EMAN Namespace Reference

E2Exception class. More...

Namespaces
namespace	Gatan
namespace	GatanDM4

Classes
class	_BadAllocException
	Used when memory allocation goes wrong... i.e. More...
class	_EmptyContainerException
	Used when an argument container is empty, such as a vector. More...
class	_FileAccessException
	Used when a file access error occurs. More...
class	_ImageDimensionException
	Used when an image is not in the expected dimension. More...
class	_ImageFormatException
	Used when an image is not in the expected format. More...
class	_ImageReadException
	Used when an error occurs at image reading time. More...
class	_ImageWriteException
	Used when an error occurs at image writing time. More...
class	_InvalidCallException
class	_InvalidParameterException
class	_InvalidStringException
	Used when an invalid (format) string is given. More...
class	_InvalidValueException
	Used when an invalid integer value is given. More...
class	_NotExistingObjectException
	Used when an object type, like an EMObject type, doesn't exist. More...
class	_NullPointerException
	Used when a NULL is given to a pointer that should not be NULL. More...
class	_OutofRangeException
	Used when the given value is out of range. More...
class	_TypeException
	Used when a type cast error occurs. More...
class	_UnexpectedBehaviorException
	Used when internal behavior is unexpected A generic kind of exception. More...
class	AboveToZeroProcessor
	f(x) = x if x <= maxval; f(x) = 0 if x > maxval More...
class	AbsoluteValueProcessor
	f(x) = |x| More...
class	ACFCenterProcessor
	Center image using auto convolution with 180 degree rotation. More...
class	AddMaskShellProcessor
	Add additional shells/rings to an existing 1/0 mask image. More...
class	AddNoiseProcessor
	add noise to an image More...
class	AddRandomNoiseProcessor
	add spectral noise to a complex image More...
class	AddShapeProcessor
	Rotate by 180 using pixel swapping, works for 2D only. More...
class	AddSigmaNoiseProcessor
	add sigma noise, multiply image's sigma value to noise More...
class	Aligner
	Aligner class defines image alignment method. More...
class	AmiraIO
	Amira file = ASCII header + binary data. More...
class	AmpMultProcessor
class	AmpweightFourierProcessor
	Multiplies each Fourier pixel by its amplitude. More...
class	Analyzer
	Analyzer class defines a way to take a List of images as input, and returns a new List of images. More...
class	ApplyPolynomialProfileToHelix
class	ApplySymProcessor
	Applies a symmetry to a 3D model. More...
class	AreaProcessor
	AreaProcessor use pixel values and coordinates of a real-space square area. More...
class	AutoMask2DProcessor
	Attempts to automatically mask out the particle, excluding other particles in the box, etc. More...
class	AutoMask3D2Processor
	Tries to mask out only interesting density. More...
class	AutoMask3DProcessor
	Tries to mask out only interesting density. More...
class	AutoMaskAsymUnit
	Tries to mask out only interesting density. More...
class	AutoMaskDustProcessor
	A "dust removal" filter which will remove above threshold densities smaller than a given size. More...
class	Averager
	Averager class defines a way to do averaging on a set of images. More...
class	AverageXProcessor
	Average along Y and replace with average. More...
class	Axis0FourierProcessor
	Zeroes the values on the X=0 and y=0 Fourier axes (except x=y=0) More...
class	AzSharpProcessor
	Similar to FourierProcessor, but enhances or compresses azimuthal contrast rather than the typical radial linear filter. More...
class	BackProjectionReconstructor
	Real space 3D reconstruction using back projection. More...
class	BadLineXYProcessor
	This processor will remove specified bad lines from CCD/DDD images, generally due to faulty lines/rows in the detector. More...
class	BeamstopProcessor
	Try to eliminate beamstop in electron diffraction patterns. More...
class	BilateralProcessor
	Bilateral processing on 2D or 3D volume data. More...
class	BinarizeFourierProcessor
	A thresholding processor for Fourier images based on the amplitude component. More...
class	BinarizeProcessor
	f(x) = 0 if x < value; f(x) = 1 if x >= value. More...
class	BinaryBlackHatProcessor
	Performs a morphological black hat operation on an image. More...
class	BinaryClosingProcessor
	Performs a morphological closing operation on an image. More...
class	BinaryDilationProcessor
	Performs a morphological dilation operation on an image. More...
class	BinaryErosionProcessor
	Performs a morphological erosion operation on an image. More...
class	BinaryExternalGradientProcessor
	Computes an external morphological gradient operation on an image. More...
class	BinaryInternalGradientProcessor
	Computes an internal morphological gradient operation on an image. More...
class	BinaryMorphGradientProcessor
	Computes the morphological gradient operation on an image. More...
class	BinaryOpeningProcessor
	Performs a morphological opening operation on an image. More...
class	BinaryOperateProcessor
	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. More...
class	BinarySkeletonizerProcessor
class	BinaryTopHatProcessor
	Performs a morphological top hat operation on an image. More...
class	BispecSliceProcessor
	This processor computes 2-D slices of the 4-D bispectrum of a 2-D image. More...
class	BitReader
class	BitStream
class	BooleanProcessor
	f(x) = 0 if x = 0; f(x) = 1 if x != 0 More...
class	BooleanShrinkProcessor
	BooleanShrinkProcessor encapsulates code common to MaxShrinkProcessor and MinShrinkProcessor - the processors use more or less identical code, the main difference being the logical operator. More...
class	BoxingTools
	BoxingTools is class for encapsulating common boxing operations that may become expensive if they are implemented in python. More...
class	BoxMaxProcessor
	peak processor: pixel = max of values surrounding pixel. More...
class	BoxMedianProcessor
	A processor for noise reduction. More...
class	BoxSigmaProcessor
	pixel = standard deviation of values surrounding pixel. More...
class	BoxStatProcessor
	BoxStatProcessor files are a kind of neighborhood processors. More...
class	BoxSVDClassifier
class	BwMajorityProcessor
	Set a pixel to white when >= N neighbors are white. More...
class	BwThinningProcessor
	Thinning a binary map to skelton using the Zhang-Suen thinning algorithm. More...
class	ByteOrder
	ByteOrder defines functions to work on big/little endian byte orders. More...
class	CccCmp
	Compute the cross-correlation coefficient between two images. More...
class	CCCSNRProcessor
	Convert an image containing normalized correlation coefficients to SNR or a Wiener filter value used in conjunction with local resolution filtration. More...
class	CCDNormProcessor
	Try to normalize the 4 quadrants of a CCD image. More...
class	ChaoProjector
	Fast real space projection using Bi-Linear interpolation. More...
class	CircularAverageAnalyzer
	Calculate the circular average around the center in real space. More...
class	CircularAverageBinarizeProcessor
	Binarize an image based on the circular average around each pixel in real space. More...
class	CircularMaskProcessor
	CircularMaskProcessor applies a circular mask to the data.This is the base class for specific circular mask processors.Its subclass must implement process_dist_pixel(). More...
class	ClampingProcessor
	f(x) = maxval if f(x) > maxval; f(x) = minval if f(x) < minval More...
class	Cmp
	Cmp class defines image comparison method. More...
class	CollapseProcessor
	f(x): if v-r<x<v+r -> v; if x>v+r -> x-r; if x<v-r -> x+r More...
class	ColorRGBGenerator
	Class 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. More...
class	ComplexNormPixel
	Each Fourier pixel will be normalized. More...
class	ComplexPixelProcessor
	The base class for fourier space processor working on individual pixels. More...
class	ConvolutionKernelProcessor
class	ConvolutionProcessor
	This processor performs fast convolution in Fourier space. More...
class	CoordinateProcessor
	CoordinateProcessor applies processing based on a pixel's value and it coordinates. More...
class	CSym
	An encapsulation of cyclic 3D symmetry. More...
class	Ctf
	Ctf is the base class for all CTF model. More...
class	CtfCAutoAverager
	CtfCWautoAverager averages the images with CTF correction with a Wiener filter. More...
class	CTFCorrProcessor
	Processor 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. More...
class	CtfCWautoAverager
	CtfCWautoAverager averages the images with CTF correction with a Wiener filter. More...
class	CtfSimProcessor
	CTF simulation processor. More...
class	CTFSNRWeightProcessor
class	CtfWtAverager
	CtfWtAverager. More...
class	CtfWtFiltAverager
	CtfWtAverager. More...
class	CUDA_Aligner
class	CUDA_multiref_aligner
class	CustomVector
	CustomVector has some trivial optimizations of the STL vector. More...
class	CutoffBlockProcessor
	Block processor, val1 is dx/dy, val2 is lp freq cutoff in pixels. More...
class	CutToZeroProcessor
	f(x) = x-minval if x >= minval; f(x) = 0 if x < minval More...
class	DecayEdgeProcessor
	Decay edges of image to zero. More...
class	Decoder
struct	DecoderIx
class	Df3IO
class	Dict
	Dict is a dictionary to store <string, EMObject> pair. More...
class	DiffBlockProcessor
	averages over cal_half_width, then sets the value in a local block More...
class	DirectionalSumProcessor
	Does a projection in one the axial directions Doesn't support process_inplace (because the output has potentially been compressed in one dimension) More...
class	DiscritizeProcessor
class	DistanceSegmentProcessor
	Segment a volume about:homeinto subvolumes based on a center separation value. More...
class	DM3IO
	Gatan DM3 file is a hierarchical binary image format. More...
class	DM4IO
	Gatan DM$ was introduced with the GMS 2.0 release. More...
class	DoGFourierProcessor
	processor radial function: f(x) = 1/sqrt(2*pi)*[1/sigma1*exp-(x^2/2*sigma1^2) - 1/sigma2*exp-(x^2/2*sigma2^2)] More...
class	DotCmp
	Use dot product of 2 same-size images to do the comparison. More...
class	DSym
	An encapsulation of dihedral 3D symmetry. More...
class	E2Exception
	E2Exception class is the parent class of all EMAN2 E2Exceptions. More...
class	EerIO
class	EMAN1Ctf
	EMAN1Ctf is the CTF model used in EMAN1. More...
class	EMAN2Ctf
	EMAN2Ctf is the default CTF model used in EMAN2. More...
class	EmanOrientationGenerator
	EmanOrientationGenerator generates orientations quasi-evenly distributed in the asymmetric unit. More...
class	EMBytes
class	EMConsts
class	EMData
	EMData stores an image's data and defines core image processing routines. More...
class	EMFTGL
	EMFTGL is an interface for rendering fonts in EMAN2 using FTGL. More...
class	EmIO
	EmIO defines I/O operations on EM image format. More...
class	EMObject
	EMObject is a wrapper class for types including int, float, double, etc as defined in ObjectType. More...
class	EMUtil
class	EnhanceProcessor
	This processor filters an image to improve the visibility of particles. More...
class	EvenOrientationGenerator
	Sparx 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. More...
class	ExpProcessor
	f(x) = exp( x / low - high) More...
class	Factory
	Factory is used to store objects to create new instances. More...
class	FactoryBase
	A class one may inherit from to ensure that the responsibilities of being incorporated into an EMAN2::Factory are met. More...
class	FFTConeProcessor
	Mask out (or in) peaks in Fourier space based on the average amplitude at each spatial frequency. More...
class	FFTPeakProcessor
	Mask out (or in) peaks in Fourier space based on the average amplitude at each spatial frequency. More...
class	FFTProcessor
	Perform a FFT transform by calling EMData::do_fft() and EMData::do_ift() More...
class	FFTResampleProcessor
	FFTResampleProcessor 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. More...
class	FFTWedgeProcessor
	Mask out (or in) peaks in Fourier space based on the average amplitude at each spatial frequency. More...
class	file_store
class	FileFourierProcessor
	A fourier processor specified in a 2 column text file. More...
class	FiniteProcessor
	f(x) = f(x) if f(x) is finite | to if f(x) is not finite More...
class	FitsIO
	MRC file = header + data (nx x ny x nz). More...
class	FixSignProcessor
	This processor can be used to correct errors when reading signed data as unsigned and vice-versa. More...
class	FlattenBackgroundProcessor
	Flattens the background by subtracting the local mean. More...
class	FlipProcessor
	flip/mirror an image around an axis More...
class	FloatPoint
	FloatPoint defines a float-coordinate point in a 1D/2D/3D space. More...
class	FloatSize
	FloatSize is used to describe a 1D, 2D or 3D rectangular size in floating numbers. More...
class	FloorValueProcessor
	f(x) = floor(x) More...
class	FourierAnlProcessor
	Same as FourierProcessor, except first computes the current image radial power spectrum and passes it to the processor (no radial oversampling, number of elements = radius) More...
class	FourierGriddingProjector
	Fourier gridding projection routine. More...
class	FourierInserter3DMode1
	FourierPixelInserter3DMode1 - encapsulates "method 1" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode10
	FourierPixelInserter3DMode10 - encapsulates "method 10" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode11
	FourierPixelInserter3DMode7 - encapsulates "method 7" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode2
	FourierPixelInserter3DMode2 - encapsulates "method 2" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode2l
	FourierPixelInserter3DMode2l - trilinear 2x2x2 inserter See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode3
	FourierPixelInserter3DMode3 - encapsulates "method 3" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode5
	FourierPixelInserter3DMode5 - encapsulates "method 5" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode6
	FourierPixelInserter3DMode6 - encapsulates "method 6" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode7
	FourierPixelInserter3DMode7 - encapsulates "method 7" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode8
	FourierPixelInserter3DMode8 - encapsulates "method 8" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierInserter3DMode9
	FourierPixelInserter3DMode9 - encapsulates "method 9" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class	FourierIterReconstructor
	Fourier 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. More...
class	FourierPixelInserter3D
	FourierPixelInserter3D 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. More...
class	FourierProcessor
	base class for Fourier filters More...
class	FourierReconstructor
	Fourier 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. More...
class	FourierReconstructorSimple2D
	This class originally added for 2D experimentation and prototying. More...
class	FourierToCenterProcessor
	Translates 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. More...
class	FourierToCornerProcessor
	Undo the effects of the FourierToCenterProcessor. More...
class	FourierWeightAverager
	FourierWeightAverager makes an average of a set of images in Fourier space using a per-image radial weight. More...
class	FRCCmp
	FRCCmp returns a quality factor based on FRC between images. More...
class	FRM2DAligner
class	FSCFourierProcessor
	This processor will apply a Wiener filter to a volume based on a provided FSC curve. More...
class	Gatan2IO
	Gatan2 Image file = header + data. More...
class	GaussFFTProjector
	Gaussian FFT 3D projection. More...
class	GaussSegmentProcessor
	Segment a volume by sequentially finding the highest peak and subtracting a Gaussian at that point from the density after strongly filtering the map to a specified resolvability. More...
class	GaussZFourierProcessor
	Zeroes the values on the X=0 and y=0 Fourier axes (except x=y=0) More...
class	GLUtil
class	GradientDirectionProcessor
	Determines the direction of an approximate image gradient using David's image gradient processors. More...
class	GradientMagnitudeProcessor
	Determines the magnitude of an approximate image gradient using David's image gradient processors. More...
class	GradientPlaneRemoverProcessor
	Gradient removed by least square plane fit. More...
class	GradientRemoverProcessor
	Gradient remover, does a rough plane fit to find linear gradients. More...
class	GridKernelFixProcessor
	Multiplies 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. More...
class	GrowSkeletonProcessor
	Grow a skeleton map toward a local direction. More...
class	HarmonicProcessor
	This processor computes what I've dubbed the 'harmonic power spectrum'. More...
class	HighpassAutoPeakProcessor
	This processor attempts to remove the low resolution peak present in all cryoEM data. More...
class	HistogramBin
	Bins pixel values, similar to calculating a histogram. More...
class	HSym
	An encapsulation of helical 3D symmetry. More...
class	Icosahedral2Sym
	An encapsulation of icosahedral symmetry 222. More...
class	IcosahedralSym
	An encapsulation of icosahedral symmetry Doctor Phil has this to say about icosahedral symmetry: "Each Platonic Solid has 2E symmetry elements. More...
class	IcosIO
	ICOS file = header + data. More...
class	ImageAverager
	ImageAverager averages a list of images. More...
class	ImageDivergenceProcessor
	Computes the image divergence using David's partial derivative processors. More...
class	ImageIO
	ImageIO classes are designed for reading/writing various electron micrography image formats, including MRC, IMAGIC, SPIDER, PIF, etc. More...
class	ImageProcessor
struct	ImageScore
class	ImageSort
class	ImagicIO
	IMAGIC-5 Header File Format. More...
class	ImagicIO2
	IMAGIC-5 Header File Format. More...
class	IndexMaskFileProcessor
	Multiplies the image by the specified file using pixel indices. More...
class	InertiaMatrixAnalyzer
	Inertia Matrix computer Computes the Inertia Matrix for a 3-D volume. More...
class	Interp
	Interp defines the interpolation function used to generate a e^-x^4 function in real space. More...
class	IntPoint
	IntPoint defines an integer-coordinate point in a 1D/2D/3D space. More...
class	IntSize
	IntSize is used to describe a 1D, 2D or 3D rectangular size in integers. More...
class	IntTranslateProcessor
	Translate the image an integer amount Uses EMData::clip_inplace (inplace) and EMData::get_clip (out of place) to do the translation. More...
class	Isosurface
class	IterAverager
	IterAverager performs iterative averaging of 3x3 pixel zones around each pixel, computing the mean of the 9 pixels initially, then iteratively refining the average to produce something self-consistent, but hopefully less noisy. More...
class	IterBinMaskProcessor
	Iterative 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. More...
class	IterMultiMaskProcessor
	This expands a multilevel mask volume so inter-mask boundaries are preserved. More...
class	KMeansAnalyzer
	KMeansAnalyzer Performs k-means classification on a set of input images (shape/size arbitrary) returned result is a set of classification vectors. More...
class	KmeansSegmentProcessor
	Segment a volume into ~n subvolumes using K-means classification. More...
class	LaplacianDirectionProcessor
	Determines the direction of an approximate image laplacian using David's image gradient processors. More...
class	LaplacianMagnitudeProcessor
	Determines the direction of an approximate image laplacian using David's image gradient processors. More...
class	LaplacianProcessor
	Discrete approximation to Laplacian. More...
class	LinearPyramidProcessor
	Multiplies 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. More...
class	LinearRampFourierProcessor
class	LinearRampProcessor
	processor radial function: f(x) = slope * x + intercept More...
class	LinearXformProcessor
	linear transform processor: f(x) = x * scale + shift More...
class	LocalMinAbsProcessor
class	LocalNormProcessor
	This 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. More...
class	LocalWeightAverager
	LocalWeightAverager makes an average of a set of images in Fourier space using a per-image radial weight. More...
class	LodCmp
class	Log
	Log defines a way to output logging information. More...
class	LoGFourierProcessor
	processor radial function: f(x) = ((x^2 - s^2)/s^4)e^-(x^2/2s^2) More...
class	LogProcessor
	f(x) = log10(x) if x > 0; else f(x) = 0 More...
class	LowpassAutoBProcessor
	processor radial function: if lowpass > 0, f(x) = exp(-x*x/(lowpass*lowpass)); else f(x) = exp(x*x/(lowpass*lowpass)) More...
class	LowpassRandomPhaseProcessor
	Lowpass Phase Randomization processor applied in Fourier space. More...
class	LstFastIO
	A LSX file is a high performance ASCII file that contains a list of image numbers and file names. More...
class	LstIO
	A LST file is an ASCII file that contains a list of image file names. More...
class	MakeRadiusProcessor
	overwrites input, f(x) = radius More...
class	MakeRadiusSquaredProcessor
	overwrites input, f(x) = radius * radius More...
class	ManhattanDistanceProcessor
	Sets pixel values in a binary image equal to their element wise manhattan distance. More...
class	MarchingCubes
class	MaskAzProcessor
	MaskAzProcessor masks out pixels within a specified cylindrical (or circular) arc. More...
class	MaskEdgeMeanProcessor
	A step cutoff to the the mean value in a ring centered on the outer radius. More...
class	MaskGaussInvProcessor
	f(x) = f(x) / exp(-radius*radius * gauss_width / (ny*ny)) More...
class	MaskGaussNonuniformProcessor
	a gaussian falloff to zero, with anisotropic widths along x,y,z More...
class	MaskGaussProcessor
	a gaussian falloff to zero, radius is the 1/e of the width. More...
class	MaskNoiseProcessor
	fills masked region More...
class	MaskPackProcessor
	This processor will take a mask and extract the values inside the mask as a new 1-D image as well as performing the inverse operation. More...
class	MaskSharpProcessor
	step cutoff to a user-given value in both inner and outer circles. More...
class	MaskSoftProcessor
	step cutoff to a user-given value in both inner and outer circles. More...
class	MatchSFProcessor
	Sets the structure factor To match a second provided image/volume. More...
class	Matrix3
class	Matrix4
class	MaxPixelOperator
class	MaxShrinkProcessor
	MaxShrinkProcessors shrinks an image by in an integer amount, keeping the maximum pixel value - useful when constructing binary search trees in the marching cubes algorithm. More...
class	MaxValProjector
	Real-space projection which computes the maximum value along each line projection rather than a sum. More...
class	MeanShrinkProcessor
	MeanShrinkProcessor shrinks an image by in an integer amount (and optionally by 1.5) taking the mean of the pixel neighbourhood. More...
class	MeanZeroEdgeProcessor
	Fill zeroes at edges with nearest horizontal/vertical value damped towards Mean2. More...
class	MedianAverager
	MedianAverager averages a list of images to the maximum(or minimum of the absolute pixel value) It optionally makes a sigma image. More...
class	MedianShrinkProcessor
	MeanShrinkProcessor shrinks an image by in an integer amount taking the median of the pixel neighbourhood. More...
class	MinMaxAverager
	ImageAverager averages a list of images. More...
class	MinPixelOperator
class	MinShrinkProcessor
	MinShrinkProcessor shrinks an image by in an integer amount, keeping the minimum pixel value - useful when constructing binary search trees in the marching cubes algorithm. More...
class	MinusPeakProcessor
	peak processor: pixel = pixel - max of values surrounding pixel. More...
class	ModelEMCylinderProcessor
class	ModelHelixProcessor
class	MorphologicalProcessor
class	MrcIO
	MRC file = header + data (nx x ny x nz). More...
class	newfile_store
class	nn4_ctf_rectReconstructor
	nn4_ctf_rectDirect Fourier Inversion Reconstructor More...
class	nn4_ctfReconstructor
	nn4_ctf Direct Fourier Inversion Reconstructor More...
class	nn4_ctfwReconstructor
	nn4_ctfw Direct Fourier Weighted Inversion Reconstructor More...
class	nn4_ctfwsReconstructor
	nn4_ctfws Direct Fourier Weighted Inversion Reconstructor for sorting More...
class	nn4_rectReconstructor
	Direct Fourier inversion Reconstructor for extremly rectangular object. More...
class	nn4Reconstructor
class	nnSSNR_ctfReconstructor
class	nnSSNR_Reconstructor
class	NonConvexProcessor
	Make a curve or surface non-convex (planar or concave), iteratively. More...
class	NormalizeByMassProcessor
	Normalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3). More...
class	NormalizeCircleMeanProcessor
	normalizes an image, mean value equals to mean of 2 pixel circular border. More...
class	NormalizeEdgeMeanProcessor
	normalizes an image, mean value equals to edge mean. More...
class	NormalizeHistPeakProcessor
	Normalize such that the estimated histogram peak value is zero. More...
class	NormalizeLREdgeMeanProcessor
	normalizes an image, uses 2 pixels on left and right edge More...
class	NormalizeMaskProcessor
	Uses a 1/0 mask defining a region to use for the zero-normalization.if no_sigma is 1, standard deviation not modified. More...
class	NormalizeMaxMinProcessor
	normalizes an image. More...
class	NormalizeProcessor
	Base class for normalization processors. More...
class	NormalizeRampNormVar
	Normalize the image whilst also removing any ramps. More...
class	NormalizeRowProcessor
	normalizes each row in the image individually More...
class	NormalizeStdProcessor
	do a standard normalization on an image. More...
class	NormalizeToLeastSquareProcessor
	use least square method to normalize More...
class	NormalizeUnitProcessor
	Normalize an image so its vector length is 1.0. More...
class	NormalizeUnitSumProcessor
	Normalize an image so its elements sum to 1.0 (fails if mean=0) More...
class	NSigmaClampingProcessor
	This function clamps the min and max vals in the image at minval and maxval at mean-n*sigma and mean+n*sigma, respectively. More...
class	ObjDensityProcessor
	Replace the value of each pixel with the sum of density of the object it belongs to. More...
class	ObjLabelProcessor
	Label each object in a black-white image. More...
class	OctahedralSym
	An encapsulation of octahedral symmetry Doctor Phil has this to say about the octahedral symmetry: "Each Platonic Solid has 2E symmetry elements. More...
class	OmapIO
	DSN6 MAP is composed of a series of records which are all 512 bytes long. More...
class	OptimumOrientationGenerator
	Optimum orientation generator. More...
class	OptSubCmp
	Uses math.sub.optimal to remove the density of the reference from the image as much as possible. More...
class	OptVarianceCmp
	Variance between two data sets after various modifications. More...
class	OrientationGenerator
	An 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. More...
class	OutlierProcessor
	This processor will try and remove outliers (and optionally exactly zero values), replacing any identified values with the local mean value. More...
class	PaintProcessor
	Multiplies the image by the specified file using pixel coordinates instead of pixel indices. More...
class	PawelProjector
	Pawel Penczek's optimized projection routine. More...
class	PDBReader
	PointArray defines a double array of points with values in a 3D space. More...
class	PeakOnlyProcessor
	peak processor -> if npeaks or more surrounding values >= value, value->0 More...
class	PgmIO
	A PGM file = header + data. More...
class	Phase180Processor
	This class is abstract. More...
class	PhaseCmp
	Amplitude weighted mean phase difference (radians) with optional SNR weight. More...
class	PhaseToCenterProcessor
	Translates a cornered image to the center Undoes the PhaseToCornerProcessor. More...
class	PhaseToCornerProcessor
	Translates a centered image to the corner works for 1D, 2D and 3D images, for all combinations of even and oddness. More...
class	PhaseToMassCenterProcessor
	ToMassCenterProcessor centers image at center of mass, ignores old dx, dy. More...
class	PifIO
	PIF(Portable Image Format for EM Data) is an image format from Purdue University. More...
class	Pixel
	Pixel describes a 3D pixel's coordinates and its intensity value. More...
class	PlatonicSym
	A base (or parent) class for the Platonic symmetries. More...
class	Point3
struct	point_t
class	PointArray
	PointArray defines a double array of points with values in a 3D space. More...
class	PolarData
	a specialized image class for storing the results of a transform from EMData to polar coordinates, currently support 2D only. More...
class	PolyMaskProcessor
class	PriorityQueue
	Template class for a priority queue. More...
class	Processor
	Typical usage of Processors are as follows: More...
class	Projector
	Projector class defines a method to generate 2D projections from a 3D model. More...
class	PruneSkeletonProcessor
	Prune branches from the skeleton. More...
class	QuadMinDotCmp
	This will calculate the dot product for each quadrant of the image and return the worst value. More...
class	Quaternion
	Quaternion is used in Rotation and Transformation to replace Euler angles. More...
class	RadialProcessor
	Perform a multiplication of real image with a radial table. More...
class	RampProcessor
	Ramp processor – Fits a least-squares plane to the picture, and subtracts the plane from the picture. More...
class	Randnum
	The wrapper class for gsl's random number generater. More...
class	RandomOrientationGenerator
	Random Orientation Generator - carefully generates uniformly random orientations in any asymmetric unit. More...
class	RangeThresholdProcessor
	f(x) = 1 if (low <= x <= high); else f(x) = 0 More...
class	RangeZeroProcessor
	Set any values in a range to zero. More...
class	RealMedianReconstructor
	Real space 3D reconstruction using per-voxel median. More...
class	RealPixelProcessor
	The base class for real space processor working on individual pixels. More...
class	RealToFFTProcessor
	This will replace the image with a full-circle 2D fft amplitude rendering. More...
class	RecipCarefullyProcessor
	Reciprocal image as if f(x) != 0: f(x) = 1/f(x) else: f(x) = zero_to. More...
class	Reconstructor
	Reconstructor class defines a way to do 3D recontruction. More...
class	ReconstructorVolumeData
	This is a Mixin class A class object encapsulating the volume data required by Reconstructors It basically stores two (pointers) to EMData objects and stores the dimensions of the image volume. More...
class	Refine3DAlignerGrid
	Refine alignment. More...
class	Refine3DAlignerQuaternion
	Refine alignment. More...
class	RefineAligner
	refine alignment. More...
class	RefineAlignerCG
	Conjugate gradient refine alignment. More...
class	Region
	Region defines a 2D or 3D rectangular region specified by its origin coordinates and all edges' sizes. More...
class	ReplaceValuefromListProcessor
	Replace the value of each pixel with a value in a given array. More...
class	ReverseProcessor
	mirror an image around an axis (reverse pixels) More...
class	Rotate180Processor
	Rotate by 180 using pixel swapping, works for 2D only. More...
class	RotateFlipAligner
	rotational and flip alignment More...
class	RotateFlipAlignerIterative
	rotational and flip alignment, iterative style More...
class	RotateInFSProcessor
class	RotatePrecenterAligner
	rotational alignment assuming centers are correct More...
class	RotateTranslateAligner
	rotational, translational alignment More...
class	RotateTranslateAlignerBispec
	rotational, translational alignment More...
class	RotateTranslateAlignerIterative
	Iterative rotational, translational alignment. More...
class	RotateTranslateAlignerPawel
	Rotational, translational alignment by resampling to polar coordinates. More...
class	RotateTranslateBestAligner
	rotational, translational alignment More...
class	RotateTranslateFlipAligner
	rotational, translational and flip alignment More...
class	RotateTranslateFlipAlignerIterative
	rotational, translational and flip alignment, iterative style More...
class	RotateTranslateFlipAlignerPawel
	Rotational, translational alignment by resampling to polar coordinates. More...
class	RotateTranslateFlipScaleAligner
	rotational, translational, flip, scaling alignment More...
class	RotateTranslateFlipScaleAlignerIterative
	Iterative rotational, translational alignment with flipping and scaling. More...
class	RotateTranslateScaleAligner
	rotational, translational, scaling alignment More...
class	RotateTranslateScaleAlignerIterative
	Iterative rotational, translational alignment with scaling. More...
class	RotationalAligner
	rotational alignment using angular correlation More...
class	RotationalAlignerBispec
	rotational alignment using invariants More...
class	RotationalAlignerIterative
	rotational alignment using the iterative method (in this case we only do one iteration b/c we are not doing a translation. More...
class	RotationalAverageProcessor
	makes image circularly symmetric. More...
class	RotationalSubstractProcessor
	subtracts circularly symmetric part of an image. More...
class	RT2Dto3DTreeAligner
	Alignment of a 2D image into a 3D volume using a hierarchical method with gradually decreasing downsampling in Fourier space. More...
class	RT2DTreeAligner
	2D rotational and translational alignment using a hierarchical method with gradually decreasing downsampling in Fourier space. More...
class	RT3DGridAligner
	rotational 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). More...
class	RT3DLocalTreeAligner
	3D rotational and translational alignment using a hierarchical method with gradually decreasing downsampling in Fourier space. More...
class	RT3DSphereAligner
	3D rotational and translational alignment using spherical sampling, can reduce the search space based on symmetry. More...
class	RT3DSymmetryAligner
	3D rotational symmetry aligner. More...
class	RT3DTreeAligner
	3D rotational and translational alignment using a hierarchical method with gradually decreasing downsampling in Fourier space. More...
class	RTFExhaustiveAligner
	rotational, translational and flip alignment using real-space methods. More...
class	RTFSlowExhaustiveAligner
	rotational, translational and flip alignment using exhaustive search. More...
class	SaffOrientationGenerator
	Saff orientation generator - based on the work of Saff and Kuijlaars, 1997 E.B. More...
class	SalIO
	A SAL image is an image from Perkin Elmer PDS Microdensitometer. More...
class	ScaleAligner
	Scale aligner. More...
class	ScaleAlignerABS
	This is an ABS for use in constructing, rt_scale, rt_flip, etc scale aligners. More...
class	ScaleTransformProcessor
	Scale the image with control over the output dimensions. More...
class	ScreenPoint
class	ScreenVector
class	SDGDProcessor
	Determines the second derivative in the gradient direction using David's image gradient processors. More...
class	SegmentSubunitProcessor
	This tries to extract a single subunit from a symmetric structure. More...
class	SerIO
	SER (Series File Format) is a file format created by Dr. More...
class	SetBitsProcessor
class	SetIsoPowProcessor
	Makes the radial power distribution spherically symmetric with a profile defined by "strucfac". More...
class	SetSFProcessor
	Sets the structure factor based on a 1D s/intensity curve as an XYData object. More...
class	ShapeAnalyzer
	Shape characterization Computes a set of values characteristic of the shape of a volume. More...
class	SigmaAverager
	SigmaAverager averages a list of images. More...
class	SigmaProcessor
	f(x) = mean if x<(mean-v2*sigma) or x>(mean+v1*sigma); else f(x) = x; More...
class	SigmaZeroEdgeProcessor
	Fill zeroes at edges with nearest horizontal/vertical value. More...
class	SingleOrientationGenerator
	SingleOrientationGenerator generates a single orientation with the specified EMAN-style Euler angles. More...
class	SingleSpiderIO
	Single Spider Image I/O class. More...
class	SitusIO
	situs is a a Situs-specific format on a cubic lattice. More...
class	SmartMaskProcessor
	Smart mask processor. More...
class	SNREvalProcessor
	Evaluate individual particle images using a tenchique similar to that used for CTF evaluation. More...
class	SNRProcessor
	Processor 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. More...
class	SpiderIO
	SPIDER: (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy. More...
class	SqEuclideanCmp
	Squared Euclidean distance normalized by n between 'this' and 'with'. More...
class	StandardProjector
	Fast real-space 3D projection. More...
class	StripeXYProcessor
	This processor will remove localized 'striping' along the x/y axes, caused by issues with CCD/CMOS readout. More...
class	SubtractOptProcessor
	Sorry for the pun. More...
class	SVDAnalyzer
	Singular Value Decomposition from GSL. More...
class	SymAlignProcessor
	Aligns a particle with the specified symmetry into the standard orientation for that symmetry. More...
class	SymAlignProcessorQuat
	Aligns a particle with a specified symetry to its symmetry axis using the simplex multidimensional minimization algorithm. More...
class	Symmetry3D
	Symmetry3D - A base class for 3D Symmetry objects. More...
class	SymSearchProcessor
	Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel. More...
class	TestImageAxes
	Make an image consisting of a single cross, with lines going in the axial directions, intersecting at the origin. More...
class	TestImageCirclesphere
	Replace a source image as a circle or sphere depends on 2D or 3D of the source image. More...
class	TestImageCylinder
	Replace a source image with a cylinder. More...
class	TestImageDisc
	Replace source image with a disc (generalized cylinder) More...
class	TestImageEllipse
	Generate an ellipse or ellipsoid image. More...
class	TestImageFourierGaussianBand
	Replace a source image with a Gaussian band in Fourier space with a given center and width. More...
class	TestImageFourierNoiseGaussian
	Replace a source image as a strict Gaussian. More...
class	TestImageFourierNoiseProfile
class	TestImageGaussian
	Replace a source image as a Gaussian Blob. More...
class	TestImageGradient
	Put 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. More...
class	TestImageHollowEllipse
	Generate an ellipse/ellipsoid image with an inner hollow ellipse/ellipsoid. More...
class	TestImageLineWave
	Treats 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) More...
class	TestImageNoiseGauss
	Replace 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). More...
class	TestImageNoiseUniformRand
	Replace 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) More...
class	TestImageProcessor
	Base class for a group of 'processor' used to create test image. More...
class	TestImagePureGaussian
	Replace a source image as a strict Gaussian. More...
class	TestImageScurve
	Replace a source image with a lumpy S-curve used for alignment testing. More...
class	TestImageSinewave
	Replace a source image as a sine wave in specified wave length. More...
class	TestImageSinewaveCircular
	Replace a source image as a circular sine wave in specified wave length. More...
class	TestImageSphericalWave
	Replace a source image as a sine wave in specified wave length. More...
class	TestImageSquarecube
	Replace a source image as a square or cube depends on 2D or 3D of the source image. More...
class	TestTomoImage
	Make 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". More...
class	TestUtil
class	TetrahedralSym
	An encapsulation of tetrahedral symmetry Doctor Phil has this to say about tetrahedral symmetry: " Each Platonic Solid has 2E symmetry elements. More...
class	ToCenterProcessor
	ToCenterProcessor centers image, ignores old dx, dy. More...
class	ToMassCenterProcessor
	ToMassCenterProcessor centers image at center of mass, ignores old dx, dy. More...
class	ToMinvalProcessor
	f(x) = x if x >= minval; f(x) = minval if x < minval More...
class	TomoAverager
	TomoAverager averages a list of volumes in Fourier space. More...
class	TomoCccCmp
	This implements the technique of Mike Schmid where by the cross correlation is normalized in an effort to remove the effects of the missing wedge. More...
class	TomoFscCmp
	This is a FSC comparitor for tomography. More...
class	TomoObject
class	TomoSeg
class	TomoTiltAngleWeightProcessor
	A 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. More...
class	TomoTiltEdgeMaskProcessor
	A processor designed specifically for tomographic tilt series data. More...
class	TomoWedgeCccCmp
	Both images should be FFTs. More...
class	TomoWedgeFscCmp
	Both images should be FFTs. More...
class	ToZeroProcessor
	f(x) = x if x >= minval; f(x) = 0 if x < minval More...
class	Transform
	A Transform object is a somewhat specialized object designed specifically for EMAN2/Sparx storage of alignment parameters and euler orientations. More...
class	TransformProcessor
	Transform the image using a Transform object. More...
class	TranslationalAligner
	Translational 2D Alignment using cross correlation. More...
class	TransposeProcessor
	Transpose a 2D image. More...
class	TypeDict
	TypeDict is a dictionary to store <string, EMObject::ObjectType> pair. More...
class	U3DWriter
	A work in progress by David Woolford. More...
class	UnevenMatrix
	a general data structure for a matrix with variable x dim size for different y More...
class	Util
	Util is a collection of utility functions. More...
class	V4L2IO
	Read-only. More...
class	ValuePowProcessor
	Do a math power operation on image, f(x) = x ^ pow;. More...
class	ValueSqrtProcessor
	f(x) = sqrt(x) More...
class	ValueSquaredProcessor
	Do a square operation on image, f(x) = x * x;. More...
class	Vec2
	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. More...
class	Vec3
	The Vec3 object is a templated object, intended to instantiated with basic types such as int, float, double etc. More...
class	Vec4
	The Vec4 object is a templated object, intended to instantiated with basic types such as int, float, double etc. More...
class	Vector3
class	Vector4
class	VerticalCmp
class	VerticalStripeProcessor
	Tries to fix images scanned on the zeiss for poor ccd normalization. More...
class	VtkIO
	VtkIO reads/writes VTK image file. More...
class	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 More...
class	WaveletProcessor
	Perform a Wavelet transform using GSL. More...
class	WedgeFillProcessor
	Fill missing wedge with information from another image. More...
class	Wiener2DAutoAreaProcessor
	Automatically 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. More...
class	Wiener2DFourierProcessor
	Wiener filter based on a Ctf object either in the image header. More...
class	WienerFourierReconstructor
	Fourier 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". More...
class	XGradientProcessor
	Determines the partial derivatives in the x direction Does this by constructing edge kernels in real space but convoluting in Fourier space. More...
class	XplorIO
	XPLOR image format is in ASCII: More...
class	XYData
	XYData defines a 1D (x,y) data set. More...
class	XYZAligner
	XYZAligner is an aligner template for defining new aligners. More...
class	XYZAverager
	XYZAverager is an averager template for defining new averagers. More...
class	XYZCmp
	XYZCmp is a cmp template for defining new cmps. More...
class	XYZIO
	XYZIO is a sample Image IO class. More...
class	XYZProcessor
	XYZProcessor is a processor template for defining new processors. More...
class	XYZProjector
	XYZProjector is an projector template for defining new projectors. More...
class	XYZReconstructor
	XYZReconstructor is a reconstructor template for defining new reconstructors. More...
class	YGradientProcessor
class	ZeroConstantProcessor
	Contraction of data, if any nearest neighbor is 0, value -> 0, generally used iteratively. More...
class	ZeroEdgePlaneProcessor
	zero edges of volume on all sides More...
class	ZeroEdgeRowProcessor
	zero edges of image on top and bottom, and on left and right. More...
class	ZGradientProcessor
class	ZThicknessProcessor
	Calculate the z thickness of each pixel in a binarized 3d image. More...

Typedefs
typedef boost::multi_array_ref< float, 2 >	MArray2D
typedef boost::multi_array_ref< float, 3 >	MArray3D
typedef boost::multi_array_ref< std::complex< float >, 2 >	MCArray2D
typedef boost::multi_array_ref< std::complex< float >, 3 >	MCArray3D
typedef boost::multi_array< int, 2 >	MIArray2D
typedef boost::multi_array< int, 3 >	MIArray3D
template<unsigned int T, class U >
using	Rle = BitReader< T, true, U >
template<unsigned int T, class U >
using	SubPix = BitReader< T, false, U >
using	EerWord = uint64_t
using	EerStream = BitStream< EerWord >
using	EerRle = Rle< 7, EerWord >
using	EerSubPix = SubPix< 4, EerWord >
typedef Vec4< float >	Vec4f
typedef Vec4< int >	Vec4i
typedef Vec4< double >	Vec4d
typedef Vec3< float >	Vec3f
typedef Vec3< int >	Vec3i
typedef Vec3< double >	Vec3d
typedef Vec2< float >	Vec2f
typedef Vec2< int >	Vec2i
typedef Vec2< double >	Vec2d

Enumerations
enum	MapInfoType {   NORMAL , ICOS2F_FIRST_OCTANT , ICOS2F_FULL , ICOS2F_HALF ,   ICOS3F_HALF , ICOS3F_FULL , ICOS5F_HALF , ICOS5F_FULL ,   ICOS_UNKNOWN }

Functions
void	dump_aligners ()
map< string, vector< string > >	dump_aligners_list ()
void	dump_analyzers ()
map< string, vector< string > >	dump_analyzers_list ()
void	dump_averagers ()
map< string, vector< string > >	dump_averagers_list ()
void	dump_cmps ()
map< string, vector< string > >	dump_cmps_list ()
EMData *	operator+ (const EMData &em, float n)
EMData *	operator- (const EMData &em, float n)
EMData *	operator* (const EMData &em, float n)
EMData *	operator/ (const EMData &em, float n)
EMData *	operator+ (float n, const EMData &em)
EMData *	operator- (float n, const EMData &em)
EMData *	operator* (float n, const EMData &em)
EMData *	operator/ (float n, const EMData &em)
EMData *	rsub (const EMData &em, float n)
EMData *	rdiv (const EMData &em, float n)
EMData *	operator+ (const EMData &a, const EMData &b)
EMData *	operator- (const EMData &a, const EMData &b)
EMData *	operator* (const EMData &a, const EMData &b)
EMData *	operator/ (const EMData &a, const EMData &b)
bool	operator== (const EMObject &e1, const EMObject &e2)
bool	operator!= (const EMObject &e1, const EMObject &e2)
bool	operator== (const Dict &d1, const Dict &d2)
bool	operator!= (const Dict &d1, const Dict &d2)
template<class T >
void	dump_factory ()
template<class T >
map< string, vector< string > >	dump_factory_list ()
IntPoint	operator- (const IntPoint &p)
bool	operator< (const Pixel &p1, const Pixel &p2)
bool	operator== (const Pixel &p1, const Pixel &p2)
bool	operator!= (const Pixel &p1, const Pixel &p2)
int	multi_processors (EMData *image, vector< string > processornames)
void	dump_processors ()
map< string, vector< string > >	dump_processors_list ()
map< string, vector< string > >	group_processors ()
void	dump_projectors ()
map< string, vector< string > >	dump_projectors_list ()
Quaternion	operator+ (const Quaternion &q1, const Quaternion &q2)
Quaternion	operator- (const Quaternion &q1, const Quaternion &q2)
Quaternion	operator* (const Quaternion &q1, const Quaternion &q2)
Quaternion	operator* (const Quaternion &q, float s)
Quaternion	operator* (float s, const Quaternion &q)
Quaternion	operator/ (const Quaternion &q1, const Quaternion &q2)
bool	operator== (const Quaternion &q1, const Quaternion &q2)
bool	operator!= (const Quaternion &q1, const Quaternion &q2)
EMData *	padfft_slice (const EMData *const slice, const Transform &t, int npad)
	Direct Fourier inversion Reconstructor. More...
void	dump_reconstructors ()
map< string, vector< string > >	dump_reconstructors_list ()
void	dump_symmetries ()
	dump symmetries, useful for obtaining symmetry information More...
map< string, vector< string > >	dump_symmetries_list ()
	dump_symmetries_list, useful for obtaining symmetry information More...
void	dump_orientgens ()
	Dumps useful information about the OrientationGenerator factory. More...
map< string, vector< string > >	dump_orientgens_list ()
	Can be used to get useful information about the OrientationGenerator factory. More...
Transform	operator* (const Transform &M2, const Transform &M1)
	Matrix times Matrix, a pure mathematical operation. More...
template<typename Type >
Vec3f	operator* (const Transform &M, const Vec3< Type > &v)
	Matrix times Vector, a pure mathematical operation. More...
template<typename Type >
Vec2f	operator* (const Transform &M, const Vec2< Type > &v)
	Matrix times Vector, a pure mathematical operation. More...
template<typename Type >
Vec3f	operator* (const Vec3< Type > &v, const Transform &M)
	Vector times a matrix. More...
template<typename Type , typename Type2 >
Vec3< Type >	operator+ (const Vec3< Type > &v1, const Vec3< Type2 > &v2)
template<typename Type , typename Type2 >
Vec3< Type >	operator+ (const Vec3< Type > &v, const Type2 &n)
template<typename Type , typename Type2 >
Vec3< Type >	operator- (const Vec3< Type > &v1, const Vec3< Type2 > &v2)
template<typename Type , typename Type2 >
Vec3< Type >	operator- (const Vec3< Type > &v, const Type2 &n)
template<typename Type >
Vec3< Type >	operator- (const Vec3< Type > &v)
template<typename Type , typename Type2 >
Type	operator* (const Vec3< Type > &v1, const Vec3< Type2 > &v2)
template<typename Type , typename Type2 >
Vec3< Type2 >	operator* (const Type &d, const Vec3< Type2 > &v)
template<typename Type , typename Type2 >
Vec3< Type >	operator* (const Vec3< Type > &v, const Type2 &d)
template<typename Type , typename Type2 >
Vec3< Type2 >	operator/ (const Type &d, const Vec3< Type2 > &v)
template<typename Type , typename Type2 >
Vec3< Type >	operator/ (const Vec3< Type > &v, const Type2 &d)
template<typename Type , typename Type2 >
bool	operator== (const Vec3< Type > &v1, const Vec3< Type2 > &v2)
template<typename Type , typename Type2 >
bool	operator!= (const Vec3< Type > &v1, const Vec3< Type2 > &v2)
template<typename Type , typename Type2 >
Vec2< Type >	operator+ (const Vec2< Type > &v1, const Vec2< Type2 > &v2)
template<typename Type , typename Type2 >
Vec2< Type >	operator+ (const Vec2< Type > &v, const Type2 &n)
template<typename Type , typename Type2 >
Vec2< Type >	operator- (const Vec2< Type > &v1, const Vec2< Type2 > &v2)
template<typename Type , typename Type2 >
Vec2< Type >	operator- (const Vec2< Type > &v, const Type2 &n)
template<typename Type >
Vec2< Type >	operator- (const Vec2< Type > &v)
template<typename Type , typename Type2 >
Type	operator* (const Vec2< Type > &v1, const Vec2< Type2 > &v2)
template<typename Type , typename Type2 >
Vec2< Type2 >	operator* (const Type &d, const Vec2< Type2 > &v)
template<typename Type , typename Type2 >
Vec2< Type >	operator* (const Vec2< Type > &v, const Type2 &d)
template<typename Type , typename Type2 >
Vec2< Type2 >	operator/ (const Type &d, const Vec2< Type2 > &v)
template<typename Type , typename Type2 >
Vec2< Type >	operator/ (const Vec2< Type > &v, const Type2 &d)
template<typename Type , typename Type2 >
bool	operator== (const Vec2< Type > &v1, const Vec2< Type2 > &v2)
template<typename Type , typename Type2 >
bool	operator!= (const Vec2< Type > &v1, const Vec2< Type2 > &v2)
bool	isZero (double in_d, double in_dEps=1e-16)
ScreenVector	operator* (const double s, const ScreenVector &v)
std::ostream &	operator<< (std::ostream &os, const ScreenVector &v)
std::ostream &	operator<< (std::ostream &os, const ScreenPoint &p)
Vector3	operator* (const double s, const Vector3 &v)
double	dot (const Vector3 &w, const Vector3 &v)
Vector3	cross (const Vector3 &w, const Vector3 &v)
double	length (const Vector3 &v)
Vector3	unit (const Vector3 &v)
std::ostream &	operator<< (std::ostream &os, const Vector3 &v)
Point3	lerp (const Point3 &p0, const Point3 &p1, double dT)
std::ostream &	operator<< (std::ostream &os, const Point3 &p)
Vector3	operator* (const Vector3 &v, const Matrix3 &m)
Point3	operator* (const Point3 &p, const Matrix3 &m)
std::ostream &	operator<< (std::ostream &os, const Matrix3 &m)
Vector4	operator* (const double s, const Vector4 &v)
double	length (const Vector4 &v)
Vector4	unit (const Vector4 &v)
std::ostream &	operator<< (std::ostream &os, const Vector4 &v)
std::ostream &	operator<< (std::ostream &os, const Matrix4 &m)

Variables
const int	EMDataTypeBits [] = { 0,8,8,16,16,32,32,32,64,32,32,64,0 }
static DecoderIx< 0 >	decoder0x
static DecoderIx< 1 >	decoder1x
static DecoderIx< 2 >	decoder2x
static const int	MAXFFT =32768

Detailed Description

E2Exception class.

df3 file format (http://www.povray.org/documentation/view/3.6.1/374) Header: The df3 format consists of a 6 byte header of three 16-bit integers with high order byte first.

E2Exception class is a subclass of std::exception; All EMAN2 exception classes are subclass of E2Exception class.

A XYZ Exception class is defined in the following way: 0) It will extend E2Exception class. 1) The class is named _XYZException. 2) The class has a function to return its name "XYZException". 3) A macro called "XYZException" is defined to simplify the usage of _XYZException class. So that filename, function name, and line number can be handled automatically.

How to use XYZException:

1) To throw exception, use "throw XYZException(...)"; 2) To catch exception, use "catch (_XYZException & e) ...".

These three values give the x,y,z size of the data in pixels (or more appropriately called voxels ). Data: The header is followed by x*y*z unsigned integer bytes of data with a resolution of 8, 16 or 32 bit. The data are written with high order byte first (big-endian). The resolution of the data is determined by the size of the df3-file. That is, if the file is twice (minus header, of course) as long as an 8 bit file then it is assumed to contain 16 bit ints and if it is four times as long 32 bit ints.

Typedef Documentation

EerRle

using EMAN::EerRle = typedef Rle <7, EerWord>

Definition at line 116 of file eerio.h.

EerStream

using EMAN::EerStream = typedef BitStream<EerWord>

Definition at line 115 of file eerio.h.

EerSubPix

using EMAN::EerSubPix = typedef SubPix<4, EerWord>

Definition at line 117 of file eerio.h.

EerWord

using EMAN::EerWord = typedef uint64_t

Definition at line 114 of file eerio.h.

MArray2D

typedef boost::multi_array_ref<float, 2> EMAN::MArray2D

Definition at line 68 of file emdata.h.

MArray3D

typedef boost::multi_array_ref<float, 3> EMAN::MArray3D

Definition at line 69 of file emdata.h.

MCArray2D

typedef boost::multi_array_ref<std::complex<float>, 2> EMAN::MCArray2D

Definition at line 70 of file emdata.h.

MCArray3D

typedef boost::multi_array_ref<std::complex<float>, 3> EMAN::MCArray3D

Definition at line 71 of file emdata.h.

MIArray2D

typedef boost::multi_array<int, 2> EMAN::MIArray2D

Definition at line 72 of file emdata.h.

MIArray3D

typedef boost::multi_array< int, 3 > EMAN::MIArray3D

Definition at line 73 of file emdata.h.

Rle

template<unsigned int T, class U >

using EMAN::Rle = typedef BitReader<T, true, U>

Definition at line 109 of file eerio.h.

SubPix

template<unsigned int T, class U >

using EMAN::SubPix = typedef BitReader<T, false, U>

Definition at line 112 of file eerio.h.

Vec2d

typedef Vec2<double> EMAN::Vec2d

Definition at line 1073 of file vec3.h.

Vec2f

typedef Vec2<float> EMAN::Vec2f

Definition at line 1071 of file vec3.h.

Vec2i

typedef Vec2<int> EMAN::Vec2i

Definition at line 1072 of file vec3.h.

Vec3d

typedef Vec3<double> EMAN::Vec3d

Definition at line 695 of file vec3.h.

Vec3f

typedef Vec3<float> EMAN::Vec3f

Definition at line 693 of file vec3.h.

Vec3i

typedef Vec3<int> EMAN::Vec3i

Definition at line 694 of file vec3.h.

Vec4d

typedef Vec4<double> EMAN::Vec4d

Definition at line 254 of file vec3.h.

Vec4f

typedef Vec4<float> EMAN::Vec4f

Definition at line 252 of file vec3.h.

Vec4i

typedef Vec4<int> EMAN::Vec4i

Definition at line 253 of file vec3.h.

Enumeration Type Documentation

MapInfoType

enum EMAN::MapInfoType

Enumerator
NORMAL
ICOS2F_FIRST_OCTANT
ICOS2F_FULL
ICOS2F_HALF
ICOS3F_HALF
ICOS3F_FULL
ICOS5F_HALF
ICOS5F_FULL
ICOS_UNKNOWN

Definition at line 94 of file emobject.h.

                         {
                NORMAL,
                ICOS2F_FIRST_OCTANT,
                ICOS2F_FULL,
                ICOS2F_HALF,
                ICOS3F_HALF,
                ICOS3F_FULL,
                ICOS5F_HALF,
                ICOS5F_FULL,
                ICOS_UNKNOWN
        };

Function Documentation

cross()

Vector3 EMAN::cross ( const Vector3 &  w, const Vector3 &  v  )

inline

Definition at line 309 of file vecmath.h.

                                                                   {
            return w ^ v;
        }

Referenced by EMAN::PointArray::remove_helix_from_map().

dot()

double EMAN::dot ( const Vector3 &  w, const Vector3 &  v  )

inline

Definition at line 305 of file vecmath.h.

                                                                {
            return w * v;
        }

Referenced by EMAN::FourierReconstructor::do_compare_slice_work(), EMAN::WienerFourierReconstructor::do_compare_slice_work(), EMAN::EMData::little_big_dot(), EMAN::EMData::make_footprint(), EMAN::PointArray::remove_helix_from_map(), EMAN::EMUtil::vertical_acf(), and EMAN::Util::windowdot().

dump_aligners()

void EMAN::dump_aligners

(

)

Definition at line 5436 of file aligner.cpp.

{
        dump_factory < Aligner > ();
}

dump_aligners_list()

map< string, vector< string > > EMAN::dump_aligners_list

(

)

Definition at line 5441 of file aligner.cpp.

{
        return dump_factory_list < Aligner > ();
}

dump_analyzers()

void EMAN::dump_analyzers

(

)

Definition at line 1022 of file analyzer.cpp.

{
        dump_factory < Analyzer > ();
}

dump_analyzers_list()

map< string, vector< string > > EMAN::dump_analyzers_list

(

)

Definition at line 1027 of file analyzer.cpp.

{
        return dump_factory_list < Analyzer > ();
}

dump_averagers()

void EMAN::dump_averagers

(

)

Definition at line 1597 of file averager.cpp.

{
        dump_factory < Averager > ();
}

dump_averagers_list()

map< string, vector< string > > EMAN::dump_averagers_list

(

)

Definition at line 1602 of file averager.cpp.

{
        return dump_factory_list < Averager > ();
}

dump_cmps()

void EMAN::dump_cmps

(

)

Definition at line 1664 of file cmp.cpp.

{
        dump_factory < Cmp > ();
}

dump_cmps_list()

map< string, vector< string > > EMAN::dump_cmps_list

(

)

Definition at line 1669 of file cmp.cpp.

{
        return dump_factory_list < Cmp > ();
}

dump_factory()

template<class T >

void EMAN::dump_factory

(

)

Definition at line 848 of file emobject.h.

        {
                auto item_names = Factory<T>::get_list();
 
                for (size_t i = 0; i < item_names.size(); i++) {
                        T* item = Factory<T>::get(item_names[i]);
                        printf("%s :  %s\n", item->get_name().c_str(),item->get_desc().c_str());
                        TypeDict td = item->get_param_types();
                        td.dump();
                }
        }

References EMAN::TypeDict::dump(), EMAN::Factory< T >::get(), and EMAN::Factory< T >::get_list().

dump_factory_list()

template<class T >

map< string, vector< string > > EMAN::dump_factory_list

(

)

Definition at line 861 of file emobject.h.

        {
                vector<string> item_names = Factory<T>::get_list();
                map<string, vector<string> >    factory_list;
 
                for(auto p = item_names.begin(); p !=item_names.end(); ++p) {
                        T* item = Factory<T>::get(*p);
 
                        string name = item->get_name();
 
                        vector<string> content;
                        content.push_back(item->get_desc());
                        TypeDict td = item->get_param_types();
                        vector<string> keys = td.keys();
                        for(unsigned int i=0; i<td.size(); ++i) {
                                content.push_back(keys[i]);
                                content.push_back( td.get_type(keys[i]) );
                                content.push_back( td.get_desc(keys[i]) );
                        }
                        factory_list[name] = content;
                }
 
                return factory_list;
        }

References EMAN::Factory< T >::get(), EMAN::TypeDict::get_desc(), EMAN::Factory< T >::get_list(), EMAN::TypeDict::get_type(), EMAN::TypeDict::keys(), and EMAN::TypeDict::size().

dump_orientgens()

void EMAN::dump_orientgens

(

)

Dumps useful information about the OrientationGenerator factory.

Definition at line 157 of file symmetry.cpp.

{
        dump_factory < OrientationGenerator > ();
}

dump_orientgens_list()

map< string, vector< string > > EMAN::dump_orientgens_list

(

)

Can be used to get useful information about the OrientationGenerator factory.

Definition at line 162 of file symmetry.cpp.

{
        return dump_factory_list < OrientationGenerator > ();
}

dump_processors()

void EMAN::dump_processors

(

)

Definition at line 13086 of file processor.cpp.

{
        dump_factory < Processor > ();
}

dump_processors_list()

map< string, vector< string > > EMAN::dump_processors_list

(

)

Definition at line 13091 of file processor.cpp.

{
        return dump_factory_list < Processor > ();
}

dump_projectors()

void EMAN::dump_projectors

(

)

Definition at line 2153 of file projector.cpp.

{
        dump_factory < Projector > ();
}

dump_projectors_list()

map< string, vector< string > > EMAN::dump_projectors_list

(

)

Definition at line 2158 of file projector.cpp.

{
        return dump_factory_list < Projector > ();
}

dump_reconstructors()

void EMAN::dump_reconstructors

(

)

Definition at line 6280 of file reconstructor.cpp.

{
        dump_factory < Reconstructor > ();
}

dump_reconstructors_list()

map< string, vector< string > > EMAN::dump_reconstructors_list

(

)

Definition at line 6285 of file reconstructor.cpp.

{
        return dump_factory_list < Reconstructor > ();
}

dump_symmetries()

void EMAN::dump_symmetries

(

)

dump symmetries, useful for obtaining symmetry information

Definition at line 65 of file symmetry.cpp.

{
        dump_factory < Symmetry3D > ();
}

dump_symmetries_list()

map< string, vector< string > > EMAN::dump_symmetries_list

(

)

dump_symmetries_list, useful for obtaining symmetry information

Definition at line 70 of file symmetry.cpp.

{
        return dump_factory_list < Symmetry3D > ();
}

group_processors()

map< string, vector< string > > EMAN::group_processors

(

)

Definition at line 13096 of file processor.cpp.

{
        map<string, vector<string> > processor_groups;
 
        vector <string> processornames = Factory<Processor>::get_list();
 
        for (size_t i = 0; i < processornames.size(); i++) {
                Processor * f = Factory<Processor>::get(processornames[i]);
                if (dynamic_cast<RealPixelProcessor*>(f) != 0) {
                        processor_groups["RealPixelProcessor"].push_back(f->get_name());
                }
                else if (dynamic_cast<BoxStatProcessor*>(f)      != 0) {
                        processor_groups["BoxStatProcessor"].push_back(f->get_name());
                }
                else if (dynamic_cast<ComplexPixelProcessor*>(f)  != 0) {
                        processor_groups["ComplexPixelProcessor"].push_back(f->get_name());
                }
                else if (dynamic_cast<CoordinateProcessor*>(f)  != 0) {
                        processor_groups["CoordinateProcessor"].push_back(f->get_name());
                }
                else if (dynamic_cast<FourierProcessor*>(f)      != 0) {
                        processor_groups["FourierProcessor"].push_back(f->get_name());
                }
                else if (dynamic_cast<NewFourierProcessor*>(f)  != 0) {
                        processor_groups["FourierProcessor"].push_back(f->get_name());
                }
                else if (dynamic_cast<NormalizeProcessor*>(f)  != 0) {
                        processor_groups["NormalizeProcessor"].push_back(f->get_name());
                }
                else {
                        processor_groups["Others"].push_back(f->get_name());
                }
        }
 
        return processor_groups;
}

References EMAN::Factory< T >::get(), EMAN::Factory< T >::get_list(), and EMAN::Processor::get_name().

isZero()

bool EMAN::isZero ( double  in_d, double  in_dEps = 1e-16  )

inline

Definition at line 44 of file vecmath.h.

        { 
            return (in_d < in_dEps && in_d > -in_dEps)? true : false; 
        }

Referenced by EMAN::Matrix3::approxEqual(), EMAN::Matrix4::approxEqual(), EMAN::Point3::approxEqual(), EMAN::Vector3::approxEqual(), EMAN::Vector4::approxEqual(), EMAN::Matrix3::inverse(), EMAN::Matrix4::inverse(), and EMAN::Matrix4::operator*().

length() [1/2]

double EMAN::length ( const Vector3 &  v )

inline

Definition at line 313 of file vecmath.h.

{ return v.length(); }

References EMAN::Vector3::length().

Referenced by EMAN::PointArray::distmx(), EMAN::TestImageFourierNoiseGaussian::process_inplace(), EMAN::TestImageFourierNoiseProfile::process_inplace(), EMAN::CTFSNRWeightProcessor::process_inplace(), and EMAN::PointArray::remove_helix_from_map().

length() [2/2]

double EMAN::length ( const Vector4 &  v )

inline

Definition at line 684 of file vecmath.h.

{ return v.length(); }

References EMAN::Vector4::length().

lerp()

Point3 EMAN::lerp ( const Point3 &  p0, const Point3 &  p1, double  dT  )

inline

Definition at line 402 of file vecmath.h.

        {
            const double dTMinus = 1.0 - dT;
            return Point3( dTMinus * p0[0] + dT * p1[0], dTMinus * p0[1] + dT * p1[1], dTMinus * p0[2] + dT * p1[2] ); 
        }

multi_processors()

int EMAN::multi_processors	(	EMData *	image,
		vector< string >	processornames
	)

Definition at line 10685 of file processor.cpp.

{
        Assert(image != 0);
        Assert(processornames.size() > 0);
 
        for (size_t i = 0; i < processornames.size(); i++) {
                image->process_inplace(processornames[i]);
        }
        return 0;
}

References Assert.

operator!=() [1/6]

bool EMAN::operator!=	(	const Dict &	d1,
		const Dict &	d2
	)

Definition at line 1027 of file emobject.cpp.

{
        return !(d1 == d2);
}

operator!=() [2/6]

bool EMAN::operator!=	(	const EMObject &	e1,
		const EMObject &	e2
	)

Definition at line 873 of file emobject.cpp.

{
        return !(e1 == e2);
}

operator!=() [3/6]

bool EMAN::operator!=	(	const Pixel &	p1,
		const Pixel &	p2
	)

Definition at line 58 of file geometry.cpp.

{
        return !(p1 == p2);
}

operator!=() [4/6]

bool EMAN::operator!=	(	const Quaternion &	q1,
		const Quaternion &	q2
	)

Definition at line 366 of file quaternion.cpp.

{
        return (!(q1 == q2));
}

operator!=() [5/6]

template<typename Type , typename Type2 >

bool EMAN::operator!= ( const Vec2< Type > &  v1, const Vec2< Type2 > &  v2  )

inline

Definition at line 1064 of file vec3.h.

                                                                             {
                if (v1[0] != v2[0] || v1[1] != v2[1] ) {
                        return true;
                }
                return false;
        }

operator!=() [6/6]

template<typename Type , typename Type2 >

bool EMAN::operator!= ( const Vec3< Type > &  v1, const Vec3< Type2 > &  v2  )

inline

Definition at line 686 of file vec3.h.

                                                                             {
                if (v1[0] != v2[0] || v1[1] != v2[1] || v1[2] != v2[2]) {
                        return true;
                }
                return false;
        }

operator*() [1/21]

ScreenVector EMAN::operator* ( const double  s, const ScreenVector &  v  )

inline

Definition at line 129 of file vecmath.h.

                                                                               {
            return ScreenVector( (int)(v[0] * s), (int)(v[1] * s) );
        }

operator*() [2/21]

Vector3 EMAN::operator* ( const double  s, const Vector3 &  v  )

inline

Definition at line 301 of file vecmath.h.

                                                                     {
            return Vector3( v[0] * s, v[1] * s, v[2] * s );
        }

operator*() [3/21]

Vector4 EMAN::operator* ( const double  s, const Vector4 &  v  )

inline

Definition at line 680 of file vecmath.h.

                                                                     {
            return Vector4( v[0] * s, v[1] * s, v[2] * s, v[3] * s );
        }

operator*() [4/21]

EMData * EMAN::operator*	(	const EMData &	a,
		const EMData &	b
	)

Definition at line 3272 of file emdata.cpp.

{
        EMData * r = a.copy();
        r->mult(b);
        return r;
}

operator*() [5/21]

EMData * EMAN::operator*	(	const EMData &	em,
		float	n
	)

Definition at line 3201 of file emdata.cpp.

{
        EMData* r = em.copy();
        r ->mult(n);
        return r;
}

operator*() [6/21]

Point3 EMAN::operator* ( const Point3 &  p, const Matrix3 &  m  )

inline

Definition at line 574 of file vecmath.h.

                                                                   {
            return Point3(m(0,0) * p[0] + m(1,0) * p[1] + m(2,0) * p[2],
                          m(0,1) * p[0] + m(1,1) * p[1] + m(2,1) * p[2],
                          m(0,2) * p[0] + m(1,2) * p[1] + m(2,2) * p[2]);
        }

operator*() [7/21]

Quaternion EMAN::operator*	(	const Quaternion &	q,
		float	s
	)

Definition at line 326 of file quaternion.cpp.

{
        Quaternion q1 = q;
        q1 *= s;
        return q1;
}

operator*() [8/21]

Quaternion EMAN::operator*	(	const Quaternion &	q1,
		const Quaternion &	q2
	)

Definition at line 319 of file quaternion.cpp.

{
        Quaternion q = q1;
        q *= q2;
        return q;
}

operator*() [9/21]

template<typename Type >

Vec2f EMAN::operator*	(	const Transform &	M,
		const Vec2< Type > &	v
	)

Matrix times Vector, a pure mathematical operation.

Definition at line 538 of file transform.h.

        {
                return M.transform(v);
        }

References EMAN::Transform::transform().

operator*() [10/21]

template<typename Type >

Vec3f EMAN::operator*	(	const Transform &	M,
		const Vec3< Type > &	v
	)

Matrix times Vector, a pure mathematical operation.

Definition at line 531 of file transform.h.

        {
                return M.transform(v);
        }

References EMAN::Transform::transform().

operator*() [11/21]

Transform EMAN::operator*	(	const Transform &	M2,
		const Transform &	M1
	)

Matrix times Matrix, a pure mathematical operation.

Definition at line 1353 of file transform.cpp.

{
        Transform result;
        for (int i=0; i<3; i++) {
                for (int j=0; j<4; j++) {
                        result[i][j] = M2[i][0] * M1[0][j] +  M2[i][1] * M1[1][j] + M2[i][2] * M1[2][j];
                }
                result[i][3] += M2[i][3];
        }
 
        return result;
}

operator*() [12/21]

template<typename Type , typename Type2 >

Vec2< Type2 > EMAN::operator* ( const Type &  d, const Vec2< Type2 > &  v  )

inline

Definition at line 1022 of file vec3.h.

        {
                // Preserve the vector type
                Vec2<Type2> v1(v);
                v1 *= d;
                return v1;
        }

operator*() [13/21]

template<typename Type , typename Type2 >

Vec3< Type2 > EMAN::operator* ( const Type &  d, const Vec3< Type2 > &  v  )

inline

Definition at line 644 of file vec3.h.

        {
                // Preserve the vector type
                Vec3<Type2> v1(v);
                v1 *= d;
                return v1;
        }

operator*() [14/21]

template<typename Type , typename Type2 >

Vec2< Type > EMAN::operator* ( const Vec2< Type > &  v, const Type2 &  d  )

inline

Definition at line 1031 of file vec3.h.

                                                                          {
        // Preserve the vector type
                Vec2<Type> v1(v);
                v1 *= d;
                return v1;
        }

operator*() [15/21]

template<typename Type , typename Type2 >

Type EMAN::operator* ( const Vec2< Type > &  v1, const Vec2< Type2 > &  v2  )

inline

Definition at line 1016 of file vec3.h.

        {
                return v1.dot(v2);
        }

References EMAN::Vec2< Type >::dot().

operator*() [16/21]

template<typename Type >

Vec3f EMAN::operator*	(	const Vec3< Type > &	v,
		const Transform &	M
	)

Vector times a matrix.

Highly specialized. Useful when the upper 3x3 only contains rotations and you want to quickly multiply by the rotation matrix inverse (transpose)

Definition at line 547 of file transform.h.

        {
                float x = v[0] * M[0][0] + v[1] * M[1][0] + v[2] * M[2][0] ;
                float y = v[0] * M[0][1] + v[1] * M[1][1] + v[2] * M[2][1];
                float z = v[0] * M[0][2] + v[1] * M[1][2] + v[2] * M[2][2];
                return Vec3f(x, y, z);
        }

References x, and y.

operator*() [17/21]

template<typename Type , typename Type2 >

Vec3< Type > EMAN::operator* ( const Vec3< Type > &  v, const Type2 &  d  )

inline

Definition at line 653 of file vec3.h.

                                                                          {
                // Preserve the vector type
                Vec3<Type> v1(v);
                v1 *= d;
                return v1;
        }

operator*() [18/21]

template<typename Type , typename Type2 >

Type EMAN::operator* ( const Vec3< Type > &  v1, const Vec3< Type2 > &  v2  )

inline

Definition at line 638 of file vec3.h.

        {
                return v1.dot(v2);
        }

References EMAN::Vec3< Type >::dot().

operator*() [19/21]

Vector3 EMAN::operator* ( const Vector3 &  v, const Matrix3 &  m  )

inline

Definition at line 567 of file vecmath.h.

                                                                     {
            return Vector3(m(0,0) * v[0] + m(1,0) * v[1] + m(2,0) * v[2],
                           m(0,1) * v[0] + m(1,1) * v[1] + m(2,1) * v[2],
                           m(0,2) * v[0] + m(1,2) * v[1] + m(2,2) * v[2]);
        }

operator*() [20/21]

EMData * EMAN::operator*	(	float	n,
		const EMData &	em
	)

Definition at line 3231 of file emdata.cpp.

{
        EMData * r = em.copy();
        r->mult(n);
        return r;
}

operator*() [21/21]

Quaternion EMAN::operator*	(	float	s,
		const Quaternion &	q
	)

Definition at line 333 of file quaternion.cpp.

{
        Quaternion q1 = q;
        q1 *= s;
        return q1;
}

operator+() [1/8]

EMData * EMAN::operator+	(	const EMData &	a,
		const EMData &	b
	)

Definition at line 3258 of file emdata.cpp.

{
        EMData * r = a.copy();
        r->add(b);
        return r;
}

operator+() [2/8]

EMData * EMAN::operator+	(	const EMData &	em,
		float	n
	)

Definition at line 3187 of file emdata.cpp.

{
        EMData * r = em.copy();
        r->add(n);
        return r;
}

operator+() [3/8]

Quaternion EMAN::operator+	(	const Quaternion &	q1,
		const Quaternion &	q2
	)

Definition at line 304 of file quaternion.cpp.

{
        Quaternion q = q1;
        q += q2;
        return q;
}

operator+() [4/8]

template<typename Type , typename Type2 >

Vec2< Type > EMAN::operator+ ( const Vec2< Type > &  v, const Type2 &  n  )

inline

Definition at line 987 of file vec3.h.

        {
                Vec2<Type> v1(v);
                v1 += n;
                return v1;
        }

operator+() [5/8]

template<typename Type , typename Type2 >

Vec2< Type > EMAN::operator+ ( const Vec2< Type > &  v1, const Vec2< Type2 > &  v2  )

inline

Definition at line 981 of file vec3.h.

        {
                return Vec2<Type>(static_cast<Type>(v1[0] + v2[0]), static_cast<Type>(v1[1] + v2[1]));;
        }

operator+() [6/8]

template<typename Type , typename Type2 >

Vec3< Type > EMAN::operator+ ( const Vec3< Type > &  v, const Type2 &  n  )

inline

Definition at line 593 of file vec3.h.

        {
                Vec3<Type> v1(v);
                v1 += n;
                return v1;
        }

operator+() [7/8]

template<typename Type , typename Type2 >

Vec3< Type > EMAN::operator+ ( const Vec3< Type > &  v1, const Vec3< Type2 > &  v2  )

inline

Definition at line 586 of file vec3.h.

        {
 
                return Vec3<Type>(static_cast<Type>(v1[0] + v2[0]), static_cast<Type>(v1[1] + v2[1]),static_cast<Type>(v1[2] + v2[2]));;
        }

operator+() [8/8]

EMData * EMAN::operator+	(	float	n,
		const EMData &	em
	)

Definition at line 3216 of file emdata.cpp.

{
        EMData * r = em.copy();
        r->add(n);
        return r;
}

operator-() [1/11]

EMData * EMAN::operator-	(	const EMData &	a,
		const EMData &	b
	)

Definition at line 3265 of file emdata.cpp.

{
        EMData * r = a.copy();
        r->sub(b);
        return r;
}

operator-() [2/11]

EMData * EMAN::operator-	(	const EMData &	em,
		float	n
	)

Definition at line 3194 of file emdata.cpp.

{
        EMData* r = em.copy();
        r->sub(n);
        return r;
}

Referenced by rsub().

operator-() [3/11]

IntPoint EMAN::operator-

(

const IntPoint &

p

)

Definition at line 37 of file geometry.cpp.

{
        return IntPoint(-p[0],-p[1],-p[2]);
}

operator-() [4/11]

Quaternion EMAN::operator-	(	const Quaternion &	q1,
		const Quaternion &	q2
	)

Definition at line 311 of file quaternion.cpp.

{
        Quaternion q = q1;
        q -= q2;
        return q;
}

operator-() [5/11]

template<typename Type >

Vec2< Type > EMAN::operator- ( const Vec2< Type > &  v )

inline

Definition at line 1009 of file vec3.h.

        {
                return Vec2<Type>(-v[0],-v[1]);
        }

operator-() [6/11]

template<typename Type , typename Type2 >

Vec2< Type > EMAN::operator- ( const Vec2< Type > &  v, const Type2 &  n  )

inline

Definition at line 1001 of file vec3.h.

        {
                Vec2<Type> v1(v);
                v1 -= n;
                return v1;
        }

operator-() [7/11]

template<typename Type , typename Type2 >

Vec2< Type > EMAN::operator- ( const Vec2< Type > &  v1, const Vec2< Type2 > &  v2  )

inline

Definition at line 995 of file vec3.h.

        {
                return Vec2<Type>(static_cast<Type>(v1[0] - v2[0]),     static_cast<Type>(v1[1] - v2[1]));
        }

operator-() [8/11]

template<typename Type >

Vec3< Type > EMAN::operator- ( const Vec3< Type > &  v )

inline

Definition at line 624 of file vec3.h.

        {
                return Vec3<Type>(-v[0],-v[1],-v[2]);
        }

operator-() [9/11]

template<typename Type , typename Type2 >

Vec3< Type > EMAN::operator- ( const Vec3< Type > &  v, const Type2 &  n  )

inline

Definition at line 617 of file vec3.h.

        {
                Vec3<Type> v1(v);
                v1 -= n;
                return v1;
        }

operator-() [10/11]

template<typename Type , typename Type2 >

Vec3< Type > EMAN::operator- ( const Vec3< Type > &  v1, const Vec3< Type2 > &  v2  )

inline

Definition at line 609 of file vec3.h.

        {
                return Vec3<Type>(static_cast<Type>(v1[0] - v2[0]),
                                                  static_cast<Type>(v1[1] - v2[1]),
                                                  static_cast<Type>(v1[2] - v2[2]));
        }

operator-() [11/11]

EMData * EMAN::operator-	(	float	n,
		const EMData &	em
	)

Definition at line 3223 of file emdata.cpp.

{
        EMData * r = em.copy();
        r->mult(-1.0f);
        r->add(n);
        return r;
}

operator/() [1/8]

EMData * EMAN::operator/	(	const EMData &	a,
		const EMData &	b
	)

Definition at line 3279 of file emdata.cpp.

{
        EMData * r = a.copy();
        r->div(b);
        return r;
}

operator/() [2/8]

EMData * EMAN::operator/	(	const EMData &	em,
		float	n
	)

Definition at line 3208 of file emdata.cpp.

{
        EMData * r = em.copy();
        r->div(n);
        return r;
}

Referenced by rdiv().

operator/() [3/8]

Quaternion EMAN::operator/	(	const Quaternion &	q1,
		const Quaternion &	q2
	)

Definition at line 340 of file quaternion.cpp.

{
        Quaternion q = q1;
        q /= q2;
        return q;
}

operator/() [4/8]

template<typename Type , typename Type2 >

Vec2< Type2 > EMAN::operator/ ( const Type &  d, const Vec2< Type2 > &  v  )

inline

Definition at line 1039 of file vec3.h.

        {
        // Preserve the vector type
                Vec2<Type2> v1(v);
                v1 /= d;
                return v1;
        }

operator/() [5/8]

template<typename Type , typename Type2 >

Vec3< Type2 > EMAN::operator/ ( const Type &  d, const Vec3< Type2 > &  v  )

inline

Definition at line 661 of file vec3.h.

        {
                // Preserve the vector type
                Vec3<Type2> v1(v);
                v1 /= d;
                return v1;
        }

operator/() [6/8]

template<typename Type , typename Type2 >

Vec2< Type > EMAN::operator/ ( const Vec2< Type > &  v, const Type2 &  d  )

inline

Definition at line 1048 of file vec3.h.

                                                                          {
                // Preserve the vector type
                Vec2<Type> v1(v);
                v1 /= d;
                return v1;
        }

operator/() [7/8]

template<typename Type , typename Type2 >

Vec3< Type > EMAN::operator/ ( const Vec3< Type > &  v, const Type2 &  d  )

inline

Definition at line 670 of file vec3.h.

                                                                          {
                // Preserve the vector type
                Vec3<Type> v1(v);
                v1 /= d;
                return v1;
        }

operator/() [8/8]

EMData * EMAN::operator/	(	float	n,
		const EMData &	em
	)

Definition at line 3238 of file emdata.cpp.

{
        EMData * r = em.copy();
        r->to_one();
        r->mult(n);
        r->div(em);
 
        return r;
}

operator<()

bool EMAN::operator<	(	const Pixel &	p1,
		const Pixel &	p2
	)

Definition at line 42 of file geometry.cpp.

{
        if (p1.value < p2.value) {
                return true;
        }
        return false;
}

References EMAN::Pixel::value.

operator<<() [1/7]

std::ostream & EMAN::operator<< ( std::ostream &  os, const Matrix3 &  m  )

inline

Definition at line 580 of file vecmath.h.

                                                                        {
            os << m.row(0) << std::endl;
            os << m.row(1) << std::endl;
            os << m.row(2) << std::endl;
            return os;
        }

References EMAN::Matrix3::row().

operator<<() [2/7]

std::ostream & EMAN::operator<< ( std::ostream &  os, const Matrix4 &  m  )

inline

Definition at line 948 of file vecmath.h.

                                                                        {
            os << m.row(0) << std::endl;
            os << m.row(1) << std::endl;
            os << m.row(2) << std::endl;
            os << m.row(3) << std::endl;
            return os;
        }

References EMAN::Matrix4::row().

operator<<() [3/7]

std::ostream & EMAN::operator<< ( std::ostream &  os, const Point3 &  p  )

inline

Definition at line 408 of file vecmath.h.

                                                                       {
            os << "(" << p[0] << ", " << p[1] << ", " << p[2] << ")";
            return os;
        }

operator<<() [4/7]

std::ostream & EMAN::operator<< ( std::ostream &  os, const ScreenPoint &  p  )

inline

Definition at line 196 of file vecmath.h.

                                                                            {
            os << "(" << p[0] << ", " << p[1] << ")";
            return os;
        }

operator<<() [5/7]

std::ostream & EMAN::operator<< ( std::ostream &  os, const ScreenVector &  v  )

inline

Definition at line 133 of file vecmath.h.

                                                                             {
            os << "(" << v[0] << ", " << v[1] << ")";
            return os;
        }

operator<<() [6/7]

std::ostream & EMAN::operator<< ( std::ostream &  os, const Vector3 &  v  )

inline

Definition at line 316 of file vecmath.h.

                                                                        {
            os << "(" << v[0] << ", " << v[1] << ", " << v[2] << ")";
            return os;
        }

operator<<() [7/7]

std::ostream & EMAN::operator<< ( std::ostream &  os, const Vector4 &  v  )

inline

Definition at line 686 of file vecmath.h.

                                                                        {
            os << "(" << v[0] << ", " << v[1] << ", " << v[2] << ", " << v[3] << ")";
            return os;
        }

operator==() [1/6]

bool EMAN::operator==	(	const Dict &	d1,
		const Dict &	d2
	)

Definition at line 1021 of file emobject.cpp.

{
        // Just make use of map's version of operator==
        return (d1.dict == d2.dict);
}

References EMAN::Dict::dict.

operator==() [2/6]

bool EMAN::operator==	(	const EMObject &	e1,
		const EMObject &	e2
	)

Definition at line 770 of file emobject.cpp.

{
 
        if (e1.type != e2.type) {
                return false;
        }
 
        switch (e1.type) {
        case  EMObject::BOOL:
                return (e1.b == e2.b);
        break;
        case EMObject::SHORT:
                return (e1.si == e2.si);
        break;
        case  EMObject::INT:
                return (e1.n == e2.n);
        break;
        case  EMObject::UNSIGNEDINT:
                return (e1.ui == e2.ui);
        break;
        case  EMObject::FLOAT:
                return (e1.f == e2.f);
        break;
        case  EMObject::DOUBLE:
                return (e1.d == e2.d);
        break;
        case EMObject::CTF:
        case  EMObject::STRING:
                return (e1.str == e2.str);
        break;
        case  EMObject::FLOAT_POINTER:
                return (e1.fp == e2.fp);
        break;
        case  EMObject::INT_POINTER:
                return (e1.ip == e2.ip);
        break;
        case  EMObject::VOID_POINTER:
                return (e1.vp == e2.vp);
        break;
        case  EMObject::EMDATA:
                return (e1.emdata == e2.emdata);
        break;
        case  EMObject::XYDATA:
                return (e1.xydata == e2.xydata);
        break;
        case  EMObject::TRANSFORM:
        case  EMObject::FLOATARRAY:
                if (e1.farray.size() == e2.farray.size()) {
                        for (size_t i = 0; i < e1.farray.size(); i++) {
                                if (e1.farray[i] != e2.farray[i]) {
                                        return false;
                                }
                        }
                        return true;
                }
                else {
                        return false;
                }
        break;
        case  EMObject::INTARRAY:
                if (e1.iarray.size() == e2.iarray.size()) {
                        for (size_t i = 0; i < e1.iarray.size(); i++) {
                                if (e1.iarray[i] != e2.iarray[i]) {
                                        return false;
                                }
                        }
                        return true;
                }
        break;
        case  EMObject::STRINGARRAY:
                if (e1.strarray.size() == e2.strarray.size()) {
                        for (size_t i = 0; i < e1.strarray.size(); i++) {
                                if (e1.strarray[i] != e2.strarray[i]) {
                                        return false;
                                }
                        }
                        return true;
                }
                else {
                        return false;
                }
        break;
        case EMObject::TRANSFORMARRAY:
                if (e1.transformarray.size() == e2.transformarray.size()) {
                        for (size_t i = 0; i < e1.transformarray.size(); i++) {
                                if (e1.transformarray[i] != e2.transformarray[i]) {
                                        return false;
                                }
                        }
                }
        break;
        case  EMObject::UNKNOWN:
                // UNKNOWN really means "no type" and if two objects both have
                // type UNKNOWN they really are the same
                return (e1.type == e2.type);
        break;
        default:
                return false;
        break;
        }
        return false;
}

References EMAN::EMObject::b, EMAN::EMObject::BOOL, EMAN::EMObject::CTF, EMAN::EMObject::d, EMAN::EMObject::DOUBLE, EMAN::EMObject::EMDATA, EMAN::EMObject::emdata, EMAN::EMObject::f, EMAN::EMObject::farray, EMAN::EMObject::FLOAT, EMAN::EMObject::FLOAT_POINTER, EMAN::EMObject::FLOATARRAY, EMAN::EMObject::fp, EMAN::EMObject::iarray, EMAN::EMObject::INT, EMAN::EMObject::INT_POINTER, EMAN::EMObject::INTARRAY, EMAN::EMObject::ip, EMAN::EMObject::n, EMAN::EMObject::SHORT, EMAN::EMObject::si, EMAN::EMObject::str, EMAN::EMObject::strarray, EMAN::EMObject::STRING, EMAN::EMObject::STRINGARRAY, EMAN::EMObject::TRANSFORM, EMAN::EMObject::TRANSFORMARRAY, EMAN::EMObject::transformarray, EMAN::EMObject::type, EMAN::EMObject::ui, EMAN::EMObject::UNKNOWN, EMAN::EMObject::UNSIGNEDINT, EMAN::EMObject::VOID_POINTER, EMAN::EMObject::vp, EMAN::EMObject::XYDATA, and EMAN::EMObject::xydata.

operator==() [3/6]

bool EMAN::operator==	(	const Pixel &	p1,
		const Pixel &	p2
	)

Definition at line 50 of file geometry.cpp.

{
        if (p1.x == p2.x && p1.y == p2.y && p1.z == p2.z && p1.value == p2.value) {
                return true;
        }
        return false;
}

References EMAN::Pixel::value, EMAN::Pixel::x, EMAN::Pixel::y, and EMAN::Pixel::z.

operator==() [4/6]

bool EMAN::operator==	(	const Quaternion &	q1,
		const Quaternion &	q2
	)

Definition at line 348 of file quaternion.cpp.

{
        bool result = true;
        const float err_limit = 0.00001f;
        
        vector < float >v1 = q1.as_list();
        vector < float >v2 = q2.as_list();
 
        for (size_t i = 0; i < v1.size(); i++) {
                if (fabs(v1[i] - v2[i]) > err_limit) {
                        result = false;
                        break;
                }
        }
 
        return result;
}

References EMAN::Quaternion::as_list().

operator==() [5/6]

template<typename Type , typename Type2 >

bool EMAN::operator== ( const Vec2< Type > &  v1, const Vec2< Type2 > &  v2  )

inline

Definition at line 1056 of file vec3.h.

                                                                             {
                if (v1[0] == v2[0] && v1[1] == v2[1] ) {
                        return true;
                }
                return false;
        }

operator==() [6/6]

template<typename Type , typename Type2 >

bool EMAN::operator== ( const Vec3< Type > &  v1, const Vec3< Type2 > &  v2  )

inline

Definition at line 678 of file vec3.h.

                                                                             {
                if (v1[0] == v2[0] && v1[1] == v2[1] && v1[2] == v2[2]) {
                        return true;
                }
                return false;
        }

padfft_slice()

EMData * EMAN::padfft_slice	(	const EMData *const	slice,
		const Transform &	t,
		int	npad
	)

Direct Fourier inversion Reconstructor.

Definition at line 2924 of file reconstructor.cpp.

{
        int nx = slice->get_xsize();
        int ny = slice->get_ysize();
        int padffted= slice->get_attr_default("padffted", 0);
        int ndim = (ny==1) ? 1 : 2;
        int iext = slice->is_fftodd();
        int extension = (2-iext)*padffted;  //  If 2, it means it is a Fourier file.
 
        if( ndim==2 && (nx-extension)!=ny ) {
                LOGERR("Input image must be square!");
                throw ImageDimensionException("Input image must be square!");
        }
 
        EMData* padfftslice = NULL;
        if( padffted == 0) {
                // process 2D slice or 1D line -- subtract the average outside of the circle, zero-pad, fft extend, and fft
                EMData* temp = slice->average_circ_sub();
 
                padfftslice = temp->norm_pad( false, npad );
                checked_delete( temp );
 
                padfftslice->do_fft_inplace();
        } else {
                padfftslice = new EMData(*slice);
        }
 
        // shift the projection
        Vec2f trans = t.get_trans_2d();
        float sx = -trans[0];
        float sy = -trans[1];
        if(sx != 0.0f || sy != 0.0) padfftslice->process_inplace("filter.shift", Dict("x_shift", sx, "y_shift", sy, "z_shift", 0.0f));
 
        int remove = slice->get_attr_default("remove", 0);
        padfftslice->set_attr( "remove", remove );
        padfftslice->center_origin_fft();
        return padfftslice;
}

References checked_delete(), EMAN::Transform::get_trans_2d(), ImageDimensionException, and LOGERR.

Referenced by EMAN::newfile_store::add_image(), EMAN::file_store::add_image(), EMAN::nn4Reconstructor::insert_slice(), EMAN::nn4_rectReconstructor::insert_slice(), EMAN::nnSSNR_Reconstructor::insert_slice(), EMAN::nn4_ctfReconstructor::insert_slice(), EMAN::nn4_ctfwReconstructor::insert_slice(), EMAN::nn4_ctfwsReconstructor::insert_slice(), EMAN::nn4_ctf_rectReconstructor::insert_slice(), and EMAN::nnSSNR_ctfReconstructor::insert_slice().

rdiv()

EMData * EMAN::rdiv	(	const EMData &	em,
		float	n
	)

Definition at line 3253 of file emdata.cpp.

{
        return EMAN::operator/(n, em);
}

References operator/().

rsub()

EMData * EMAN::rsub	(	const EMData &	em,
		float	n
	)

Definition at line 3248 of file emdata.cpp.

{
        return EMAN::operator-(n, em);
}

References operator-().

unit() [1/2]

Vector3 EMAN::unit ( const Vector3 &  v )

inline

Definition at line 314 of file vecmath.h.

{ const double len = v.length(); return v / len; }

References EMAN::Vector3::length().

unit() [2/2]

Vector4 EMAN::unit ( const Vector4 &  v )

inline

Definition at line 685 of file vecmath.h.

{ const double len = v.length(); return v / len; }

References EMAN::Vector4::length().

Variable Documentation

decoder0x

DecoderIx<0> EMAN::decoder0x

static

Definition at line 175 of file eerio.h.

Referenced by EMAN::EMUtil::get_imageio().

decoder1x

DecoderIx<1> EMAN::decoder1x

static

Definition at line 176 of file eerio.h.

Referenced by EMAN::EMUtil::get_imageio().

decoder2x

DecoderIx<2> EMAN::decoder2x

static

Definition at line 177 of file eerio.h.

Referenced by EMAN::EMUtil::get_imageio().

EMDataTypeBits

const int EMAN::EMDataTypeBits[] = { 0,8,8,16,16,32,32,32,64,32,32,64,0 }

Definition at line 82 of file emutil.h.

MAXFFT

const int EMAN::MAXFFT =32768

static

Definition at line 45 of file polardata.h.