

Aligns completely two matrices (rotationally and translationally). Uses the autocorrelation function to speed up the rotational alignment

Parameters

[in]	input	Reference matrix
[in]	m_to_align	Matrix to align to the reference
[in]	apply	if true, apply the transformation to m_to_align after alignment

Returns

The result. Check the definition of ResultAlign2D

em2d::ResultAlign2D IMP::em2d::get_complete_alignment_no_preprocessing	(	const cv::Mat &	input,
		const cv::Mat &	INPUT,
		const cv::Mat &	POLAR1,
		cv::Mat &	m_to_align,
		const cv::Mat &	POLAR2,
		bool	apply = false
	)

Aligns two matrices rotationally and translationally without performing preprocessing. Preprocessed data must be provided.

Parameters

[in]	input	first matrix
[in]	INPUT	fft of the first matrix
[in]	POLAR1	fft of the autocorrelation (in polars) of the input.
[in]	m_to_align	the matrix to align with the input
[in]	POLAR2	fft of the autocorrelation (in polars) of m_to_align
[in]	apply	true if m_to_align is transformed at the end

Returns

The result. Check the definition of ResultAlign2D

ResultAlign2D IMP::em2d::get_complete_alignment_with_centers_no_preprocessing	(	const algebra::Vector2D &	center1,
		const algebra::Vector2D &	center2,
		const cv::Mat &	AUTOC_POLAR1,
		const cv::Mat &	AUTOC_POLAR2
	)

Aligns two matrices (rotation and translation) using centers and no preprocessing. Preprocessed data must be provided.

Parameters

[in]	center1	weighted centroid of the reference matrix
[in]	center2	weighted centroid of the matrix to align
[in]	AUTOC_POLAR1	fft of the autocorrelation (in polars) of the input.
[in]	AUTOC_POLAR2	fft of the autocorrelation (in polars) of m_to_align

Returns

The result. Check the definition of ResultAlign2D

void IMP::em2d::get_correlation2d	(	const cv::Mat &	A,
		const cv::Mat &	B,
		cv::Mat &	corr
	)

Parameters

[in]	A	first matrix
[in]	B	second matrix
[out]	corr	matrix of results

void IMP::em2d::get_correlation2d	(	Image *	im1,
		Image *	im2,
		Image *	corr
	)

Compute the cross correlation matrix between two images

Parameters

im1	First input image
im2	First second image
corr	The output image of cross correlation values

Definition at line 264 of file Image.h.

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void IMP::em2d::get_correlation2d_no_preprocessing	(	const cv::Mat &	M1,
		const cv::Mat &	M2,
		cv::Mat &	corr
	)

Correlation without preprocessing Returns the correlation matrix between two 2D matrices using FFT

Parameters

[in]	M1	matrix containing the dft of the first matrix
[in]	M2	matrix containing the dft of the second matrix
[out]	corr	matrix of results (It MUST have the right size in advance)

double IMP::em2d::get_cross_correlation_coefficient	(	Image *	im1,
		Image *	im2
	)

Get the cross correlation coefficient between 2 images

Parameters

im1	First image
im2	Second image

Returns

The value of the coefficient. Ranges from 0 to 1

std::string IMP::em2d::get_data_path

(

std::string

file_name

)

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

void IMP::em2d::get_diffusion_filtering_partial_derivative	(	const cv::Mat &	m,
		cv::Mat &	der,
		double	dx,
		double	dy,
		double	ang
	)

Partial derivative with respect to time for an image filtered with difusion-reaction

Parameters

[in]	m	input matrix
[in]	der	output derivative matrix
[in]	dx	- step for x
[in]	dy	- step for y
[in]	ang	- parameter for weight diffusion and edge detection (90-0)

void IMP::em2d::get_domes	(	cv::Mat &	m,
		cv::Mat &	result,
		double	h
	)

Parameters

[in]	m	the input matrix
[in]	result	the result matrix
[in]	h	the height

Note

The function does not work in-place

unsigned int IMP::em2d::get_enclosing_image_size	(	const ParticlesTemp &	ps,
		double	pixel_size,
		unsigned int	slack
	)

Get an automatic size for an image that contains the particles

Parameters

[in]

slack

is the number of pixels left as border

RegistrationResults IMP::em2d::get_evenly_distributed_registration_results

(

unsigned int

n_projections

)

Provides a set of registration results with directions of projection evenly distributed in the semisphere

Parameters

[in]

n_projections

the number of requested projections

std::string IMP::em2d::get_example_path

(

std::string

file_name

)

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb", model));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

void IMP::em2d::get_fft_using_optimal_size	(	const cv::Mat &	m,
		cv::Mat &	M
	)

Get the FFT of a matrix using padding with other matrix that can be computed with FFT in an optimal way. i.e. with a size that makes the FFT algorithm work faster

Parameters

m	The input matrix
M	The output matrix with the FFT

Note

The output matrix can have (and frequently will have) different dimensions than the input matrix

double IMP::em2d::get_global_score

(

const RegistrationResults &

RRs

)

Get the gloal score given a set of individual registration results from images

Note

The function checks what time of registration results are given.

• If the registration results correspond to a coarse registration, the score is based on the cross-correlation (currently, the score is a mean of the cross-correlation coefficients.
• If the registration results are obtained after a fine registration, the score is the average of all the registration scores. This score g depends on the function selected. Eg. EM2DScore.

Floats IMP::em2d::get_histogram	(	const cv::Mat &	m,
		int	bins
	)

Parameters

[in]	m	Matrix with the data
[in]	bins	Number of bins to use in the histogram
[out]	vector	with the values for each bin

Floats IMP::em2d::get_histogram	(	Image *	img,
		int	bins
	)

Gets an histogram of the values of the image

Parameters

img	The image
bins	The number of bins to use to build the histogram

Returns

The histogram: number of points per bin

Definition at line 284 of file Image.h.

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double IMP::em2d::get_mean	(	const cv::Mat &	mat,
		const cvIntMat &	mask
	)

Mean of an matrix inside a mask

Parameters

[in]	mat	The matrix
[in]	mask	If a pixel is not zero, is considered for computing the mean

Returns

The mean

void IMP::em2d::get_morphologic_gradient	(	const cv::Mat &	m,
		cv::Mat &	result,
		const cv::Mat &	kernel
	)

Morphologic gradient: dilation-erosion

Parameters

[in]	m	Input matrix
[out]	result
[in]	kernel	morphologic kernel

double IMP::em2d::get_overlap_percentage	(	cv::Mat &	m1,
		cv::Mat &	m2,
		const IntPair &	center
	)

Get the percentage of overlap between two matrices. Two images are overlapping in a pixel if both have values > 0. The overlap is (pixels overlapping) / (pixels > 0 in m2)

Parameters

[in]	m1	First matrix
[in]	m2	Matrix used to check the overlap. This matrix can be of the same size of m1 or smaller.
[in]	center	Indicates the position of m1 where to put the center m2. E.g., if center is (32,16) the center of m2 will be in the pixel (32,16) of m1.

void IMP::em2d::get_projection	(	em2d::Image *	img,
		const ParticlesTemp &	ps,
		const RegistrationResult &	reg,
		const ProjectingOptions &	options,
		MasksManagerPtr	masks = MasksManagerPtr(),
		String	name = ""
	)

Parameters

[in]	ps	particles to project
[in]	reg	Registration value with the parameters of the projection
[in]	masks	Precomputed masks for projecting the particles. Very useful for speeding the projection procedure if they are given. If nullptr, they are computed
[out]	img	the projection will be stored here

Note

See the function get_projections() for the rest of the parameters

em2d::Images IMP::em2d::get_projections	(	const ParticlesTemp &	ps,
		const algebra::SphericalVector3Ds &	vs,
		int	rows,
		int	cols,
		const ProjectingOptions &	options,
		Strings	names = Strings()
	)

Parameters

[in]	ps	particles to project
[in]	vs	set of spherical vectors with the directions of projection
[in]	rows	size of the images
[in]	cols
[in]	options	Options for control the projecting
[in]	names	names of the images

em2d::Images IMP::em2d::get_projections	(	const ParticlesTemp &	ps,
		const RegistrationResults &	registration_values,
		int	rows,
		int	cols,
		const ProjectingOptions &	options,
		Strings	names = Strings()
	)

Parameters

[in]

registration_values

Registration values with the parameters of the projections to generate

Note

See the function get_projections() for the rest of the parameters

RegistrationResults IMP::em2d::get_random_registration_results	(	unsigned int	n,
		double	maximum_shift = 5.0
	)

Parameters

[in]	n	the number of requested results
[in]	maximum_shift	shift from the center in pixels

double IMP::em2d::get_rotation_error	(	const RegistrationResult &	rr1,
		const RegistrationResult &	rr2
	)

angle in the axis-angle representation of the rotation that takes first to second

em2d::ResultAlign2D IMP::em2d::get_rotational_alignment	(	const cv::Mat &	input,
		cv::Mat &	m_to_align,
		bool	apply = false
	)

Aligns two matrices rotationally. Based on the autocorrelation function of the matrices.

Parameters

[in]	input	Reference matrix
[in]	m_to_align	Matrix to align to the reference
[in]	apply	if true, apply the transformation to m_to_align after alignment

Returns

The result. Check the definition of ResultAlign2D

ResultAlign2D IMP::em2d::get_rotational_alignment_no_preprocessing	(	const cv::Mat &	POLAR1,
		const cv::Mat &	POLAR2
	)

Computes the rotational alignment for two autocorrelation matrices It is assumed that the arguments are FFTs

Parameters

[in]	M1	fft of the first autocorrelation (in polars)
[in]	M2	fft of the second autocorrelation (in polars)

Returns

The result. Check the definition of ResultAlign2D

void IMP::em2d::get_spectrum	(	const cv::Mat &	m,
		cv::Mat &	real,
		cv::Mat &	imag
	)

Computes the fft of a matrix and returns the real and imaginary matrices

Parameters

m	The input matrix
real	The matrix with the real part of the FFT matrix
imag	The imaginary part of the FFT matrix

void IMP::em2d::get_transformed	(	const cv::Mat &	input,
		cv::Mat &	transformed,
		const algebra::Transformation2D &	T
	)

Applies a transformation to a matrix. First rotates the matrix using the matrix center as the origin of the rotation, and then applies the translation

ResultAlign2D IMP::em2d::get_translational_alignment	(	const cv::Mat &	input,
		cv::Mat &	m_to_align,
		bool	apply = false
	)

Parameters

[in]	input	Reference matrix
[in]	m_to_align	Matrix to align to the reference
[in]	apply	if true, apply the transformation to m_to_align after alignment

Returns

The result. Check the definition of ResultAlign2D

ResultAlign2D IMP::em2d::get_translational_alignment_no_preprocessing	(	const cv::Mat &	M1,
		const cv::Mat &	M2
	)

Aligns two matrices translationally without preprocessing. The preprocessed data must be provided.

Parameters

[in]	M1	the dft the first matrix (input)
[in]	M2	the dft of the matrix to align with the input

Returns

The result. Check the definition of ResultAlign2D

Images IMP::em2d::read_images	(	const Strings &	names,
		const ImageReaderWriter *	rw
	)

Reads images from files (For compatibility with SPIDER format, the images are read from floats)

Parameters

[in]	names	filenames of the images
[in]	rw	reader/writer to use

void IMP::em2d::save_images	(	Images	images,
		const Strings &	names,
		const ImageReaderWriter *	rw
	)

Saves images to files (For compatibility with SPIDER format, the images are written to floats)

Parameters

[in]	images	Images to save
[in]	names	filenames of the images
[in]	rw	reader/writer to use

void IMP::em2d::write_vectors_as_pdb	(	const algebra::Vector2Ds	vs,
		const String	filename
	)

Generate a PDB file from a set of Vector2D (all the points are C-alpha) and the Z coordinate is set to 0.

Note

This version deals with the problem of having more than 10000 points