Reconstruction library

Collaboration diagram for Reconstruction library:

Modules
	Homogenizer
	art_xray (ART for xrays)
	Classify Kmeans 2D
	Classify a set of images into a discrete set of classes
	Common Lines (find common lines between projections)
	ctf_correct_idr (Iterative Data Refinement for CTF amplitude correction)
	(phase flipping)
	Evaluate Coordinates
	Extracting Particles From Metadata
	IDR Xray Tomography
	Make spectra
	ml_refine3d (Maximum likelihood 3D refinement)
	Maximum likelihood for tomograms
	Construct a low and high resolution dictionary
	Restore a volume with a low/high dictionary
	project_xr (project for tilt series)
	Reconstruct Alternating Direction Method of Multipliers
	reconstruct_art_pseudo (Reconstruct with pseudo atoms)
	Program ART
	Measure resolution through the inverse of border widths
	resolution_ssnr (Spectral Signal to Noise Ratio)
	score_micrograph (Evaluates the score of a micrograph)
	Align two dual tilt series
	angular_assign_for_tomogram (Discrete angular assignment for tomography)
	angular_assign_for_tilt_series
	Tomo Extract Subvolume
	Remove fluctuations in tilt series
	align_tilt_pairs (Align tilted and untilted images in a random conical tilt experiment)
	Enhance constrast
	Volume PCA
	Validation of volume consistency with respect to the provided classes
	Xray import
	GPU Correlation
	GPU MultidimArray At CPU
	Fourier reconstruction
	Resolution
	FFTwT
	Masks in Fourier space
	Fourier projection
	Micrograph Downsample
	Core analysis for CL2D
	Classification with Fourier Transform based Translational and Rotational Invariants
	Rotational invariant PCA
	Alignment Estimation
	adjust_volume_grey_values (Adjust volume grey values to a set of projections)
	ExtremaFinder
	GeoTransformerSettings
	align2d (Align a set of 2D images)
	MeritSettings
	accuracy to angular assignment by pca
	AngularAssignmentMag
	angular_distance (Distance between two angular assignments)
	angular_common_lines
	angular_continuous_assign (Continuous angular assignment)
	angular_continuous_assign2 (Continuous angular assignment)
	angular_discrete_assign (Discrete angular assignment)
	Estimate the tilt axis position in a pair of micrographs
	angular_neighbourhood (Projection neighbourhood)
	new_projmatch (Discrete angular assignment using a new projection matching)
	Rotation Estimation Setting
	art_crystal (ART for crystals)
	AShiftCorrEstimator
	AShiftEstimator
	ART Reconstruction stuff
	Parameters and common ART Reconstruction stuff
	BSpline Transform Settings
	BSplineHelper
	Compare Classes
	Evaluate Classes
	ProgExtractFeatures
	Classification first split
	Deform a volume using spherical harmonics
	Coordinates Micrograph Filter
	Correlation Computer
	CTF Phase flip in 2D particles
	ctf_correct_amplitude3D (3D Wiener filtering)
	psd_enhance (Enhance visualization of the PSD)
	ctf_estimate_from_micrograph (CTF estimation from a micrograph)
	adjust_ctf (Adjust CTF parameters to PSD)
	Program CTF Basic Parameters
	adjust_ctf (Adjust CTF parameters to PSD)
	Spectrum modelling by ARMA filters
	ctf_group
	psd_Sort (Sort visualization of the PSD)
	Image denoising
	Operations for projection directions
	Alignment with Normal modes
	Routines to work with fringes
	Image Assignment Tilt Pair
	Eliminate images whose energy is extremely large or extremely low
	Eliminate Empty Particles
	Even
	Image sort by statistics
	Iterative Alignment Estimator
	Split a metadata according to a 3D volume
	Image denoising
	ml_align2d (Maximum likelihood in 2D)
	mlf_align2d (Maximum likelihood in 2D in Fourier space)
	Movie alignment correlation
	Movie Alignment Correlation
	Estimate gain from a movie
	Movie alignment by correlation
	Multireference Aligneability
	Alignment of volumes with Normal modes
	Different statistics of the PDB
	convert_pdb2vol (PDB Phantom program)
	Deform PDB according to NMA
	Pdb Reduce
	Phantom Movie
	phantom_simulate_microscope (Microscope simulation)
	Polar Rotation Estimator
	precompute_sampling (Precompute samplin points in the projection sphere)
	Filter Operation
	Image Residuals
	Estimate the SSNR
	project (Generate projections from a volume)
	project_crystal (Project crystals)
	projectTomograpy (project for tilt series)
	PSD Estimator
	radon (Radon transform)
	Reconstruct multiple volumes analyzing significant correlations
	reconstruct_wbp (Weighted Back Projection)
	refinement (Shift refinement)
	Local Filter
	Shift Correlation Estimator
	Single Extrema Finder
	Subtomogram subtraction
	Subtract projections
	symmetrize (Symmetrize a volume or image)
	Threshold
	Change the image gray values to match a volume projection
	without tilt
	Restoration of a volume given two halves
	Heuristic Initial Volume
	Sharpening
	Volume segmentation
	ConvertVol2Pseudo
	Volume Set Align
	Align Significant GPU
	Volume Halves Restoration GPU
	Cuda BSpline GeoTransformer
	Cuda Correlation Computer
	CudaFFT
	Cuda GPU Correlation
	GeoShift Transformer
	Cuda GPU GeoTransformer
	Cuda GPU Reconstruct Fourier
	Cuda Rotation Polar Estimator
	CudaShiftCorrEstimator
	CudaExtremaFinder
	Volume Halves Restorator
	Volume Restoration Kernels
	Cuda Xmipp Utils
	GPU
	Detect missing wedge
	Tomo map back

Detailed Description