EMAN2
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
EMAN::_BadAllocExceptionUsed when memory allocation goes wrong..
EMAN::_EmptyContainerExceptionUsed when an argument container is empty, such as a vector
EMAN::_FileAccessExceptionUsed when a file access error occurs
EMAN::_ImageDimensionExceptionUsed when an image is not in the expected dimension
EMAN::_ImageFormatExceptionUsed when an image is not in the expected format
EMAN::_ImageReadExceptionUsed when an error occurs at image reading time
EMAN::_ImageWriteExceptionUsed when an error occurs at image writing time
EMAN::_InvalidCallException
EMAN::_InvalidParameterException
EMAN::_InvalidStringExceptionUsed when an invalid (format) string is given
EMAN::_InvalidValueExceptionUsed when an invalid integer value is given
EMAN::_NotExistingObjectExceptionUsed when an object type, like an EMObject type, doesn't exist
EMAN::_NullPointerExceptionUsed when a NULL is given to a pointer that should not be NULL
EMAN::_OutofRangeExceptionUsed when the given value is out of range
EMAN::_TypeExceptionUsed when a type cast error occurs
EMAN::_UnexpectedBehaviorExceptionUsed when internal behavior is unexpected A generic kind of exception
EMAN::AboveToZeroProcessorF(x) = x if x <= maxval; f(x) = 0 if x > maxval
EMAN::AbsMaxMinAveragerAbsMaxMinAverager averages a list of images to the maximum(or minimum of the absolute pixel value) It optionally makes a sigma image
EMAN::AbsoluateValueProcessorF(x) = |x|
EMAN::ACFCenterProcessorCenter image using auto convolution with 180 degree rotation
EMAN::AddMaskShellProcessorAdd additional shells/rings to an existing 1/0 mask image
EMAN::AddNoiseProcessorAdd noise to an image
EMAN::AddRandomNoiseProcessorAdd spectral noise to a complex image
EMAN::AddShapeProcessorRotate by 180 using pixel swapping, works for 2D only
EMAN::AddSigmaNoiseProcessorAdd sigma noise, multiply image's sigma value to noise
EMAN::AlignerAligner class defines image alignment method
AlignOptions
EMAN::AmiraIOAmira file = ASCII header + binary data
EMAN::AmpweightFourierProcessorMultiplies each Fourier pixel by its amplitude
EMAN::AnalyzerAnalyzer class defines a way to take a List of images as input, and returns a new List of images
APMDopt
APMQopt
EMAN::ApplyPolynomialProfileToHelix
EMAN::ApplySymProcessorApplies a symmetry to a 3D model
EMAN::AreaProcessorAreaProcessor use pixel values and coordinates of a real-space square area
assign_groups_comparator
EMAN::AutoMask2DProcessorAttempts to automatically mask out the particle, excluding other particles in the box, etc
EMAN::AutoMask3D2ProcessorTries to mask out only interesting density
EMAN::AutoMask3DProcessorTries to mask out only interesting density
EMAN::AutoMaskAsymUnitTries to mask out only interesting density
EMAN::AutoMaskDustProcessorA "dust removal" filter which will remove above threshold densities smaller than a given size
EMAN::AveragerAverager class defines a way to do averaging on a set of images
EMAN::AverageXProcessorAverage along Y and replace with average
EMAN::Axis0FourierProcessorZeroes the values on the X=0 and y=0 Fourier axes (except x=y=0)
EMAN::BackProjectionReconstructorReal space 3D reconstruction using back projection
EMAN::BeamstopProcessorTry to eliminate beamstop in electron diffraction patterns
EMAN::BilateralProcessorBilateral processing on 2D or 3D volume data
EMAN::BinarizeFourierProcessorA thresholding processor for Fourier images based on the amplitude component
EMAN::BinarizeProcessorF(x) = 0 if x < value; f(x) = 1 if x >= value
EMAN::BinaryOperateProcessor< Type >Operates on two images, returning an image containing the maximum/minimum/multiplied pixel (etc, you choose) at each location The actual operation depends on what template argument you use
EMAN::BinarySkeletonizerProcessor
EMAN::BooleanProcessorF(x) = 0 if x = 0; f(x) = 1 if x != 0
EMAN::BooleanShrinkProcessorBooleanShrinkProcessor encapsulates code common to MaxShrinkProcessor and MinShrinkProcessor - the processors use more or less identical code, the main difference being the logical operator
EMAN::BoxingToolsBoxingTools is class for encapsulating common boxing operations that may become expensive if they are implemented in python
EMAN::BoxMaxProcessorPeak processor: pixel = max of values surrounding pixel
EMAN::BoxMedianProcessorA processor for noise reduction
EMAN::BoxSigmaProcessorPixel = standard deviation of values surrounding pixel
EMAN::BoxStatProcessorBoxStatProcessor files are a kind of neighborhood processors
EMAN::BoxSVDClassifier
BPKT
EMAN::ByteOrderByteOrder defines functions to work on big/little endian byte orders
EMAN::CccCmpCompute the cross-correlation coefficient between two images
EMAN::CCDNormProcessorTry to normalize the 4 quadrants of a CCD image
ccf_point
ccf_value
EMAN::ChaoProjectorFast real space projection using Bi-Linear interpolation
cilist
EMAN::CircularMaskProcessorCircularMaskProcessor applies a circular mask to the data.This is the base class for specific circular mask processors.Its subclass must implement process_dist_pixel()
EMAN::ClampingProcessorF(x) = maxval if f(x) > maxval; f(x) = minval if f(x) < minval
EMAN::EMData::ClipInplaceVariables
EMAN::CmpCmp class defines image comparison method
cmpang
EMAN::CollapseProcessorF(x): if v-r<x<v+r -> v; if x>v+r -> x-r; if x<v-r -> x+r
Maxclique::ColorClass
EMAN::ColorRGBGeneratorClass to encapsulate an RGB color generator for marching cubes isosurface generator For now you can only color by radius, but in the near future you will be able to color by map, etc
EMAN::ComplexNormPixelEach Fourier pixel will be normalized
EMAN::ComplexPixelProcessorThe base class for fourier space processor working on individual pixels
EMAN::Dict::const_iteratorConst iterator support for the Dict object This is just a wrapper, everything is inherited from the map<string,EMObject>::cons_iterator so the interface is the same as you would expect i.e for ( Dict::const_iterator it = params.begin(); it != params.end(); ++it )
EMAN::ConvolutionKernelProcessor
EMAN::ConvolutionProcessorThis processor performs fast convolution in Fourier space
EMAN::CoordinateMaskFileProcessorMultiplies the image by the specified file using pixel coordinates instead of pixel indices
EMAN::CoordinateProcessorCoordinateProcessor applies processing based on a pixel's value and it coordinates
EMAN::CSymAn encapsulation of cyclic 3D symmetry
EMAN::CtfCtf is the base class for all CTF model
EMAN::CTF_Processor
ctf_store
ctf_store_new
EMAN::CtfCAutoAveragerCtfCWautoAverager averages the images with CTF correction with a Wiener filter
EMAN::CtfCWautoAveragerCtfCWautoAverager averages the images with CTF correction with a Wiener filter
EMAN::CtfSimProcessorCTF simulation processor
EMAN::CTFSNRWeightProcessor
EMAN::CUDA_Aligner
EMAN::CUDA_multiref_aligner
CudaPeakInfo
CudaPeakInfoFloat
EMAN::CustomVector< type >CustomVector has some trivial optimizations of the STL vector
EMAN::CutoffBlockProcessorBlock processor, val1 is dx/dy, val2 is lp freq cutoff in pixels
EMAN::CutToZeroProcessorF(x) = x-minval if x >= minval; f(x) = 0 if x < minval
d_ang
EMAN::Gatan::DataType
EMAN::GatanDM4::DataType
EMAN::DecayEdgeProcessorDecay edges of image to zero
EMAN::Df3IO
EMAN::DictDict is a dictionary to store <string, EMObject> pair
EMAN::DiffBlockProcessorAverages over cal_half_width, then sets the value in a local block
EMAN::DirectionalSumProcessorDoes a projection in one the axial directions Doesn't support process_inplace (because the output has potentially been compressed in one dimension)
EMAN::DistanceSegmentProcessorSegment a volume about:homeinto subvolumes based on a center separation value
EMAN::DM3IOGatan DM3 file is a hierarchical binary image format
EMAN::DM4IOGatan DM$ was introduced with the GMS 2.0 release
EMAN::DoGFourierProcessorProcessor radial function: f(x) = 1/sqrt(2*pi)*[1/sigma1*exp-(x^2/2*sigma1^2) - 1/sigma2*exp-(x^2/2*sigma2^2)]
EMAN::DotCmpUse dot product of 2 same-size images to do the comparison
EMAN::DSymAn encapsulation of dihedral 3D symmetry
EMAN::E2ExceptionE2Exception class is the parent class of all EMAN2 E2Exceptions
EMAN::EMAN1CtfEMAN1Ctf is the CTF model used in EMAN1
EMAN::EMAN2CtfEMAN2Ctf is the default CTF model used in EMAN2
EMAN::EmanOrientationGeneratorEmanOrientationGenerator generates orientations quasi-evenly distributed in the asymmetric unit
EMAN::EMArray< T >EMArray -- 1-, 2-, or 3-D array of types T
EMAN::EMConsts
EMAN::EMDataEMData stores an image's data and defines core image processing routines
EMDataForCudaA struct for passing EMData objects to and from things like processors
EMAN::EMFTGLEMFTGL is an interface for rendering fonts in EMAN2 using FTGL
EMAN::EMFTGL::EMFTGLFontInstanceA class for encapsulatiing a particular instance of an FTFont (pointer) Each FTFont is characterised by 5 parameters, them being the font mode, the font file name, the face size, whether or not display lists are being used, and depth (which is redundant, except when the font mode is EXTRUDE)
EMAN::EMFTGL::EMFTGLManagerA class for managing multiple instances of EMFTGLFontInstances, in particular for caching them, for constructing news ones if they don't exist, and for returning appropriate instances
EMAN::EmIO::EMHeader
EMAN::EmIOEmIO defines I/O operations on EM image format
EMAN::EMObjectEMObject is a wrapper class for types including int, float, double, etc as defined in ObjectType
EMAN::EMUtil
EMAN::EvenOrientationGeneratorSparx even orientation generator - see util_sparx.cpp - Util::even_angles(...) This orientation generator is based on work presented in Penczek et al., 1994 P.A
EMAN::ExpProcessorF(x) = exp( x / low - high)
EMAN::Factory< T >Factory is used to store objects to create new instances
EMAN::FactoryBaseA class one may inherit from to ensure that the responsibilities of being incorporated into an EMAN2::Factory are met
FakeKaiserBessel
EMAN::Util::FakeKaiserBessel
EMAN::MrcIO::FeiMrcExtHeaderThe extended header used by Fei MRC image
EMAN::MrcIO::FeiMrcHeaderExtended MRC format for tomography As used by Fei; original definition of extended header by Dave Agard and Bram Koster Contact Dustin Morado <Dustin.Morado@uth.tmc.edu> for details
EMAN::FFTProcessorPerform a FFT transform by calling EMData::do_fft() and EMData::do_ift()
EMAN::FFTResampleProcessorFFTResampleProcessor resamples an image by clipping the Fourier Transform This is the same as multipyling the FT by a box window, in real space this is a convolution that will induce rippling
EMAN::file_store
EMAN::FileFourierProcessorA fourier processor specified in a 2 column text file
EMAN::FiniteProcessorF(x) = f(x) if f(x) is finite | to if f(x) is not finite
EMAN::FitsIOMRC file = header + data (nx x ny x nz)
EMAN::FlattenBackgroundProcessorFlattens the background by subtracting the local mean
EMAN::FlipProcessorFlip an image around an axis
EMAN::FloatPointFloatPoint defines a float-coordinate point in a 1D/2D/3D space
EMAN::FloatSizeFloatSize is used to describe a 1D, 2D or 3D rectangular size in floating numbers
EMAN::FloorValueProcessorF(x) = floor(x)
EMAN::FourierAnlProcessorSame as FourierProcessor, except first computes the current image radial power spectrum and passes it to the processor (no radial oversampling, number of elements = radius)
EMAN::FourierGriddingProjectorFourier gridding projection routine
EMAN::FourierInserter3DMode1FourierPixelInserter3DMode1 - encapsulates "method 1" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations
EMAN::FourierInserter3DMode2FourierPixelInserter3DMode2 - encapsulates "method 2" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations
EMAN::FourierInserter3DMode3FourierPixelInserter3DMode3 - encapsulates "method 3" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations
EMAN::FourierInserter3DMode5FourierPixelInserter3DMode5 - encapsulates "method 5" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations
EMAN::FourierInserter3DMode6FourierPixelInserter3DMode6 - encapsulates "method 6" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations
EMAN::FourierInserter3DMode7FourierPixelInserter3DMode7 - encapsulates "method 7" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations
EMAN::FourierInserter3DMode8FourierPixelInserter3DMode8 - encapsulates "method 8" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations
EMAN::FourierPixelInserter3DFourierPixelInserter3D class defines a way a continuous pixel in 3D is inserted into the discrete 3D volume - there are various schemes for doing this including simply finding the nearest neighbor to more elaborate schemes that involve interpolation using the nearest 8 voxels and so on
EMAN::FourierPlaneReconstructorFourier space 3D reconstruction The Fourier reconstructor is designed to work in an iterative fashion, where similarity ("quality") metrics are used to determine if a slice should be inserted into the 3D in each subsequent iteration
EMAN::FourierProcessorBase class for Fourier filters
EMAN::FourierReconstructorFourier space 3D reconstruction The Fourier reconstructor is designed to work in an iterative fashion, where similarity ("quality") metrics are used to determine if a slice should be inserted into the 3D in each subsequent iteration
EMAN::FourierReconstructorSimple2DThis class originally added for 2D experimentation and prototying
EMAN::FourierToCenterProcessorTranslates the origin in Fourier space from the corner to the center in y and z Handles 2D and 3D, and handles all combinations of even and oddness Typically you call this function after Fourier transforming a real space image
EMAN::FourierToCornerProcessorUndo the effects of the FourierToCenterProcessor
EMAN::FourierWeightAveragerFourierWeightAverager makes an average of a set of images in Fourier space using a per-image radial weight
EMAN::FRCCmpFRCCmp returns a quality factor based on FRC between images
EMAN::FRM2DAligner
EMAN::FSCFourierProcessorThis processor will apply a Wiener filter to a volume based on a provided FSC curve
EMAN::Gatan2IO::Gatan2Header
EMAN::Gatan2IOGatan2 Image file = header + data
EMAN::GaussFFTProjectorGaussian FFT 3D projection
EMAN::Util::GaussianGaussian function class
GaussianGaussian function class
EMAN::TomoTiltEdgeMaskProcessor::GaussianFunctoid
EMAN::GLUtil
EMAN::GradientPlaneRemoverProcessorGradient removed by least square plane fit
EMAN::GradientRemoverProcessorGradient remover, does a rough plane fit to find linear gradients
EMAN::MaxShrinkProcessor::GreaterThan
wustl_mm::SkeletonMaker::gridPoint
wustl_mm::SkeletonMaker::GridQueue
wustl_mm::SkeletonMaker::GridQueue2
wustl_mm::SkeletonMaker::gridQueueEle
EMAN::HighpassAutoPeakProcessorThis processor attempts to remove the low resolution peak present in all cryoEM data
EMAN::HistogramBinBins pixel values, similar to calculating a histogram
EMAN::HSymAn encapsulation of helical 3D symmetry
EMAN::Icosahedral2SymAn encapsulation of icosahedral symmetry 222
EMAN::IcosahedralSymAn encapsulation of icosahedral symmetry Doctor Phil has this to say about icosahedral symmetry: "Each Platonic Solid has 2E symmetry elements
EMAN::IcosIO::IcosHeader
EMAN::IcosIOICOS file = header + data
EMAN::ImageAveragerImageAverager averages a list of images
EMAN::ImageIOImageIO classes are designed for reading/writing various electron micrography image formats, including MRC, IMAGIC, SPIDER, PIF, etc
EMAN::ImageProcessor
EMAN::ImageScore
EMAN::ImageSort
EMAN::ImagicIO2::Imagic4DIMAGIC-4D file format http://www.imagescience.de/formats/formats.htm
EMAN::ImagicIO::ImagicHeader
EMAN::ImagicIOIMAGIC-5 Header File Format
EMAN::ImagicIO2IMAGIC-5 Header File Format
EMAN::IndexMaskFileProcessorMultiplies the image by the specified file using pixel indices
EMAN::InertiaMatrixAnalyzerInertia Matrix computer Computes the Inertia Matrix for a 3-D volume
EMAN::InterpInterp defines the interpolation function used to generate a e^-x^4 function in real space
EMAN::IntPointIntPoint defines an integer-coordinate point in a 1D/2D/3D space
EMAN::IntSizeIntSize is used to describe a 1D, 2D or 3D rectangular size in integers
EMAN::IntTranslateProcessorTranslate the image an integer amount Uses EMData::clip_inplace (inplace) and EMData::get_clip (out of place) to do the translation
EMAN::InverseKaiserI0ProcessorDivide by a Kaiser-Bessel I0 func in Fourier space
EMAN::InverseKaiserSinhProcessorDivide by a Kaiser-Bessel Sinh func in Fourier space
EMAN::PawelProjector::IPCube
EMAN::Isosurface
EMAN::IterationAveragerIterationAverager averages images by doing the smoothing iteration
EMAN::Dict::iteratorNon const iterator support for the Dict object This is just a wrapper, everything is inherited from the map<string,EMObject>::iterator so the interface is the same as you would expect i.e for ( Dict::iterator it = params.begin(); it != params.end(); ++it )
EMAN::IterBinMaskProcessorIterative expansion of a binary mask, val1 is number of pixels to expand, if val2!=0 will make a soft Gaussian edge starting after val2 pixels
EMAN::IterMultiMaskProcessorThis expands a multilevel mask volume so inter-mask boundaries are preserved
KaiserBessel1-D Kaiser-Bessel window function class
EMAN::Util::KaiserBessel1-D Kaiser-Bessel window function class
KaiserBessel::kbi0_winI0 window function object
EMAN::Util::KaiserBessel::kbi0_winI0 window function object
EMAN::Util::KaiserBessel::kbsinh_winSinh window function object
KaiserBessel::kbsinh_winSinh window function object
EMAN::KMeansAnalyzerKMeansAnalyzer Performs k-means classification on a set of input images (shape/size arbitrary) returned result is a set of classification vectors
EMAN::KmeansSegmentProcessorSegment a volume into ~n subvolumes using K-means classification
EMAN::LaplacianProcessorDiscrete approximation to Laplacian
EMAN::MinShrinkProcessor::LessThan
EMAN::LinearPyramidProcessorMultiplies image by a 'linear pyramid' 1-(|x-xsize/2|*|y-ysize/2|*4/(xsize*ysize)) This is useful in averaging together boxed out regions with 50% overlap
EMAN::LinearRampFourierProcessor
EMAN::LinearRampProcessorProcessor radial function: f(x) = slope * x + intercept
EMAN::LinearXformProcessorLinear transform processor: f(x) = x * scale + shift
EMAN::LocalNormProcessorThis processor attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display
EMAN::LodCmp
EMAN::LogLog defines a way to output logging information
EMAN::LoGFourierProcessorProcessor radial function: f(x) = ((x^2 - s^2)/s^4)e^-(x^2/2s^2)
EMAN::LogProcessorF(x) = log10(x) if x > 0; else f(x) = 0
EMAN::LowpassAutoBProcessorProcessor radial function: if lowpass > 0, f(x) = exp(-x*x/(lowpass*lowpass)); else f(x) = exp(x*x/(lowpass*lowpass))
EMAN::LowpassRandomPhaseProcessorLowpass Phase Randomization processor applied in Fourier space
EMAN::LstFastIOA LSX file is a high performance ASCII file that contains a list of image numbers and file names
EMAN::LstIOA LST file is an ASCII file that contains a list of image file names
EMAN::MakeRadiusProcessorOverwrites input, f(x) = radius
EMAN::MakeRadiusSquaredProcessorOverwrites input, f(x) = radius * radius
EMAN::MarchingCubes
EMAN::MaskEdgeMeanProcessorA step cutoff to the the mean value in a ring centered on the outer radius
EMAN::MaskGaussInvProcessorF(x) = f(x) / exp(-radius*radius * gauss_width / (ny*ny))
EMAN::MaskGaussNonuniformProcessorGaussian falloff to zero, with nonisotropic widths along x,y,z
EMAN::MaskGaussProcessorGaussian falloff to zero, radius is the 1/e of the width
EMAN::MaskNoiseProcessorFills masked region
EMAN::MaskSharpProcessorStep cutoff to a user-given value in both inner and outer circles
EMAN::MaskSoftProcessorStep cutoff to a user-given value in both inner and outer circles
EMAN::MatchSFProcessorSets the structure factor To match a second provided image/volume
EMAN::Matrix3
EMAN::Matrix4
Maxclique
EMAN::MaxPixelOperator
EMAN::MaxShrinkProcessorMaxShrinkProcessors shrinks an image by in an integer amount, keeping the maximum pixel value - useful when constructing binary search trees in the marching cubes algorithm
EMAN::MaxValProjectorReal-space projection which computes the maximum value along each line projection rather than a sum
EMAN::MeanShrinkProcessorMeanShrinkProcessor shrinks an image by in an integer amount (and optionally by 1.5) taking the mean of the pixel neighbourhood
EMAN::MeanZeroEdgeProcessorFill zeroes at edges with nearest horizontal/vertical value damped towards Mean2
EMAN::MedianShrinkProcessorMeanShrinkProcessor shrinks an image by in an integer amount taking the median of the pixel neighbourhood
methodName
EMAN::MinMaxAveragerImageAverager averages a list of images
EMAN::MinPixelOperator
EMAN::MinShrinkProcessorMinShrinkProcessor shrinks an image by in an integer amount, keeping the minimum pixel value - useful when constructing binary search trees in the marching cubes algorithm
EMAN::MinusPeakProcessorPeak processor: pixel = pixel - max of values surrounding pixel
EMAN::MirrorProcessorMirror an image
EMAN::ModelEMCylinderProcessor
EMAN::ModelHelixProcessor
EMAN::MrcIO::MrcHeader
EMAN::MrcIOMRC file = header + data (nx x ny x nz)
EMAN::NewBandpassGaussProcessorBandpass Gauss filter processor applied in Fourier space
EMAN::NewBandpassTanhProcessorBandpass tanh processor applied in Fourier space
EMAN::NewBandpassTopHatProcessorBandpass top-hat filter processor applied in Fourier space
EMAN::newfile_store
EMAN::NewFourierProcessorBase class for Fourier processors
EMAN::NewHighpassButterworthProcessorHighpass Butterworth filter processor applied in Fourier space
EMAN::NewHighpassGaussProcessorHighpass Gauss filter processor applied in Fourier space
EMAN::NewHighpassTanhProcessorHighpass tanh filter processor applied in Fourier space
EMAN::NewHighpassTopHatProcessorHighpass top-hat filter applied in Fourier NewLowpassGaussProcessorspace
EMAN::NewHomomorphicButterworthProcessorHomomorphic Butterworth filter processor applied in Fourier space
EMAN::NewHomomorphicGaussProcessorHomomorphic Gauss filter processor applied in Fourier space
EMAN::NewHomomorphicTanhProcessorHomomorphic Tanh processor applied in Fourier space
EMAN::NewHomomorphicTopHatProcessorHomomorphic top-hat filter processor applied in Fourier space
EMAN::NewInverseGaussProcessorDivide by a Gaussian in Fourier space
EMAN::NewLowpassButterworthProcessorLowpass Butterworth filter processor applied in Fourier space
EMAN::NewLowpassGaussProcessorLowpass Gauss filter processor applied in Fourier space
EMAN::NewLowpassTanhProcessorLowpass tanh filter processor applied in Fourier space
EMAN::NewLowpassTopHatProcessorLowpass top-hat filter processor applied in Fourier space
EMAN::NewRadialTableProcessorFilter with tabulated data in Fourier space
EMAN::nn4_ctf_rectReconstructorNn4_ctf_rectDirect Fourier Inversion Reconstructor
EMAN::nn4_ctfReconstructorNn4_ctf Direct Fourier Inversion Reconstructor
EMAN::nn4_ctfwReconstructorNn4_ctfw Direct Fourier Weighted Inversion Reconstructor
EMAN::nn4_rectReconstructorDirect Fourier inversion Reconstructor for extremly rectangular object
EMAN::nn4Reconstructor
EMAN::nnSSNR_ctfReconstructor
EMAN::nnSSNR_Reconstructor
EMAN::NonConvexProcessorMake a curve or surface non-convex (planar or concave), iteratively
EMAN::NormalizeByMassProcessorNormalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3)
EMAN::NormalizeCircleMeanProcessorNormalizes an image, mean value equals to mean of 2 pixel circular border
EMAN::NormalizeEdgeMeanProcessorNormalizes an image, mean value equals to edge mean
EMAN::NormalizeLREdgeMeanProcessorNormalizes an image, uses 2 pixels on left and right edge
EMAN::NormalizeMaskProcessorUses a 1/0 mask defining a region to use for the zero-normalization.if no_sigma is 1, standard deviation not modified
EMAN::NormalizeMaxMinProcessorNormalizes an image
EMAN::NormalizeProcessorBase class for normalization processors
EMAN::NormalizeRampNormVarNormalize the image whilst also removing any ramps
EMAN::NormalizeRowProcessorNormalizes each row in the image individually
EMAN::NormalizeStdProcessorDo a standard normalization on an image
EMAN::NormalizeToLeastSquareProcessorUse least square method to normalize
EMAN::NormalizeUnitProcessorNormalize an image so its vector length is 1.0
EMAN::NormalizeUnitSumProcessorNormalize an image so its elements sum to 1.0 (fails if mean=0)
EMAN::NSigmaClampingProcessorThis function clamps the min and max vals in the image at minval and maxval at mean-n*sigma and mean+n*sigma, respectively
EMAN::OctahedralSymAn encapsulation of octahedral symmetry Doctor Phil has this to say about the octahedral symmetry: "Each Platonic Solid has 2E symmetry elements
olist
EMAN::OmapIO::OmapHeaderThe data in the header is composed of 256 short integers
EMAN::OmapIODSN6 MAP is composed of a series of records which are all 512 bytes long
EMAN::OptimumOrientationGeneratorOptimum orientation generator
EMAN::OptSubCmpUses math.sub.optimal to remove the density of the reference from the image as much as possible
EMAN::OptVarianceCmpVariance between two data sets after various modifications
ori_t
EMAN::OrientationGeneratorAn orientation generator is a kind of class that will generate orientations for a given symmetry If one needs to generate orientations in the unit sphere, one simply uses the C1 symmetry
EMAN::PaintProcessor'paints' a circle into the image at x,y,z with values inside r1 set to v1, values between r1 and r2 will be set to a value between v1 and v2, and values outside r2 will be unchanged
EMAN::XYData::Pair
EMAN::PawelProjectorPawel Penczek's optimized projection routine
EMAN::PCA
EMAN::PCAlarge
EMAN::PCAsmallPrincipal component analysis
EMAN::PDBReaderPointArray defines a double array of points with values in a 3D space
EMAN::PeakOnlyProcessorPeak processor -> if npeaks or more surrounding values >= value, value->0
EMAN::PgmIOA PGM file = header + data
EMAN::Phase180ProcessorThis class is abstract
EMAN::PhaseCmpAmplitude weighted mean phase difference (radians) with optional SNR weight
EMAN::PhaseToCenterProcessorTranslates a cornered image to the center Undoes the PhaseToCornerProcessor
EMAN::PhaseToCornerProcessorTranslates a centered image to the corner works for 1D, 2D and 3D images, for all combinations of even and oddness
EMAN::PhaseToMassCenterProcessorToMassCenterProcessor centers image at center of mass, ignores old dx, dy
EMAN::PifIO::PifColorMap
EMAN::PifIO::PifFileHeader
EMAN::PifIO::PifImageHeader
EMAN::PifIOPIF(Portable Image Format for EM Data) is an image format from Purdue University
EMAN::PixelPixel describes a 3D pixel's coordinates and its intensity value
EMAN::PlatonicSymA base (or parent) class for the Platonic symmetries
EMAN::Point3
point3d_t
EMAN::point_t
EMAN::PointArrayPointArray defines a double array of points with values in a 3D space
EMAN::PolarDataSpecialized image class for storing the results of a transform from EMData to polar coordinates, currently support 2D only
EMAN::PriorityQueue< ValueT, KeyT >Template class for a priority queue
EMAN::ProcessorTypical usage of Processors are as follows:
EMAN::ProjectorProjector class defines a method to generate 2D projections from a 3D model
EMAN::QuadMinDotCmpThis will calculate the dot product for each quadrant of the image and return the worst value
EMAN::QuaternionQuaternion is used in Rotation and Transformation to replace Euler angles
EMAN::RadialProcessorPerform a multiplication of real image with a radial table
EMAN::RampProcessorRamp processor -- Fits a least-squares plane to the picture, and subtracts the plane from the picture
EMAN::RandnumThe wrapper class for gsl's random number generater
EMAN::RandomOrientationGeneratorRandom Orientation Generator - carefully generates uniformly random orientations in any asymmetric unit
EMAN::RangeThresholdProcessorF(x) = 1 if (low <= x <= high); else f(x) = 0
EMAN::RealPixelProcessorThe base class for real space processor working on individual pixels
EMAN::RealToFFTProcessorThis will replace the image with a full-circle 2D fft amplitude rendering
EMAN::RecipCarefullyProcessorReciprocal image as if f(x) != 0: f(x) = 1/f(x) else: f(x) = zero_to
EMAN::ReconstructorReconstructor class defines a way to do 3D recontruction
EMAN::ReconstructorVolumeDataThis is a Mixin class A class object encapsulating the volume data required by Reconstructors It basically stores two (pointers) to EMData objectsd stores the dimensions of the image volume
EMAN::Refine3DAlignerGridRefine alignment
EMAN::Refine3DAlignerQuaternionRefine alignment
EMAN::RefineAlignerRefine alignment
EMAN::RefineAlignerCGConjugate gradient refine alignment
EMAN::RegionRegion defines a 2D or 3D rectangular region specified by its origin coordinates and all edges' sizes
EMAN::Rotate180ProcessorRotate by 180 using pixel swapping, works for 2D only
EMAN::RotateFlipAlignerRotational and flip alignment
EMAN::RotateFlipAlignerIterativeRotational and flip alignment, iterative style
EMAN::RotateInFSProcessor
EMAN::RotatePrecenterAlignerRotational alignment assuming centers are correct
EMAN::RotateTranslateAlignerRotational, translational alignment
EMAN::RotateTranslateAlignerIterativeIterative rotational, translational alignment
EMAN::RotateTranslateAlignerPawelRotational, translational alignment by resampling to polar coordinates
EMAN::RotateTranslateBestAlignerRotational, translational alignment
EMAN::RotateTranslateFlipAlignerRotational, translational and flip alignment
EMAN::RotateTranslateFlipAlignerIterativeRotational, translational and flip alignment, iterative style
EMAN::RotateTranslateFlipAlignerPawelRotational, translational alignment by resampling to polar coordinates
EMAN::RotateTranslateFlipScaleAlignerRotational, translational, flip, scaling alignment
EMAN::RotateTranslateFlipScaleAlignerIterativeIterative rotational, translational alignment with flipping and scaling
EMAN::RotateTranslateScaleAlignerRotational, translational, scaling alignment
EMAN::RotateTranslateScaleAlignerIterativeIterative rotational, translational alignment with scaling
EMAN::RotationalAlignerRotational alignment using angular correlation
EMAN::RotationalAlignerIterativeRotational alignment using the iterative method (in this case we only do one iteration b/c we are not doing a translation
EMAN::RotationalAverageProcessorMakes image circularly symmetric
EMAN::RotationalSubstractProcessorSubtracts circularly symmetric part of an image
EMAN::RT3DGridAlignerRotational and translational alignment using a square qrid of Altitude and Azimuth values (the phi range is specifiable) This aligner is ported from the original tomohunter.py - it is less efficient than searching on the sphere (RT3DSphereAligner)
EMAN::RT3DSphereAligner3D rotational and translational alignment using spherical sampling, can reduce the search space based on symmetry
EMAN::RT3DSymmetryAligner3D rotational symmetry aligner
EMAN::RTFExhaustiveAlignerRotational, translational and flip alignment using real-space methods
EMAN::RTFSlowExhaustiveAlignerRotational, translational and flip alignment using exhaustive search
EMAN::SaffOrientationGeneratorSaff orientation generator - based on the work of Saff and Kuijlaars, 1997 E.B
EMAN::SalIOA SAL image is an image from Perkin Elmer PDS Microdensitometer
EMAN::ScaleAlignerScale aligner
EMAN::ScaleAlignerABSThis is an ABS for use in constructing, rt_scale, rt_flip, etc scale aligners
EMAN::ScaleTransformProcessorScale the image with control over the output dimensions
EMAN::ScreenPoint
EMAN::ScreenVector
EMAN::SerIO::SerHeader
EMAN::SerIOSER (Series File Format) is a file format created by Dr
EMAN::SetSFProcessorSets the structure factor based on a 1D s/intensity curve as an XYData object
EMAN::ShapeAnalyzerShape characterization Computes a set of values characteristic of the shape of a volume
EMAN::SHIFTProcessorShift by phase multiplication in Fourier space
EMAN::SigmaProcessorF(x) = mean if x<(mean-v2*sigma) or x>(mean+v1*sigma); else f(x) = x;
EMAN::SigmaZeroEdgeProcessorFill zeroes at edges with nearest horizontal/vertical value
sincBlackman
EMAN::Util::sincBlackman
EMAN::SingleSpiderIOSingle Spider Image I/O class
EMAN::SitusIOSitus is a a Situs-specific format on a cubic lattice
EMAN::SmartMaskProcessorSmart mask processor
EMAN::SNREvalProcessorEvaluate individual particle images using a tenchique similar to that used for CTF evaluation
EMAN::SNRProcessorProcessor the images by the estimated SNR in each image.if parameter 'wiener' is 1, then wiener processor the images using the estimated SNR with CTF amplitude correction
EMAN::SpiderIO::SpiderHeader
EMAN::SpiderIOSPIDER: (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy
EMAN::SqEuclideanCmpSquared Euclidean distance normalized by n between 'this' and 'with'
EMAN::StandardProjectorFast real-space 3D projection
stcom_
Maxclique::StepCount
EMAN::StripeXYProcessorThis processor will remove localized 'striping' along the x/y axes, caused by issues with CCD/CMOS readout
EMAN::SubtractOptProcessorSorry for the pun
EMAN::SVDAnalyzerSingular Value Decomposition from GSL
EMAN::SymAlignProcessorAligns a particle with the specified symmetry into the standard orientation for that symmetry
EMAN::SymAlignProcessorQuatAligns a particle with a specified symetry to its symmetry axis using the simplex multidimensional minimization algorithm
EMAN::Symmetry3DSymmetry3D - A base class for 3D Symmetry objects
EMAN::SymSearchProcessorIdentifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel
t_BPCQ_line
EMAN::Gatan::TagData
EMAN::GatanDM4::TagData
EMAN::Gatan::TagEntry
EMAN::GatanDM4::TagEntry
EMAN::Gatan::TagGroup
EMAN::GatanDM4::TagGroup
EMAN::GatanDM4::TagTable
EMAN::Gatan::TagTable
EMAN::TestImageAxesMake an image consisting of a single cross, with lines going in the axial directions, intersecting at the origin
EMAN::TestImageCirclesphereReplace a source image as a circle or sphere depends on 2D or 3D of the source image
EMAN::TestImageCylinderReplace a source image with a cylinder
EMAN::TestImageEllipseGenerate an ellipse or ellipsoid image
EMAN::TestImageFourierNoiseGaussianReplace a source image as a strict Gaussian
EMAN::TestImageFourierNoiseProfile
EMAN::TestImageGaussianReplace a source image as a Gaussian Blob
EMAN::TestImageGradientPut a gradient in the image of the form y = mx+b : "x" is a string indicating any of the image axes, i.e., x,y or z
EMAN::TestImageHollowEllipseGenerate an ellipse/ellipsoid image with an inner hollow ellipse/ellipsoid
EMAN::TestImageLineWaveTreats the pixels as though they are 1D (even if the image is 2D or 3D), inserting a sine wave of pixel period extracted from the parameters (default is 10)
EMAN::TestImageNoiseGaussReplace a source image with gaussian distributed random noise If you don't provide a seed at all, it should be seeded using the best available source of randomness( time(0) in this implementation)
EMAN::TestImageNoiseUniformRandReplace a source image as a uniform random noise, random number generated from gsl_rng_mt19937, the pixel value is from 0 to 1, [0, 1)
EMAN::TestImageProcessorBase class for a group of 'processor' used to create test image
EMAN::TestImagePureGaussianReplace a source image as a strict Gaussian
EMAN::TestImageScurveReplace a source image with a lumpy S-curve used for alignment testing
EMAN::TestImageSinewaveReplace a source image as a sine wave in specified wave length
EMAN::TestImageSinewaveCircularReplace a source image as a circular sine wave in specified wave length
EMAN::TestImageSphericalWaveReplace a source image as a sine wave in specified wave length
EMAN::TestImageSquarecubeReplace a source image as a square or cube depends on 2D or 3D of the source image
EMAN::TestTomoImageMake an image useful for tomographic reconstruction testing this is a 3D phantom image based on the 2D phantom described in Delaney and Bresler, "Globally convergent edge-preserving regularized reconstruction: An application to limited-angle tomography"
EMAN::TestUtil
EMAN::TetrahedralSymAn encapsulation of tetrahedral symmetry Doctor Phil has this to say about tetrahedral symmetry: " Each Platonic Solid has 2E symmetry elements
EMAN::Util::tmpstruct
tmpstruct
EMAN::ToMassCenterProcessorToMassCenterProcessor centers image at center of mass, ignores old dx, dy
EMAN::ToMinvalProcessorF(x) = x if x >= minval; f(x) = minval if x < minval
EMAN::TomoAveragerTomoAverager averages a list of volumes in Fourier space
EMAN::TomoCccCmpThis implements the technique of Mike Schmid where by the cross correlation is normalized in an effort to remove the effects of the missing wedge
EMAN::TomoFscCmpThis is a FSC comparitor for tomography
EMAN::TomoTiltAngleWeightProcessorA processor that can be used to weight an image by 1/cos(angle) This processor evolved originally as an experimental tool for weighting tomographic data by the width of its cross section relative to the electron beam
EMAN::TomoTiltEdgeMaskProcessorA processor designed specifically for tomographic tilt series data
EMAN::ToZeroProcessorF(x) = x if x >= minval; f(x) = 0 if x < minval
EMAN::TransformA Transform object is a somewhat specialized object designed specifically for EMAN2/Sparx storage of alignment parameters and euler orientations
EMAN::TransformProcessorTransform the image using a Transform object
EMAN::TranslationalAlignerTranslational 2D Alignment using cross correlation
EMAN::TransposeProcessorTranspose a 2D image
EMAN::TypeDictTypeDict is a dictionary to store <string, EMObject::ObjectType> pair
EMAN::U3DWriterMost commonly used constructor calls set_data(em)
EMAN::UnevenMatrixGeneral data structure for a matrix with variable x dim size for different y
EMAN::UtilUtil is a collection of utility functions
EMAN::V4L2IORead-only
EMAN::ValuePowProcessorDo a math power operation on image, f(x) = x ^ pow;
EMAN::ValueSqrtProcessorF(x) = sqrt(x)
EMAN::ValueSquaredProcessorDo a square operation on image, f(x) = x * x;
EMAN::varimax
EMAN::Vec2< Type >The Vec2 is precisely the same as Vec3 except it works exclusively in 2D Note there are convenient typedef so one needn't bother about using template terminology typedef Vec2<float> Vec2f; typedef Vec2<int> Vec2i; typedef Vec2double> Vec2d; // Not recommended for use unless precision is addressed in this class
EMAN::Vec3< Type >The Vec3 object is a templated object, intended to instantiated with basic types such as int, float, double etc
EMAN::Vec4< Type >The Vec4 object is a templated object, intended to instantiated with basic types such as int, float, double etc
EMAN::Vector3
EMAN::Vector4
Maxclique::Vertices::Vertex
EMAN::VerticalStripeProcessorTries to fix images scanned on the zeiss for poor ccd normalization
Maxclique::Vertices
wustl_mm::SkeletonMaker::Volume
wustl_mm::SkeletonMaker::VolumeData
wustl_mm::GraySkeletonCPP::VolumeSkeletonizer
EMAN::VtkIOVtkIO reads/writes VTK image file
EMAN::WatershedProcessor'paints' a circle into the image at x,y,z with values inside r1 set to v1, values between r1 and r2 will be set to a value between v1 and v2, and values outside r2 will be unchanged
EMAN::WaveletProcessorPerform a Wavelet transform using GSL
EMAN::Wiener2DAutoAreaProcessorAutomatically determines the background for the image then uses this to perform Wiener filters on overlapping subregions of the image, which are then combined using linear interpolation
EMAN::Wiener2DFourierProcessorWiener filter based on a Ctf object either in the image header
EMAN::WienerFourierReconstructorFourier space 3D reconstruction This is a modified version of the normal FourierReconstructor which is aware of the SSNR information stored in individual class-average headers as "ctf_snr_total" and "ctf_wiener_filtered"
WSsortlist
EMAN::UnevenMatrix::XdimStruct to define x dimension size for each y, x0 is inclusive, x1 is one after the maximum, [x0, x1), so the corresponding x dim size is (x1-x0)
EMAN::XGradientProcessorDetermines the partial derivatives in the x direction Does this by constructing edge kernels in real space but convoluting in Fourier space
EMAN::XplorIOXPLOR image format is in ASCII:
EMAN::XYDataXYData defines a 1D (x,y) data set
EMAN::XYZAlignerXYZAligner is an aligner template for defining new aligners
EMAN::XYZAveragerXYZAverager is an averager template for defining new averagers
EMAN::XYZCmpXYZCmp is a cmp template for defining new cmps
EMAN::XYZIOXYZIO is a sample Image IO class
EMAN::XYZProcessorXYZProcessor is a processor template for defining new processors
EMAN::XYZProjectorXYZProjector is an projector template for defining new projectors
EMAN::XYZReconstructorXYZReconstructor is a reconstructor template for defining new reconstructors
EMAN::YGradientProcessor
EMAN::ZeroConstantProcessorContraction of data, if any nearest neighbor is 0, value -> 0, generally used iteratively
EMAN::ZeroEdgePlaneProcessorZero edges of volume on all sides
EMAN::ZeroEdgeRowProcessorZero edges of image on top and bottom, and on left and right
EMAN::ZGradientProcessor