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EMAN Namespace Reference

E2Exception class. More...


Classes

class  EMAN::Aligner
 Aligner class defines image alignment method. More...
class  EMAN::TranslationalAligner
 Translational 2D Alignment using cross correlation. More...
class  EMAN::RotationalAligner
 rotational alignment using angular correlation More...
class  EMAN::RotatePrecenterAligner
 rotational alignment assuming centers are correct More...
class  EMAN::RotateTranslateAligner
 rotational, translational alignment More...
class  EMAN::RotateTranslateBestAligner
 rotational, translational alignment More...
class  EMAN::RotateFlipAligner
 rotational and flip alignment More...
class  EMAN::RotateTranslateFlipAligner
 rotational, translational and flip alignment More...
class  EMAN::RTFExhaustiveAligner
 rotational, translational and flip alignment using real-space methods. More...
class  EMAN::RTFSlowExhaustiveAligner
 rotational, translational and flip alignment using exhaustive search. More...
class  EMAN::RefineAligner
 refine alignment. More...
class  EMAN::Refine3DAligner
 Refine alignment. More...
class  EMAN::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), but very useful if you want to search in a specific, small, local area. More...
class  EMAN::RT3DSphereAligner
 3D rotational and translational alignment using spherical sampling, can reduce the search space based on symmetry. More...
class  EMAN::CUDA_Aligner
class  EMAN::AmiraIO
 Amira file = ASCII header + binary data. More...
class  EMAN::Analyzer
 Analyzer class defines a way to take a List of images as input, and returns a new List of images. More...
class  EMAN::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  EMAN::SVDAnalyzer
 Singular Value Decomposition from GSL. More...
class  EMAN::Averager
 Averager class defines a way to do averaging on a set of images. More...
class  EMAN::ImageAverager
 ImageAverager averages a list of images. More...
class  EMAN::MinMaxAverager
 ImageAverager averages a list of images. More...
class  EMAN::IterationAverager
 IterationAverager averages images by doing the smoothing iteration. More...
class  EMAN::CtfAverager
 CtfAverager is the base Averager class for CTF correction or SNR weighting. More...
class  EMAN::WeightingAverager
 WeightingAverager averages the images with SNR weighting, but no CTF correction. More...
class  EMAN::CtfCAverager
 CtfCAverager averages the images with CTF correction. More...
class  EMAN::CtfCWAverager
 CtfCWAverager averages the images with CTF correction. More...
class  EMAN::CtfCWautoAverager
 CtfCWautoAverager averages the images with CTF correction with a Wiener filter. More...
class  EMAN::BoxingTools
 BoxingTools is class for encapsulating common boxing operations that may become expensive if they are implemented in python. More...
class  EMAN::BoxSVDClassifier
class  EMAN::ByteOrder
 ByteOrder defines functions to work on big/little endian byte orders. More...
class  EMAN::Cmp
 Cmp class defines image comparison method. More...
class  EMAN::CccCmp
 Compute the cross-correlation coefficient between two images. More...
class  EMAN::SqEuclideanCmp
 Squared Euclidean distance normalized by n between 'this' and 'with'. More...
class  EMAN::DotCmp
 Use dot product of 2 same-size images to do the comparison. More...
class  EMAN::TomoDotCmp
 Use dot product but normalize based on characteristics of the missing wedge. More...
class  EMAN::QuadMinDotCmp
 This will calculate the dot product for each quadrant of the image and return the worst value. More...
class  EMAN::OptVarianceCmp
 Variance between two data sets after various modifications. More...
class  EMAN::PhaseCmp
 Amplitude weighted mean phase difference (radians) with optional SNR weight. More...
class  EMAN::FRCCmp
 FRCCmp returns a quality factor based on FRC between images. More...
class  EMAN::Ctf
 Ctf is the base class for all CTF model. More...
class  EMAN::EMAN1Ctf
 EMAN1Ctf is the CTF model used in EMAN1. More...
class  EMAN::EMAN2Ctf
 EMAN2Ctf is the default CTF model used in EMAN2. More...
class  EMAN::DM3IO
 Gatan DM3 file is a hierarchical binary image format. More...
class  EMAN::EMCache< T >
 EMCache is a generic cache that can cache anything defined by 'T'. More...
class  EMAN::GlobalCache
 GlobalCache is a Singleton class that handles cache across EMAN. More...
class  EMAN::EMData
 EMData stores an image's data and defines core image processing routines. More...
class  EMAN::EMData::ClipInplaceVariables
class  EMAN::EMFTGL
 EMFTGL is an interface for rendering fonts in EMAN2 using FTGL. More...
class  EMAN::EMFTGL::EMFTGLFontInstance
 A class for encapsulatiing a particular instance of an FTFont (pointer) Each FTFont is characterised by 5 parameters, them being the font mode, the font file name, the face size, whether or not display lists are being used, and depth (which is redundant, except when the font mode is EXTRUDE). More...
class  EMAN::EMFTGL::EMFTGLManager
 A class for managing multiple instances of EMFTGLFontInstances, in particular for caching them, for constructing news ones if they don't exist, and for returning appropriate instances. More...
class  EMAN::EmimIO
 EMIM image format = 1 EmimFileHeader + n x (EmimImageHeader + data). More...
struct  EMAN::EmimIO::EmimFileHeader
struct  EMAN::EmimIO::EmimImageHeader
class  EMAN::EmIO
 EmIO defines I/O operations on EM image format. More...
struct  EMAN::EmIO::EMHeader
class  EMAN::EMConsts
class  EMAN::EMObject
 EMObject is a wrapper class for types including int, float, double, etc as defined in ObjectType. More...
class  EMAN::TypeDict
 TypeDict is a dictionary to store <string, EMObject::ObjectType> pair. More...
class  EMAN::Dict
 Dict is a dictionary to store <string, EMObject> pair. More...
class  EMAN::Dict::iterator
 Non const iterator support for the Dict object This is just a wrapper, everything is inherited from the map<string,EMObject>::iterator so the interface is the same as you would expect i.e for ( Dict::iterator it = params.begin(); it != params.end(); ++it ). More...
class  EMAN::Dict::const_iterator
 Const iterator support for the Dict object This is just a wrapper, everything is inherited from the map<string,EMObject>::cons_iterator so the interface is the same as you would expect i.e for ( Dict::const_iterator it = params.begin(); it != params.end(); ++it ). More...
class  EMAN::Factory< T >
 Factory is used to store objects to create new instances. More...
class  EMAN::FactoryBase
 A class one may inherit from to ensure that the responsibilities of being incorporated into an EMAN2::Factory are met. More...
class  EMAN::EMUtil
struct  EMAN::ImageScore
class  EMAN::ImageSort
class  EMAN::E2Exception
 E2Exception class is the parent class of all EMAN2 E2Exceptions. More...
class  EMAN::_NotExistingObjectException
 Used when an object type, like an EMObject type, doesn't exist. More...
class  EMAN::_ImageFormatException
 Used when an image is not in the expected format. More...
class  EMAN::_ImageDimensionException
 Used when an image is not in the expected dimension. More...
class  EMAN::_FileAccessException
 Used when a file access error occurs. More...
class  EMAN::_ImageReadException
 Used when an error occurs at image reading time. More...
class  EMAN::_ImageWriteException
 Used when an error occurs at image writing time. More...
class  EMAN::_NullPointerException
 Used when a NULL is given to a pointer that should not be NULL. More...
class  EMAN::_TypeException
 Used when a type cast error occurs. More...
class  EMAN::_InvalidValueException
 Used when an invalid integer value is given. More...
class  EMAN::_InvalidStringException
 Used when an invalid (format) string is given. More...
class  EMAN::_OutofRangeException
 Used when the given value is out of range. More...
class  EMAN::_InvalidCallException
class  EMAN::_InvalidParameterException
class  EMAN::_EmptyContainerException
 Used when an argument container is empty, such as a vector. More...
class  EMAN::_BadAllocException
 Used when memory allocation goes wrong... More...
class  EMAN::_UnexpectedBehaviorException
 Used when internal behavior is unexpected A generic kind of exception. More...
class  EMAN::FitsIO
 MRC file = header + data (nx x ny x nz). More...
class  EMAN::Gatan2IO
 Gatan2 Image file = header + data. More...
struct  EMAN::Gatan2IO::Gatan2Header
class  EMAN::IntSize
 IntSize is used to describe a 1D, 2D or 3D rectangular size in integers. More...
class  EMAN::FloatSize
 FloatSize is used to describe a 1D, 2D or 3D rectangular size in floating numbers. More...
class  EMAN::IntPoint
 IntPoint defines an integer-coordinate point in a 1D/2D/3D space. More...
class  EMAN::FloatPoint
 FloatPoint defines a float-coordinate point in a 1D/2D/3D space. More...
class  EMAN::Pixel
 Pixel describes a 3D pixel's coordinates and its intensity value. More...
class  EMAN::Region
 Region defines a 2D or 3D rectangular region specified by its origin coordinates and all edges' sizes. More...
class  EMAN::GLUtil
class  EMAN::PriorityQueue< ValueT, KeyT >
 Template class for a priority queue. More...
class  EMAN::IcosIO
 ICOS file = header + data. More...
struct  EMAN::IcosIO::IcosHeader
class  EMAN::ImageIO
 ImageIO classes are designed for reading/writing various electron micrography image formats, including MRC, IMAGIC, SPIDER, PIF, etc. More...
class  EMAN::ImagicIO
 IMAGIC-5 Header File Format. More...
struct  EMAN::ImagicIO::ImagicHeader
class  EMAN::ImagicIO2
 IMAGIC-5 Header File Format. More...
struct  EMAN::ImagicIO2::Imagic4D
 IMAGIC-4D file format http://www.imagescience.de/formats/formats.htm. More...
class  EMAN::Interp
 Interp defines the interpolation function used to generate a e^-x^4 function in real space. More...
class  EMAN::Isosurface
class  EMAN::Log
 Log defines a way to output logging information. More...
class  EMAN::LstFastIO
 A LSX file is a high performance ASCII file that contains a list of image numbers and file names. More...
class  EMAN::LstIO
 A LST file is an ASCII file that contains a list of image file names. More...
class  EMAN::CustomVector< type >
 CustomVector has some trivial optimizations of the STL vector. More...
class  EMAN::MarchingCubes
class  EMAN::U3DWriter
 A work in progress by David Woolford. More...
class  EMAN::MrcIO
 MRC file = header + data (nx x ny x nz). More...
struct  EMAN::MrcIO::MrcHeader
class  EMAN::PDBReader
 PointArray defines a double array of points with values in a 3D space. More...
class  EMAN::PgmIO
 A PGM file = header + data. More...
class  EMAN::PifIO
 PIF(Portable Image Format for EM Data) is an image format from Purdue University. More...
struct  EMAN::PifIO::PifFileHeader
struct  EMAN::PifIO::PifColorMap
struct  EMAN::PifIO::PifImageHeader
class  EMAN::XYZAligner
 XYZAligner is an aligner template for defining new aligners. More...
class  EMAN::XYZAverager
 XYZAverager is an averager template for defining new averagers. More...
class  EMAN::XYZCmp
 XYZCmp is a cmp template for defining new cmps. More...
class  EMAN::XYZIO
 XYZIO is a sample Image IO class. More...
class  EMAN::XYZProcessor
 XYZProcessor is a processor template for defining new processors. More...
class  EMAN::XYZProjector
 XYZProjector is an projector template for defining new projectors. More...
class  EMAN::XYZReconstructor
 XYZReconstructor is a reconstructor template for defining new reconstructors. More...
class  EMAN::PointArray
 PointArray defines a double array of points with values in a 3D space. More...
class  EMAN::UnevenMatrix
 a general data structure for a matrix with variable x dim size for different y More...
struct  EMAN::UnevenMatrix::Xdim
 struct to define x dimension size for each y, x0 is inclusive, x1 is one after the maximum, [x0, x1), so the corresponding x dim size is (x1-x0) More...
class  EMAN::PolarData
 a specialized image class for storing the results of a transform from EMData to polar coordinates, currently support 2D only. More...
class  EMAN::Processor
 Typical usage of Processors are as follows:. More...
class  EMAN::ImageProcessor
class  EMAN::FourierProcessor
 base class for Fourier filters More...
class  EMAN::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  EMAN::SNREvalProcessor
 Evaluate individual particle images using a tenchique similar to that used for CTF evaluation. More...
class  EMAN::AmpweightFourierProcessor
 Multiplies each Fourier pixel by its amplitude. More...
class  EMAN::ConvolutionProcessor
 This processor performs fast convolution in Fourier space. More...
class  EMAN::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  EMAN::YGradientProcessor
class  EMAN::ZGradientProcessor
class  EMAN::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  EMAN::KmeansSegmentProcessor
class  EMAN::Wiener2DFourierProcessor
 Wiener filter based on a Ctf object either in the image header. More...
class  EMAN::LowpassFourierProcessor
 Low-pass processor attenuates amplitudes at high spatial frequencies. More...
class  EMAN::LinearRampFourierProcessor
class  EMAN::HighpassFourierProcessor
 High-pass processor is rotationally symmetric 2D function. More...
class  EMAN::LowpassSharpCutoffProcessor
 processor radial function: if x <= lowpass, f(x) = 1; else f(x) = 0; More...
class  EMAN::HighpassSharpCutoffProcessor
 processor radial function: if x >= highpass, f(x) = 1; else f(x) = 0; More...
class  EMAN::LowpassGaussProcessor
 processor radial function: if lowpass > 0, f(x) = exp(-x*x/(lowpass*lowpass)); else f(x) = exp(x*x/(lowpass*lowpass)) More...
class  EMAN::LowpassAutoBProcessor
 processor radial function: if lowpass > 0, f(x) = exp(-x*x/(lowpass*lowpass)); else f(x) = exp(x*x/(lowpass*lowpass)) More...
class  EMAN::HighpassAutoPeakProcessor
 This processor attempts to remove the low resolution peak present in all cryoEM data. More...
class  EMAN::HighpassGaussProcessor
 processor radial function: f(x) = 1.0-exp(-x*x/(highpass*highpass)) More...
class  EMAN::LowpassTanhProcessor
 processor radial function: f(x)=tanh(lowpass-x)/2.0 + 0.5; More...
class  EMAN::HighpassTanhProcessor
 processor radial function: f(x)=tanh(x-highpass)/2.0+0.5; More...
class  EMAN::HighpassButterworthProcessor
 processor radial function: f(x) = 1/(1+t*t) More...
class  EMAN::LinearRampProcessor
 processor radial function: f(x) = slope * x + intercept More...
class  EMAN::RealPixelProcessor
 The base class for real space processor working on individual pixels. More...
class  EMAN::AbsoluateValueProcessor
 f(x) = |x| More...
class  EMAN::BooleanProcessor
 f(x) = 0 if x = 0; f(x) = 1 if x != 0 More...
class  EMAN::InvertCarefullyProcessor
 Invert image as if f(x) != 0: f(x) = 1/f(x) else: f(x) = zero_to. More...
class  EMAN::ValuePowProcessor
 Do a math power operation on image, f(x) = x ^ pow;. More...
class  EMAN::ValueSquaredProcessor
 Do a square operation on image, f(x) = x * x;. More...
class  EMAN::ValueSqrtProcessor
 f(x) = sqrt(x) More...
class  EMAN::ToZeroProcessor
 f(x) = x if x >= minval; f(x) = 0 if x < minval More...
class  EMAN::Rotate180Processor
 Rotate by 180 using pixel swapping, works for 2D only. More...
class  EMAN::TransformProcessor
 Transform the image using a Transform object. More...
class  EMAN::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  EMAN::ScaleTransformProcessor
 Scale the image with control over the output dimensions. More...
class  EMAN::ClampingProcessor
 f(x) = maxval if f(x) > maxval; f(x) = minval if f(x) < minval More...
class  EMAN::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  EMAN::ToMinvalProcessor
 f(x) = x if x >= minval; f(x) = minval if x < minval More...
class  EMAN::CutToZeroProcessor
 f(x) = x-minval if x >= minval; f(x) = 0 if x < minval More...
class  EMAN::BinarizeProcessor
 f(x) = 0 if x < value; f(x) = 1 if x >= value. More...
class  EMAN::BinarizeFourierProcessor
 A thresholding processor for Fourier images based on the amplitude component. More...
class  EMAN::CollapseProcessor
 f(x): if v-r<x<v+r -> v; if x>v+r -> x-r; if x<v-r -> x+r More...
class  EMAN::LinearXformProcessor
 linear transform processor: f(x) = x * scale + shift More...
class  EMAN::ExpProcessor
 f(x) = exp( x / low - high) More...
class  EMAN::FiniteProcessor
 f(x) = f(x) if f(x) is finite | to if f(x) is not finite More...
class  EMAN::RangeThresholdProcessor
 f(x) = 1 if (low <= x <= high); else f(x) = 0 More...
class  EMAN::SigmaProcessor
 f(x) = mean if x<(mean-v2*sigma) or x>(mean+v1*sigma); else f(x) = x; More...
class  EMAN::LogProcessor
 f(x) = log10(x) if x > 0; else f(x) = 0 More...
class  EMAN::CoordinateProcessor
 CoordinateProcessor applies processing based on a pixel's value and it coordinates. More...
class  EMAN::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  EMAN::MaskSharpProcessor
 step cutoff to a user-given value in both inner and outer circles. More...
class  EMAN::MaskEdgeMeanProcessor
 A step cutoff to the the mean value in a ring centered on the outer radius. More...
class  EMAN::MaskNoiseProcessor
 fills masked region More...
class  EMAN::MaskGaussProcessor
 a gaussian falloff to zero, radius is the 1/e of the width. More...
class  EMAN::MaskGaussNonuniformProcessor
 a gaussian falloff to zero, with nonisotropic widths along x,y,z More...
class  EMAN::MaskGaussInvProcessor
 f(x) = f(x) / exp(-radius*radius * gauss_width / (ny*ny)) More...
class  EMAN::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  EMAN::MakeRadiusSquaredProcessor
 overwrites input, f(x) = radius * radius More...
class  EMAN::MakeRadiusProcessor
 overwrites input, f(x) = radius More...
class  EMAN::ComplexPixelProcessor
 The base class for fourier space processor working on individual pixels. More...
class  EMAN::ComplexNormPixel
 Each Fourier pixel will be normalized. More...
class  EMAN::AreaProcessor
 AreaProcessor use pixel values and coordinates of a real-space square area. More...
class  EMAN::LaplacianProcessor
 Discrete approximation to Laplacian. More...
class  EMAN::ZeroConstantProcessor
 Contraction of data, if any nearest neighbor is 0, value -> 0, generally used iteratively. More...
class  EMAN::BoxStatProcessor
 BoxStatProcessor files are a kind of neighborhood processors. More...
class  EMAN::BoxMedianProcessor
 A processor for noise reduction. More...
class  EMAN::BoxSigmaProcessor
 pixel = standard deviation of values surrounding pixel. More...
class  EMAN::BoxMaxProcessor
 peak processor: pixel = max of values surrounding pixel. More...
class  EMAN::MinusPeakProcessor
 peak processor: pixel = pixel - max of values surrounding pixel. More...
class  EMAN::PeakOnlyProcessor
 peak processor -> if npeaks or more surrounding values >= value, value->0 More...
class  EMAN::DiffBlockProcessor
 averages over cal_half_width, then sets the value in a local block More...
class  EMAN::CutoffBlockProcessor
 Block processor, val1 is dx/dy, val2 is lp freq cutoff in pixels. More...
class  EMAN::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  EMAN::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...
struct  EMAN::MaxShrinkProcessor::GreaterThan
class  EMAN::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...
struct  EMAN::MinShrinkProcessor::LessThan
class  EMAN::MeanShrinkProcessor
 MeanShrinkProcessor shrinks an image by in an integer amount (and optionally by 1.5) taking the mean of the pixel neighbourhood. More...
class  EMAN::MedianShrinkProcessor
 MeanShrinkProcessor shrinks an image by in an integer amount taking the median of the pixel neighbourhood. More...
class  EMAN::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  EMAN::GradientRemoverProcessor
 Gradient remover, does a rough plane fit to find linear gradients. More...
class  EMAN::GradientPlaneRemoverProcessor
 Gradient removed by least square plane fit. More...
class  EMAN::FlattenBackgroundProcessor
 Flattens the background by subtracting the local mean. More...
class  EMAN::RampProcessor
 Ramp processor -- Fits a least-squares plane to the picture, and subtracts the plane from the picture. More...
class  EMAN::VerticalStripeProcessor
 Tries to fix images scanned on the zeiss for poor ccd normalization. More...
class  EMAN::RealToFFTProcessor
 This will replace the image with a full-circle 2D fft amplitude rendering. More...
class  EMAN::SigmaZeroEdgeProcessor
 Fill zeroes at edges with nearest horizontal/vertical value. More...
class  EMAN::BeamstopProcessor
 Try to eliminate beamstop in electron diffraction patterns. More...
class  EMAN::MeanZeroEdgeProcessor
 Fill zeroes at edges with nearest horizontal/vertical value damped towards Mean2. More...
class  EMAN::AverageXProcessor
 Average along Y and replace with average. More...
class  EMAN::DecayEdgeProcessor
 Decay edges of image to zero. More...
class  EMAN::ZeroEdgeRowProcessor
 zero edges of image on top and bottom, and on left and right. More...
class  EMAN::ZeroEdgePlaneProcessor
 zero edges of volume on all sides More...
class  EMAN::BilateralProcessor
 Bilateral processing on 2D or 3D volume data. More...
class  EMAN::NormalizeProcessor
 Base class for normalization processors. More...
class  EMAN::NormalizeUnitProcessor
 Normalize an image so its vector length is 1.0. More...
class  EMAN::NormalizeUnitSumProcessor
 Normalize an image so its elements sum to 1.0 (fails if mean=0). More...
class  EMAN::NormalizeStdProcessor
 do a standard normalization on an image. More...
class  EMAN::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  EMAN::NormalizeRampNormVar
 Normalize the image whilst also removing any ramps. More...
class  EMAN::NormalizeByMassProcessor
 Normalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3). More...
class  EMAN::NormalizeEdgeMeanProcessor
 normalizes an image, mean value equals to edge mean. More...
class  EMAN::NormalizeCircleMeanProcessor
 normalizes an image, mean value equals to mean of 2 pixel circular border. More...
class  EMAN::NormalizeLREdgeMeanProcessor
 normalizes an image, uses 2 pixels on left and right edge More...
class  EMAN::NormalizeMaxMinProcessor
 normalizes an image. More...
class  EMAN::NormalizeRowProcessor
 normalizes each row in the image individually More...
class  EMAN::NormalizeToLeastSquareProcessor
 use least square method to normalize More...
class  EMAN::RotationalAverageProcessor
 makes image circularly symmetric. More...
class  EMAN::RotationalSubstractProcessor
 subtracts circularly symmetric part of an image. More...
class  EMAN::TransposeProcessor
 Transpose a 2D image. More...
class  EMAN::FlipProcessor
 flip an image around an axis More...
class  EMAN::AddNoiseProcessor
 add noise to an image More...
class  EMAN::AddSigmaNoiseProcessor
 add sigma noise, multiply image's sigma value to noise More...
class  EMAN::AddRandomNoiseProcessor
 add spectral noise to a complex image More...
class  EMAN::FourierToCornerProcessor
 Undo the effects of the FourierToCenterProcessor. More...
class  EMAN::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  EMAN::Phase180Processor
 This class is abstract. More...
class  EMAN::PhaseToCenterProcessor
 Translates a cornered image to the center Undoes the PhaseToCornerProcessor. More...
class  EMAN::PhaseToCornerProcessor
 Translates a centered image to the corner works for 1D, 2D and 3D images, for all combinations of even and oddness. More...
class  EMAN::AutoMask2DProcessor
 Attempts to automatically mask out the particle, excluding other particles in the box, etc. More...
class  EMAN::AutoMaskAsymUnit
 Tries to mask out only interesting density. More...
class  EMAN::AutoMask3DProcessor
 Tries to mask out only interesting density. More...
class  EMAN::AutoMask3D2Processor
 Tries to mask out only interesting density. More...
class  EMAN::AddMaskShellProcessor
 Add additional shells/rings to an existing 1/0 mask image. More...
class  EMAN::PhaseToMassCenterProcessor
 ToMassCenterProcessor centers image at center of mass, ignores old dx, dy. More...
class  EMAN::ToMassCenterProcessor
 ToMassCenterProcessor centers image at center of mass, ignores old dx, dy. More...
class  EMAN::ACFCenterProcessor
 Center image using auto convolution with 180 degree rotation. More...
class  EMAN::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  EMAN::FileFourierProcessor
 A fourier processor specified in a 2 column text file. More...
class  EMAN::SymSearchProcessor
 Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel. More...
class  EMAN::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  EMAN::IndexMaskFileProcessor
 Multiplies the image by the specified file using pixel indices. More...
class  EMAN::CoordinateMaskFileProcessor
 Multiplies the image by the specified file using pixel coordinates instead of pixel indices. More...
class  EMAN::PaintProcessor
 'paints' a circle into the image at x,y,z with values inside r1 set to v1, values between r1 and r2 will be set to a value between v1 and v2, and values outside r2 will be unchanged More...
class  EMAN::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  EMAN::WatershedProcessor
 'paints' a circle into the image at x,y,z with values inside r1 set to v1, values between r1 and r2 will be set to a value between v1 and v2, and values outside r2 will be unchanged More...
class  EMAN::BinaryOperateProcessor< Type >
 Operates on two images, returning an image containing the maximum/minimum/multiplied pixel (etc, you choose) at each location The actual operation depends on what template argument you use. More...
class  EMAN::MaxPixelOperator
class  EMAN::MinPixelOperator
class  EMAN::MatchSFProcessor
 Sets the structure factor To match a second provided image/volume. More...
class  EMAN::SetSFProcessor
 Sets the structure factor based on a 1D s/intensity curve as an XYData object. More...
class  EMAN::SmartMaskProcessor
 Smart mask processor. More...
class  EMAN::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  EMAN::TestImageProcessor
 Base class for a group of 'processor' used to create test image. More...
class  EMAN::TestImagePureGaussian
 Replace a source image as a strict Gaussian. More...
class  EMAN::TestImageFourierNoiseGaussian
 Replace a source image as a strict Gaussian. More...
class  EMAN::TestImageFourierNoiseProfile
class  EMAN::CTFSNRWeightProcessor
class  EMAN::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  EMAN::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  EMAN::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  EMAN::TestImageAxes
 Make an image consisting of a single cross, with lines going in the axial directions, intersecting at the origin. More...
class  EMAN::TestImageGaussian
 Replace a source image as a Gaussian Blob. More...
class  EMAN::TestImageScurve
 Replace a source image with a lumpy S-curve used for alignment testing. More...
class  EMAN::TestImageSphericalWave
 Replace a source image as a sine wave in specified wave length. More...
class  EMAN::TestImageSinewave
 Replace a source image as a sine wave in specified wave length. More...
class  EMAN::TestImageSinewaveCircular
 Replace a source image as a circular sine wave in specified wave length. More...
class  EMAN::TestImageSquarecube
 Replace a source image as a square or cube depends on 2D or 3D of the source image. More...
class  EMAN::TestImageEllipse
 Generate an ellipse or ellipsoid image. More...
class  EMAN::TestImageHollowEllipse
 Generate an ellipse/ellipsoid image with an inner hollow ellipse/ellipsoid. More...
class  EMAN::TestImageCirclesphere
 Replace a source image as a circle or sphere depends on 2D or 3D of the source image. More...
class  EMAN::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  EMAN::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  EMAN::TestImageCylinder
 Replace a source image with a cylinder. More...
class  EMAN::CCDNormProcessor
 Try to normalize the 4 quadrants of a CCD image. More...
class  EMAN::WaveletProcessor
 Perform a Wavelet transform using GSL. More...
class  EMAN::TomoTiltEdgeMaskProcessor
 A processor designed specifically for tomographic tilt series data. More...
class  EMAN::TomoTiltEdgeMaskProcessor::GaussianFunctoid
class  EMAN::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  EMAN::FFTProcessor
 Perform a FFT transform by calling EMData::do_fft() and EMData::do_ift(). More...
class  EMAN::RadialProcessor
 Perform a multiplication of real image with a radial table. More...
class  EMAN::HistogramBin
 Bins pixel values, similar to calculating a histogram. More...
class  EMAN::ModelHelixProcessor
class  EMAN::ModelEMCylinderProcessor
class  EMAN::ApplyPolynomialProfileToHelix
class  EMAN::BinarySkeletonizerProcessor
class  EMAN::Projector
 Projector class defines a method to generate 2D projections from a 3D model. More...
class  EMAN::GaussFFTProjector
 Gaussian FFT 3D projection. More...
class  EMAN::FourierGriddingProjector
 Fourier gridding projection routine. More...
class  EMAN::PawelProjector
 Pawel Penczek's optimized projection routine. More...
struct  EMAN::PawelProjector::IPCube
class  EMAN::StandardProjector
 Fast real-space 3D projection. More...
class  EMAN::ChaoProjector
 Fast real space projection using Bi-Linear interpolation. More...
class  EMAN::Quaternion
 Quaternion is used in Rotation and Transformation to replace Euler angles. More...
class  EMAN::Randnum
 The wrapper class for gsl's random number generater. More...
class  EMAN::Reconstructor
 Reconstructor class defines a way to do 3D recontruction. More...
class  EMAN::ReconstructorVolumeData
 This is a Mixin class A class object encapsulating the volume data required by Reconstructors It basically stores two (pointers) to EMData objectsd stores the dimensions of the image volume. More...
class  EMAN::FourierReconstructorSimple2D
 This class originally added for 2D experimentation and prototying. More...
class  EMAN::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  EMAN::WienerFourierReconstructor
 Fourier space 3D reconstruction with slices already Wiener filter processed. More...
class  EMAN::BackProjectionReconstructor
 Real space 3D reconstruction using back projection. More...
class  EMAN::nn4Reconstructor
class  EMAN::nnSSNR_Reconstructor
class  EMAN::nn4_ctfReconstructor
 nn4_ctf Direct Fourier Inversion Reconstructor More...
class  EMAN::nnSSNR_ctfReconstructor
struct  EMAN::point_t
class  EMAN::newfile_store
class  EMAN::file_store
class  EMAN::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  EMAN::FourierInserter3DMode1
 FourierPixelInserter3DMode1 - encapsulates "method 1" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class  EMAN::FourierInserter3DMode2
 FourierPixelInserter3DMode2 - encapsulates "method 2" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class  EMAN::FourierInserter3DMode3
 FourierPixelInserter3DMode3 - encapsulates "method 3" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class  EMAN::FourierInserter3DMode5
 FourierPixelInserter3DMode5 - encapsulates "method 5" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class  EMAN::FourierInserter3DMode6
 FourierPixelInserter3DMode6 - encapsulates "method 6" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class  EMAN::FourierInserter3DMode7
 FourierPixelInserter3DMode7 - encapsulates "method 7" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class  EMAN::FourierInserter3DMode8
 FourierPixelInserter3DMode8 - encapsulates "method 8" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...
class  EMAN::SalIO
 A SAL image is an image from Perkin Elmer PDS Microdensitometer. More...
class  EMAN::PCAsmall
 Principal component analysis. More...
class  EMAN::PCAlarge
class  EMAN::varimax
class  EMAN::EMArray< T >
 EMArray -- 1-, 2-, or 3-D array of types T. More...
class  EMAN::PCA
class  EMAN::MirrorProcessor
 mirror an image More...
class  EMAN::NewFourierProcessor
class  EMAN::NewLowpassTopHatProcessor
 Lowpass top-hat filter processor applied in Fourier space. More...
class  EMAN::NewHighpassTopHatProcessor
 Highpass top-hat filter applied in Fourier space. More...
class  EMAN::NewBandpassTopHatProcessor
 Bandpass top-hat filter processor applied in Fourier space. More...
class  EMAN::NewHomomorphicTopHatProcessor
 Homomorphic top-hat filter processor applied in Fourier space. More...
class  EMAN::NewLowpassGaussProcessor
 Lowpass Gauss filter processor applied in Fourier space. More...
class  EMAN::NewHighpassGaussProcessor
 Highpass Gauss filter processor applied in Fourier space. More...
class  EMAN::NewBandpassGaussProcessor
 Bandpass Gauss filter processor applied in Fourier space. More...
class  EMAN::NewHomomorphicGaussProcessor
 Homomorphic Gauss filter processor applied in Fourier space. More...
class  EMAN::NewInverseGaussProcessor
 Divide by a Gaussian in Fourier space. More...
class  EMAN::SHIFTProcessor
 Shift by phase multiplication in Fourier space. More...
class  EMAN::InverseKaiserI0Processor
 Divide by a Kaiser-Bessel I0 func in Fourier space. More...
class  EMAN::InverseKaiserSinhProcessor
 Divide by a Kaiser-Bessel Sinh func in Fourier space. More...
class  EMAN::NewRadialTableProcessor
 Filter with tabulated data in Fourier space. More...
class  EMAN::NewLowpassButterworthProcessor
 Lowpass Butterworth filter processor applied in Fourier space. More...
class  EMAN::NewHighpassButterworthProcessor
 Highpass Butterworth filter processor applied in Fourier space. More...
class  EMAN::NewHomomorphicButterworthProcessor
 Homomorphic Butterworth filter processor applied in Fourier space. More...
class  EMAN::NewLowpassTanhProcessor
 Lowpass tanh filter processor applied in Fourier space. More...
class  EMAN::NewHighpassTanhProcessor
 Highpass tanh filter processor applied in Fourier space. More...
class  EMAN::NewHomomorphicTanhProcessor
 Homomorphic Tanh processor applied in Fourier space. More...
class  EMAN::NewBandpassTanhProcessor
 Bandpass tanh processor applied in Fourier space. More...
class  EMAN::CTF_Processor
class  EMAN::SpiderIO
 SPIDER: (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy. More...
struct  EMAN::SpiderIO::SpiderHeader
class  EMAN::SingleSpiderIO
 Single Spider Image I/O class. More...
class  EMAN::Symmetry3D
 Symmetry3D - A base class for 3D Symmetry objects. More...
class  EMAN::CSym
 An encapsulation of cyclic 3D symmetry. More...
class  EMAN::DSym
 An encapsulation of dihedral 3D symmetry. More...
class  EMAN::HSym
 An encapsulation of helical 3D symmetry. More...
class  EMAN::PlatonicSym
 A base (or parent) class for the Platonic symmetries. More...
class  EMAN::TetrahedralSym
 An encapsulation of tetrahedral symmetry Doctor Phil has this to say about tetrahedral symmetry: " Each Platonic Solid has 2E symmetry elements. More...
class  EMAN::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  EMAN::IcosahedralSym
 An encapsulation of icosahedral symmetry Doctor Phil has this to say about icosahedral symmetry: "Each Platonic Solid has 2E symmetry elements. More...
class  EMAN::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  EMAN::EmanOrientationGenerator
 EmanOrientationGenerator generates orientations quasi-evenly distributed in the asymmetric unit. More...
class  EMAN::RandomOrientationGenerator
 Random Orientation Generator - carefully generates uniformly random orientations in any asymmetric unit. More...
class  EMAN::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  EMAN::SaffOrientationGenerator
 Saff orientation generator - based on the work of Saff and Kuijlaars, 1997 E.B. More...
class  EMAN::OptimumOrientationGenerator
 Optimum orientation generator. More...
class  EMAN::TestUtil
class  EMAN::Transform
 A Transform object is a somewhat specialized object designed specifically for EMAN2/Sparx storage of alignment parameters and euler orientations. More...
class  EMAN::Transform3D
 Transform3D These are a collection of transformation tools: rotation, translation, and construction of symmetric objects. More...
class  EMAN::Util
 Util is a collection of utility functions. More...
class  EMAN::Util::sincBlackman
class  EMAN::Util::KaiserBessel
 1-D Kaiser-Bessel window function class. More...
class  EMAN::Util::KaiserBessel::kbsinh_win
 Sinh window function object. More...
class  EMAN::Util::KaiserBessel::kbi0_win
 I0 window function object. More...
class  EMAN::Util::FakeKaiserBessel
class  EMAN::Util::Gaussian
 Gaussian function class. More...
struct  EMAN::Util::tmpstruct
class  EMAN::V4L2IO
 Read-only. More...
class  EMAN::Vec3< Type >
 The Vec3 object is a templated object, intended to instantiated with basic types such as int, float, double etc. More...
class  EMAN::Vec2< Type >
 The Vec2 is precisely the same as Vec3 except it works exclusively in 2D Note there are convenient typedef so one needn't bother about using template terminology typedef Vec2<float> Vec2f; typedef Vec2<int> Vec2i; typedef Vec2double> Vec2d; // Not recommended for use unless precision is addressed in this class. More...
class  EMAN::ScreenVector
class  EMAN::ScreenPoint
class  EMAN::Vector3
class  EMAN::Point3
class  EMAN::Matrix3
class  EMAN::Vector4
class  EMAN::Matrix4
class  EMAN::VtkIO
 VtkIO reads/writes VTK image file. More...
class  EMAN::XplorIO
 XPLOR image format is in ASCII:. More...
class  EMAN::XYData
 XYData defines a 1D (x,y) data set. More...
struct  EMAN::XYData::Pair

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
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
}
enum  fp_flag {
  CIRCULANT = 1, CIRCULANT_NORMALIZED = 2, PADDED = 3, PADDED_NORMALIZED = 4,
  PADDED_LAG = 5, PADDED_NORMALIZED_LAG = 6
}
 Fourier Product processing flag. More...
enum  fp_type { CORRELATION, CONVOLUTION, SELF_CORRELATION, AUTOCORRELATION }
enum  kernel_shape { BLOCK = 1, CIRCULAR = 2, CROSS = 3 }
enum  morph_type { BINARY = 1, GRAYLEVEL = 2 }
 Median filter. More...

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 ()
EMDataoperator+ (const EMData &em, float n)
EMDataoperator- (const EMData &em, float n)
EMDataoperator * (const EMData &em, float n)
EMDataoperator/ (const EMData &em, float n)
EMDataoperator+ (float n, const EMData &em)
EMDataoperator- (float n, const EMData &em)
EMDataoperator * (float n, const EMData &em)
EMDataoperator/ (float n, const EMData &em)
EMDatarsub (const EMData &em, float n)
EMDatardiv (const EMData &em, float n)
EMDataoperator+ (const EMData &a, const EMData &b)
EMDataoperator- (const EMData &a, const EMData &b)
EMDataoperator * (const EMData &a, const EMData &b)
EMDataoperator/ (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)
EMDatapadfft_slice (const EMData *const slice, const Transform &t, int npad)
 Direct Fourier inversion Reconstructor.
void dump_reconstructors ()
map< string, vector< string > > dump_reconstructors_list ()
EMDataperiodogram (EMData *f)
EMDatafourierproduct (EMData *f, EMData *g, fp_flag flag, fp_type ptype, bool center)
 Fourier product of two images.
EMDatacorrelation (EMData *f, EMData *g, fp_flag myflag, bool center)
 Correlation of two images.
EMDataconvolution (EMData *f, EMData *g, fp_flag myflag, bool center)
 Convolution of two images.
EMDatarsconvolution (EMData *f, EMData *K)
 Real-space convolution of two images.
EMDatarscp (EMData *f)
 Real-space convolution with the K-B window.
EMDataautocorrelation (EMData *f, fp_flag myflag, bool center)
 Image autocorrelation.
EMDataself_correlation (EMData *f, fp_flag myflag, bool center)
 Image self-correlation.
EMDatafilt_median_ (EMData *f, int nxk, int nyk, int nzk, kernel_shape myshape)
EMDatafilt_dilation_ (EMData *f, EMData *K, morph_type mydilation)
EMDatafilt_erosion_ (EMData *f, EMData *K, morph_type myerosion)
 Dilation filter.
void dump_symmetries ()
 dump symmetries, useful for obtaining symmetry information
map< string, vector< string > > dump_symmetries_list ()
 dump_symmetries_list, useful for obtaining symmetry information
void dump_orientgens ()
 Dumps useful information about the OrientationGenerator factory.
map< string, vector< string > > dump_orientgens_list ()
 Can be used to get useful information about the OrientationGenerator factory.
Transform operator * (const Transform &M2, const Transform &M1)
 Matrix times Matrix, a pure mathematical operation.
template<typename Type>
Vec3f operator * (const Transform &M, const Vec3< Type > &v)
 Matrix times Vector, a pure mathematical operation.
template<typename Type>
Vec2f operator * (const Transform &M, const Vec2< Type > &v)
 Matrix times Vector, a pure mathematical operation.
template<typename Type>
Vec3f operator * (const Vec3< Type > &v, const Transform &M)
 Vector times a matrix.
Transform3D operator * (const Transform3D &M1, const Transform3D &M2)
template<typename Type>
Vec3f operator * (const Vec3< Type > &v, const Transform3D &M)
template<typename Type>
Vec3f operator * (const Transform3D &M, const Vec3< Type > &v)
template<typename Type>
Vec2f operator * (const Transform3D &M, const Vec2< Type > &v)
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 MAXFFT = 32768


Detailed Description

E2Exception class.

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) ...".


Typedef Documentation

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

Definition at line 75 of file emdata.h.

Referenced by EMAN::EMData::get_2dview().

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

Definition at line 76 of file emdata.h.

Referenced by EMAN::EMData::get_3dview().

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

Definition at line 77 of file emdata.h.

Referenced by EMAN::EMData::get_2dcview().

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

Definition at line 78 of file emdata.h.

Referenced by EMAN::EMData::get_3dcview(), and EMAN::EMData::get_3dcviewptr().

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

Definition at line 79 of file emdata.h.

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

Definition at line 80 of file emdata.h.

typedef Vec2<double> EMAN::Vec2d
 

Definition at line 868 of file vec3.h.

typedef Vec2<float> EMAN::Vec2f
 

Definition at line 866 of file vec3.h.

Referenced by EMAN::RTFExhaustiveAligner::align(), EMAN::Transform::get_pre_trans_2d(), EMAN::Transform::get_trans_2d(), operator *(), padfft_slice(), EMAN::Util::point_is_in_convex_polygon_2d(), EMAN::Util::point_is_in_triangle_2d(), EMAN::BackProjectionReconstructor::preprocess_slice(), EMAN::StandardProjector::project3d(), EMAN::Transform3D::set_posttrans(), EMAN::Transform3D::set_pretrans(), EMAN::Transform::set_trans(), EMAN::Transform::transform(), and EMAN::TransformProcessor::transform().

typedef Vec2<int> EMAN::Vec2i
 

Definition at line 867 of file vec3.h.

typedef Vec3<double> EMAN::Vec3d
 

Definition at line 490 of file vec3.h.

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

typedef Vec3<float> EMAN::Vec3f
 

Definition at line 488 of file vec3.h.

Referenced by ali3d_d(), EMAN::TranslationalAligner::align(), EMAN::PointArray::align_2d(), EMAN::PointArray::align_trans_2d(), EMAN::PawelProjector::backproject3d(), EMAN::Util::calc_bilinear_least_square(), EMAN::EMData::cut_slice(), EMAN::FourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_insert_slice_work(), EMAN::Util::equation_of_plane(), EMAN::EMData::extract_plane(), EMAN::TetrahedralSym::get_asym_unit_points(), EMAN::PlatonicSym::get_asym_unit_points(), EMAN::HSym::get_asym_unit_points(), EMAN::DSym::get_asym_unit_points(), EMAN::CSym::get_asym_unit_points(), EMAN::DSym::get_asym_unit_triangles(), EMAN::CSym::get_asym_unit_triangles(), EMAN::Transform3D::get_center(), EMAN::BoxingTools::get_color(), EMAN::Transform3D::get_finger(), EMAN::Transform::get_hflip_transform(), EMAN::Transform3D::get_matrix3_col(), EMAN::Transform::get_matrix3_row(), EMAN::Transform3D::get_matrix3_row(), EMAN::Transform::get_params(), EMAN::Transform::get_params_inverse(), EMAN::Transform3D::get_posttrans(), EMAN::Transform::get_pre_trans(), EMAN::Transform3D::get_pretrans(), EMAN::EMData::get_rotated_clip(), EMAN::Transform3D::get_total_posttrans(), EMAN::Transform3D::get_total_pretrans(), EMAN::Symmetry3D::get_touching_au_transforms(), EMAN::Transform::get_trans(), EMAN::PointArray::get_vector_at(), EMAN::Transform::get_vflip_transform(), EMAN::Symmetry3D::in_which_asym_unit(), EMAN::TestTomoImage::insert_rectangle(), EMAN::Transform3D::inverse(), EMAN::Transform3D::inverseUsingAngs(), EMAN::EMData::max_3D_pixel_error(), operator *(), EMAN::OptimumOrientationGenerator::optimize_distances(), EMAN::Symmetry3D::point_in_which_asym_unit(), EMAN::TestImageEllipse::process_inplace(), EMAN::TestImageHollowEllipse::process_inplace(), EMAN::AutoMaskAsymUnit::process_inplace(), EMAN::StandardProjector::project3d(), EMAN::PawelProjector::project3d(), EMAN::GaussFFTProjector::project3d(), EMAN::Quaternion::Quaternion(), refalin3d_perturb(), EMAN::PointArray::replace_by_summation(), EMAN::PointArray::right_transform(), EMAN::PDBReader::right_transform(), EMAN::EMData::rot_scale_trans(), EMAN::EMData::rot_scale_trans_background(), EMAN::Transform3D::rotate(), EMAN::Quaternion::rotate(), EMAN::EMData::rotate_translate(), EMAN::Transform3D::set_center(), EMAN::PointArray::set_from(), EMAN::Transform3D::set_posttrans(), EMAN::Transform3D::set_pretrans(), EMAN::Transform3D::set_rotation(), EMAN::Transform::set_rotation(), EMAN::Transform::set_trans(), set_translation(), EMAN::PointArray::set_vector_at(), EMAN::MarchingCubes::surface_face_z(), EMAN::TestUtil::test_Vec3f(), EMAN::Quaternion::to_angle(), EMAN::Quaternion::to_axis(), EMAN::Transform3D::to_identity(), EMAN::Transform::transform(), EMAN::Transform3D::transform(), EMAN::TransformProcessor::transform(), EMAN::PointArray::transform(), EMAN::Transform3D::Transform3D(), EMAN::EMData::translate(), EMAN::EMData::uncut_slice(), EMAN::Quaternion::unreal(), verify(), and EMAN::Util::KaiserBessel::~KaiserBessel().

typedef Vec3<int> EMAN::Vec3i
 

Definition at line 489 of file vec3.h.

Referenced by ali3d_d(), AlignOptions::AlignOptions(), EMAN::PawelProjector::backproject3d(), EMAN::ChaoProjector::backproject3d(), EMAN::ChaoProjector::bckpj3(), bckpj3(), bckpj3_Cart(), EMAN::ChaoProjector::cb2sph(), cb2sph(), CleanStack(), CleanStack_Cart(), fcalc(), fgcalc(), EMAN::WatershedProcessor::find_region(), find_region(), EMAN::ChaoProjector::fwdpj3(), fwdpj3(), fwdpj3_Cart(), EMAN::EMUtil::get_region_dims(), getcb2sph(), EMAN::ChaoProjector::getnnz(), getnnz(), LBD_Cart(), main(), EMAN::EMData::mask_contig_region(), EMAN::PawelProjector::prepcubes(), EMAN::WatershedProcessor::process_inplace(), EMAN::EMUtil::process_region_io(), EMAN::ChaoProjector::project3d(), EMAN::StandardProjector::project3d(), EMAN::PawelProjector::project3d(), recons3d_CGLS_mpi_Cart(), recons3d_HyBR_mpi_Cart(), recons3d_sirt_mpi(), recons3d_sirt_mpi_Cart(), EMAN::ChaoProjector::sph2cb(), sph2cb(), EMAN::TestUtil::test_Vec3i(), EMAN::EMData::translate(), unified(), and EMAN::WatershedProcessor::watershed().


Enumeration Type Documentation

enum fp_flag
 

Fourier Product processing flag.

Should the Fourier data be treated as manifestly periodic (CIRCULANT), padded with zeros (PADDED), or padded with a lag (PADDED_LAG). Also, in each of these cases the product may be normalized or not. Pick one, as there is no default.

Enumeration values:
CIRCULANT 
CIRCULANT_NORMALIZED 
PADDED 
PADDED_NORMALIZED 
PADDED_LAG 
PADDED_NORMALIZED_LAG 

Definition at line 71 of file fundamentals.h.

00071                      {
00072                 CIRCULANT = 1,
00073                 CIRCULANT_NORMALIZED = 2,
00074                 PADDED = 3,
00075                 PADDED_NORMALIZED = 4,
00076                 PADDED_LAG = 5,
00077                 PADDED_NORMALIZED_LAG = 6
00078         };

enum fp_type
 

Enumeration values:
CORRELATION 
CONVOLUTION 
SELF_CORRELATION 
AUTOCORRELATION 

Definition at line 81 of file fundamentals.h.

00081                      {
00082                 CORRELATION,
00083                 CONVOLUTION,
00084                 SELF_CORRELATION,
00085                 AUTOCORRELATION
00086         };

enum kernel_shape
 

Enumeration values:
BLOCK 
CIRCULAR 
CROSS 

Definition at line 232 of file fundamentals.h.

00232                           {
00233                 BLOCK = 1,
00234                 CIRCULAR = 2,
00235                 CROSS = 3
00236         };

enum MapInfoType
 

Enumeration values:
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.

00094                          {
00095                 NORMAL,
00096                 ICOS2F_FIRST_OCTANT,
00097                 ICOS2F_FULL,
00098                 ICOS2F_HALF,
00099                 ICOS3F_HALF,
00100                 ICOS3F_FULL,
00101                 ICOS5F_HALF,
00102                 ICOS5F_FULL,
00103                 ICOS_UNKNOWN
00104         };

enum morph_type
 

Median filter.

Purpose: Calculate the median filtered image.
Parameters:
[in] f First real-space image object. Image may be 1-, 2-, or 3-dimensional. Image f is not changed.
[in] nxk,nyk,nzk Size of the kernel on each dimension Note: For CIRCULAR kernel, we currently only consider circle or sphere kernel, i.e., nxk==nyk for 2 dimensional image and nxk==nyk==nzk for 3 dimensional image.
[in] myshape Shape of the kernal BLOCK is for block kernal; CIRCULAR is for circular kernel; CROSS is for cross kernal; Note: For 1-dimensional image, these three kernels degenerate into the same shape.
Returns:
Median filtered image.
Enumeration values:
BINARY 
GRAYLEVEL 

Definition at line 259 of file fundamentals.h.

00259                         {
00260                 BINARY = 1,
00261                 GRAYLEVEL = 2
00262         };


Function Documentation

EMData* autocorrelation EMData *  f,
fp_flag  myflag,
bool  center
[inline]
 

Image autocorrelation.

Purpose: Calculate the autocorrelation of a 1-, 2-,
or 3-dimensional image.
Method: This function calls fourierproduct.
Parameters:
[in] f Image object, either a real-space image or a Fourier image. Image may be 1-, 2-, or 3-dimensional. Image f is not changed.
[in] myflag Processing flag (see above).
[in] center 
Returns:
Real-space autocorrelation image.

Definition at line 192 of file fundamentals.h.

References AUTOCORRELATION, and fourierproduct().

00192                                                                                {
00193                 return fourierproduct(f, NULL, myflag, AUTOCORRELATION, center);
00194         }

EMData* convolution EMData *  f,
EMData *  g,
fp_flag  myflag,
bool  center
[inline]
 

Convolution of two images.

Purpose: Calculate the convolution of two 1-, 2-,
or 3-dimensional images.
Method: This function calls fourierproduct.
Parameters:
[in] f First image object, either a real-space image or a Fourier image. Image may be 1-, 2-, or 3-dimensional. Image f is not changed.
[in] g Second image object, either a real-space image or a Fourier image. Image may be 1-, 2-, or 3-dimensional. The size of g must be the same as the size of f. Image g is not changed.
[in] myflag Processing flag (see above).
[in] center 
Returns:
Real-space convolution image.

Definition at line 149 of file fundamentals.h.

References CONVOLUTION, and fourierproduct().

Referenced by EMAN::EMData::calc_ccf().

00149                                                                                       {
00150                 return fourierproduct(f, g, myflag, CONVOLUTION, center);
00151         }

EMData* correlation EMData *  f,
EMData *  g,
fp_flag  myflag,
bool  center
[inline]
 

Correlation of two images.

Purpose: Calculate the correlation of two 1-, 2-,
or 3-dimensional images.
Method: This function calls fourierproduct.
Parameters:
[in] f First image object, either a real-space image or a Fourier image. Image may be 1-, 2-, or 3-dimensional. Image f is not changed.
[in] g Second image object, either a real-space image or a Fourier image. Image may be 1-, 2-, or 3-dimensional. The size of g must be the same as the size of f. Image g is not changed.
[in] myflag Processing flag (see above).
[in] center 
Returns:
Real-space correlation image.

Definition at line 128 of file fundamentals.h.

References CORRELATION, and fourierproduct().

Referenced by EMAN::EMData::calc_ccf().

00128                                                                                       {
00129                 return fourierproduct(f, g, myflag, CORRELATION, center);
00130         }

Vector3 cross const Vector3 &  w,
const Vector3 &  v
[inline]
 

Definition at line 313 of file vecmath.h.

00313                                                                    {
00314             return w ^ v;
00315         }

double dot const Vector3 &  w,
const Vector3 &  v
[inline]
 

Definition at line 309 of file vecmath.h.

00309                                                                 {
00310             return w * v;
00311         }

void EMAN::dump_aligners  ) 
 

Definition at line 2208 of file aligner.cpp.

02209 {
02210         dump_factory < Aligner > ();
02211 }

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

Definition at line 2213 of file aligner.cpp.

02214 {
02215         return dump_factory_list < Aligner > ();
02216 }

void EMAN::dump_analyzers  ) 
 

Definition at line 819 of file analyzer.cpp.

00820 {
00821         dump_factory < Analyzer > ();
00822 }

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

Definition at line 824 of file analyzer.cpp.

00825 {
00826         return dump_factory_list < Analyzer > ();
00827 }

void EMAN::dump_averagers  ) 
 

Definition at line 1283 of file averager.cpp.

01284 {
01285         dump_factory < Averager > ();
01286 }

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

Definition at line 1288 of file averager.cpp.

01289 {
01290         return dump_factory_list < Averager > ();
01291 }

void EMAN::dump_cmps  ) 
 

Definition at line 1217 of file cmp.cpp.

01218 {
01219         dump_factory < Cmp > ();
01220 }

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

Definition at line 1222 of file cmp.cpp.

01223 {
01224         return dump_factory_list < Cmp > ();
01225 }

template<class T>
void dump_factory  ) 
 

Definition at line 822 of file emobject.h.

References EMAN::TypeDict::dump().

00823         {
00824                 vector < string > item_names = Factory < T >::get_list();
00825 
00826                 for (size_t i = 0; i < item_names.size(); i++) {
00827                         T *item = Factory < T >::get(item_names[i]);
00828                         printf("%s :  %s\n", item->get_name().c_str(),item->get_desc().c_str());
00829                         TypeDict td = item->get_param_types();
00830                         td.dump();
00831                 }
00832         }

template<class T>
map<string, vector<string> > dump_factory_list  ) 
 

Definition at line 834 of file emobject.h.

References EMAN::TypeDict::get_desc(), EMAN::TypeDict::get_type(), EMAN::TypeDict::keys(), and EMAN::TypeDict::size().

00835         {
00836                 vector < string > item_names = Factory < T >::get_list();
00837                 map<string, vector<string> >    factory_list;
00838 
00839                 typename vector<string>::const_iterator p;
00840                 for(p = item_names.begin(); p !=item_names.end(); ++p) {
00841                         T *item = Factory<T>::get(*p);
00842 
00843                         string name = item->get_name();
00844 
00845                         vector<string> content;
00846                         content.push_back(item->get_desc());
00847                         TypeDict td = item->get_param_types();
00848                         vector<string> keys = td.keys();
00849                         for(unsigned int i=0; i<td.size(); ++i) {
00850                                 content.push_back(keys[i]);
00851                                 content.push_back( td.get_type(keys[i]) );
00852                                 content.push_back( td.get_desc(keys[i]) );
00853                         }
00854                         factory_list[name] = content;
00855                 }
00856 
00857                 return factory_list;
00858         }

void EMAN::dump_orientgens  ) 
 

Dumps useful information about the OrientationGenerator factory.

Definition at line 136 of file symmetry.cpp.

00137 {
00138         dump_factory < OrientationGenerator > ();
00139 }

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

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

Definition at line 141 of file symmetry.cpp.

00142 {
00143         return dump_factory_list < OrientationGenerator > ();
00144 }

void EMAN::dump_processors  ) 
 

Definition at line 9732 of file processor.cpp.

09733 {
09734         dump_factory < Processor > ();
09735 }

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

Definition at line 9737 of file processor.cpp.

09738 {
09739         return dump_factory_list < Processor > ();
09740 }

void EMAN::dump_projectors  ) 
 

Definition at line 2108 of file projector.cpp.

02109 {
02110         dump_factory < Projector > ();
02111 }

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

Definition at line 2113 of file projector.cpp.

02114 {
02115         return dump_factory_list < Projector > ();
02116 }

void EMAN::dump_reconstructors  ) 
 

Definition at line 3379 of file reconstructor.cpp.

03380 {
03381         dump_factory < Reconstructor > ();
03382 }

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

Definition at line 3384 of file reconstructor.cpp.

03385 {
03386         return dump_factory_list < Reconstructor > ();
03387 }

void EMAN::dump_symmetries  ) 
 

dump symmetries, useful for obtaining symmetry information

Definition at line 62 of file symmetry.cpp.

00063 {
00064         dump_factory < Symmetry3D > ();
00065 }

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

dump_symmetries_list, useful for obtaining symmetry information

Definition at line 67 of file symmetry.cpp.

00068 {
00069         return dump_factory_list < Symmetry3D > ();
00070 }

EMData * EMAN::filt_dilation_ EMData f,
EMData K,
morph_type  mydilation
 

Definition at line 597 of file rsconvolution.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, EMAN::EMData::set_size(), and EMAN::EMData::to_zero().

00597                                                                         {
00598 
00599                 int nxf = f->get_xsize();
00600                 int nyf = f->get_ysize(); 
00601                 int nzf = f->get_zsize();
00602 
00603                 int nxk = K->get_xsize();
00604                 int nyk = K->get_ysize();
00605                 int nzk = K->get_zsize();
00606         
00607                 if ( nxf < nxk && nyf < nyk && nzf < nzk ) {
00608                         // whoops, f smaller than K
00609                         swap(f,K); swap(nxf,nxk); swap(nyf,nyk); swap(nzf,nzk);
00610                 } else if ( nxk > nxf || nyk > nyf || nzk > nzf ) {
00611                         // Incommensurate sizes
00612                         throw ImageDimensionException("Two input images are incommensurate.");
00613                 }
00614 
00615                 if ( nxk % 2 != 1 || nyk % 2 != 1 || nzk % 2 != 1 ) {
00616                         // Kernel needs to be odd in size
00617                         throw ImageDimensionException("Kernel should have odd nx,ny,nz so that the center is well-defined.");
00618                 }
00619 
00620                 int nxk2 = (nxk-1)/2;
00621                 int nyk2 = (nyk-1)/2;
00622                 int nzk2 = (nzk-1)/2;
00623 
00624                 if ( mydilation == BINARY ) {
00625                         // Check whether two images are truly binary.
00626                         for (int iz = 0; iz <= nzf-1; iz++) {
00627                                 for (int iy = 0; iy <= nyf-1; iy++) {
00628                                         for (int ix = 0; ix <= nxf-1; ix++) {
00629                                                 int fxyz=(int)(*f)(ix,iy,iz);
00630                                                 if ( fxyz != 0 && fxyz != 1 ) {
00631                                                         throw ImageDimensionException("One of the two images is not binary.");
00632                                                 }
00633                                         }
00634                                 }
00635                         }
00636                         for (int iz = 0; iz <= nzk-1; iz++) {
00637                                 for (int iy = 0; iy <= nyk-1; iy++) {
00638                                         for (int ix = 0; ix <= nxk-1; ix++) {
00639                                                 int kxyz=(int)(*K)(ix,iy,iz);
00640                                                 if ( kxyz != 0 && kxyz != 1 ) {
00641                                                         throw ImageDimensionException("One of the two images is not binary.");
00642                                                 }
00643                                         }
00644                                 }
00645                         }
00646                 }
00647 
00648                 EMData* result = new EMData();
00649                 result->set_size(nxf, nyf, nzf);
00650                 result->to_zero();
00651 
00652                 for (int iz = 0; iz <= nzf-1; iz++) {
00653                         for (int iy = 0; iy <= nyf-1; iy++) {
00654                                 for (int ix = 0; ix <= nxf-1; ix++) {
00655 //                                      int kzmin = iz-nzk2 < 0     ?   0   : iz-nzk2 ;
00656 //                                      int kzmax = iz+nzk2 > nzf-1 ? nzf-1 : iz+nzk2 ;
00657 //                                      int kymin = iy-nyk2 < 0     ?   0   : iy-nyk2 ;
00658 //                                      int kymax = iy+nyk2 > nyf-1 ? nyf-1 : iy+nyk2 ;
00659 //                                      int kxmin = ix-nxk2 < 0     ?   0   : ix-nxk2 ;
00660 //                                      int kxmax = ix+nxk2 > nxf-1 ? nxf-1 : ix+nxk2 ;
00661                                         if ( mydilation == BINARY ) {
00662                                                 int fxyz = (int)(*f)(ix,iy,iz);
00663                                                 if ( fxyz == 1 ) {
00664                                                         for (int jz = -nzk2; jz <= nzk2; jz++) {
00665                                                                 for (int jy = -nyk2; jy <= nyk2; jy++) {
00666                                                                         for (int jx= -nxk2; jx <= nxk2; jx++) {
00667                                                                                 if ( (int)(*K)(jx+nxk2,jy+nyk2,jz+nzk2) == 1 ) {
00668                                                                                         int fz = iz+jz;
00669                                                                                         int fy = iy+jy;
00670                                                                                         int fx = ix+jx;
00671                                                                                         if ( fz >= 0 && fz <= nzf-1 && fy >= 0 && fy <= nyf-1 && fx >= 0 && fx <= nxf-1 )
00672                                                                                                 (*result)(fx,fy,fz) = 1;
00673                                                                                         }
00674                                                                                 }
00675                                                                         }
00676                                                                 }
00677                                                         }
00678                                         } else if ( mydilation == GRAYLEVEL ) {
00679                                                         float pmax = (*f)(ix,iy,iz)+(*K)(nxk2,nyk2,nzk2); 
00680                                                         for (int jz = -nzk2; jz <= nzk2; jz++) {
00681                                                                 for (int jy = -nyk2; jy <= nyk2; jy++) {
00682                                                                         for (int jx = -nxk2; jx <= nxk2; jx++) {
00683                                                                                 int fz = iz+jz;
00684                                                                                 int fy = iy+jy;
00685                                                                                 int fx = ix+jx;
00686                                                                                 if ( fz >= 0 && fz <= nzf-1 && fy >= 0 && fy <= nyf-1 && fx >= 0 && fx <= nxf-1 ) {
00687                                                                                         float kxyz = (*K)(jx+nxk2,jy+nyk2,jz+nzk2);
00688                                                                                         float fxyz = (*f)(fx,fy,fz);                                                                                    
00689                                                                                         if ( kxyz+fxyz > pmax )  pmax = kxyz+fxyz;
00690                                                                                 }
00691                                                                         }
00692                                                                 }
00693                                                         }
00694                                                         (*result)(ix,iy,iz) = pmax;
00695                                         } else {
00696                                                 throw ImageDimensionException("Illegal dilation type!");
00697                                         }
00698                                 }
00699                         }
00700                 }               
00701                 return result;
00702     }

EMData * EMAN::filt_erosion_ EMData f,
EMData K,
morph_type  myerosion
 

Dilation filter.

Purpose: Calculate the Minkowski addition of the two images
Parameters:
[in] f First real-space image object. Image may be 2- or 3-dimensional. Image f is not changed. K Second real-space image object Image may be 2- or 3-dimentional. Image K is not changed. mydilation Type of dilation BINARY is for binary dilation. GRAYLEVEL is for graylevel dilation.
K 
myerosion 
Returns:
Dilation filtered image.

Definition at line 704 of file rsconvolution.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, EMAN::EMData::set_size(), and EMAN::EMData::to_one().

00704                                                                       {
00705 
00706                 int nxf = f->get_xsize();
00707                 int nyf = f->get_ysize(); 
00708                 int nzf = f->get_zsize();
00709 
00710                 int nxk = K->get_xsize();
00711                 int nyk = K->get_ysize();
00712                 int nzk = K->get_zsize();
00713         
00714                 if ( nxf < nxk && nyf < nyk && nzf < nzk ) {
00715                         // whoops, f smaller than K
00716                         swap(f,K); swap(nxf,nxk); swap(nyf,nyk); swap(nzf,nzk);
00717                 } else if ( nxk > nxf || nyk > nyf || nzk > nzf ) {
00718                         // Incommensurate sizes
00719                         throw ImageDimensionException("Two input images are incommensurate.");
00720                 }
00721 
00722                 if ( nxk % 2 != 1 || nyk % 2 != 1 || nzk % 2 != 1 ) {
00723                         // Kernel needs to be odd in size
00724                         throw ImageDimensionException("Kernel should have odd nx,ny,nz so that the center is well-defined.");
00725                 }
00726 
00727                 int nxk2 = (nxk-1)/2;
00728                 int nyk2 = (nyk-1)/2;
00729                 int nzk2 = (nzk-1)/2;
00730 
00731                 if ( myerosion == BINARY ) {
00732                         // Check whether two images are truly binary.
00733                         for (int iz = 0; iz <= nzf-1; iz++) {
00734                                 for (int iy = 0; iy <= nyf-1; iy++) {
00735                                         for (int ix = 0; ix <= nxf-1; ix++) {
00736                                                 int fxyz=(int)(*f)(ix,iy,iz);
00737                                                 if ( fxyz != 0 && fxyz != 1 ) {
00738                                                         throw ImageDimensionException("One of the two images is not binary.");
00739                                                 }
00740                                         }
00741                                 }
00742                         }
00743                         for (int iz = 0; iz <= nzk-1; iz++) {
00744                                 for (int iy = 0; iy <= nyk-1; iy++) {
00745                                         for (int ix = 0; ix <= nxk-1; ix++) {
00746                                                 int kxyz=(int)(*K)(ix,iy,iz);
00747                                                 if ( kxyz != 0 && kxyz != 1 ) {
00748                                                         throw ImageDimensionException("One of the two images is not binary.");
00749                                                 }
00750                                         }
00751                                 }
00752                         }
00753                 }
00754 
00755                 EMData* result = new EMData();
00756                 result->set_size(nxf, nyf, nzf);
00757                 result->to_one();
00758 
00759                 for (int iz = 0; iz <= nzf-1; iz++) {
00760                         for (int iy = 0; iy <= nyf-1; iy++) {
00761                                 for (int ix = 0; ix <= nxf-1; ix++) {
00762                                         if ( myerosion == BINARY ) {
00763                                                 int fxyz = (int)(*f)(ix,iy,iz);
00764                                                 if ( fxyz == 0 ) {
00765                                                         for (int jz = -nzk2; jz <= nzk2; jz++) {
00766                                                                 for (int jy = -nyk2; jy <= nyk2; jy++) {
00767                                                                         for (int jx= -nxk2; jx <= nxk2; jx++) {
00768                                                                                 if ( (int)(*K)(jx+nxk2,jy+nyk2,jz+nzk2) == 1 ) {
00769                                                                                         int fz = iz+jz;
00770                                                                                         int fy = iy+jy;
00771                                                                                         int fx = ix+jx;
00772                                                                                         if ( fz >= 0 && fz <= nzf-1 && fy >= 0 && fy <= nyf-1 && fx >= 0 && fx <= nxf-1 )
00773                                                                                                 (*result)(fx,fy,fz) = 0;
00774                                                                                         }
00775                                                                                 }
00776                                                                         }
00777                                                                 }
00778                                                         }
00779                                         } else if ( myerosion == GRAYLEVEL ) {
00780                                                         float pmin = (*f)(ix,iy,iz)-(*K)(nxk2,nyk2,nzk2); 
00781                                                         for (int jz = -nzk2; jz <= nzk2; jz++) {
00782                                                                 for (int jy = -nyk2; jy <= nyk2; jy++) {
00783                                                                         for (int jx = -nxk2; jx <= nxk2; jx++) {
00784                                                                                 int fz = iz+jz;
00785                                                                                 int fy = iy+jy;
00786                                                                                 int fx = ix+jx;
00787                                                                                 if ( fz >= 0 && fz <= nzf-1 && fy >= 0 && fy <= nyf-1 && fx >= 0 && fx <= nxf-1 ) {
00788                                                                                         float kxyz = (*K)(jx+nxk2,jy+nyk2,jz+nzk2);
00789                                                                                         float fxyz = (*f)(fx,fy,fz);                                                                                    
00790                                                                                         if ( fxyz-kxyz < pmin )  pmin = fxyz-kxyz;
00791                                                                                 }
00792                                                                         }
00793                                                                 }
00794                                                         }
00795                                                         (*result)(ix,iy,iz) = pmin;
00796                                         } else {
00797                                                 throw ImageDimensionException("Illegal dilation type!");
00798                                         }
00799                                 }
00800                         }
00801                 }               
00802                 return result;
00803     }

EMData * EMAN::filt_median_ EMData f,
int  nxk,
int  nyk,
int  nzk,
kernel_shape  myshape
 

Definition at line 559 of file rsconvolution.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, median(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().

00559                                                                                      {
00560                 
00561                 int nxf = f->get_xsize();
00562                 int nyf = f->get_ysize(); 
00563                 int nzf = f->get_zsize();
00564                 
00565                 if ( nxk > nxf || nyk > nyf || nzk > nzf ) {
00566                         // Kernel should be smaller than the size of image
00567                         throw ImageDimensionException("Kernel should be smaller than the size of image.");
00568                 }       
00569 
00570                 if ( nxk % 2 != 1 || nyk % 2 != 1 || nzk % 2 != 1 ) {
00571                         // Kernel needs to be odd in size
00572                         throw ImageDimensionException("Real-space kernel must have odd size so that the center is well-defined.");
00573                 }
00574 
00575                 if ( myshape == CIRCULAR ) {
00576                         // For CIRCULAR kernal, size must be same on all dimensions
00577                         if ( nzf != 1 && ( nxk != nyk || nxk != nzk ) || nzf == 1 && nyf != 1 && nxk != nyk ) {
00578                                 throw ImageDimensionException("For CIRCULAR kernal, size must be same on all dimensions.");
00579                         }
00580                 }
00581 
00582                 EMData* result = new EMData();
00583                 result->set_size(nxf, nyf, nzf);
00584                 result->to_zero();
00585 
00586                 for (int iz = 0; iz <= nzf-1; iz++) {
00587                         for (int iy = 0; iy <= nyf-1; iy++) {
00588                                 for (int ix = 0; ix <= nxf-1; ix++) {
00589                                         (*result)(ix,iy,iz) = median (*f, nxk, nyk, nzk, myshape, iz, iy, ix);                                  
00590                                 }
00591                         }
00592                 }
00593                 
00594                 return result;
00595         }

EMData * EMAN::fourierproduct EMData f,
EMData g,
fp_flag  myflag,
fp_type  mytype,
bool  center
 

Fourier product of two images.

Purpose: Calculate the correlation or convolution of
two images, or the autocorrelation or self-correlation of one image.
Parameters:
[in] f First image object, either a real-space image or a Fourier image. Image may be 1-, 2-, or 3-dimensional. Image f is not changed.
[in] g Second image object, either a real-space image or a Fourier image. Image may be 1-, 2-, or 3-dimensional. The size of g must be the same as the size of f. Image g is not changed.
[in] myflag Processing flag (see above).
[in] mytype Type of Fourier product to perform. (see above).
[in] center 
Returns:
1-, 2-, or 3-dimensional real fourier product image.

Definition at line 167 of file fundamentals.cpp.

References abs, AUTOCORRELATION, CIRCULANT, EMAN::EMData::cmplx(), CONVOLUTION, EMAN::EMData::copy(), CORRELATION, EMAN::EMData::depad(), EMAN::EMData::depad_corner(), EMAN::EMData::do_fft_inplace(), EMAN::EMData::do_ift_inplace(), flag, EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), imag(), InvalidValueException, EMAN::EMData::is_complex(), EMAN::EMData::is_fftodd(), EMAN::EMData::is_real(), LOGERR, EMAN::EMData::norm_pad(), nx, ny, real(), SELF_CORRELATION, EMAN::EMData::set_array_offsets(), and EMAN::EMData::update().

Referenced by autocorrelation(), convolution(), correlation(), EMAN::ConvolutionProcessor::process_inplace(), and self_correlation().

00167                                                                                        {
00168                 int normfact;
00169                 //std::complex<float> phase_mult;
00170                 // Not only does the value of "flag" determine how we handle
00171                 // periodicity, but it also determines whether or not we should
00172                 // normalize the results.  Here's some convenience bools:
00173                 bool donorm = (0 == flag%2) ? true : false;
00174                 // the 2x padding is hardcoded for now
00175                 int  npad  = (flag >= 3) ? 2 : 1;  // amount of padding used
00176                 // g may be NULL.  If so, have g point to the same object as f.  In that
00177                 // case we need to be careful later on not to try to delete g's workspace
00178                 // as well as f's workspace, since they will be the same.
00179                 bool  gexists = true;
00180                 if (!g) { g = f; gexists = false; }
00181                 if ( f->is_complex() || g->is_complex() ) {
00182                         // Fourier input only allowed for circulant
00183                         if (CIRCULANT != flag) {
00184                                 LOGERR("Cannot perform normalization or padding on Fourier type.");
00185                                 throw InvalidValueException(flag, "Cannot perform normalization or padding on Fourier type.");
00186                         }
00187                 }
00188                 // These are actual dimensions of f (and real-space sizes for ny and nz)
00189                 int nx  = f->get_xsize();
00190                 int ny  = f->get_ysize();
00191                 int nz  = f->get_zsize();
00192                 // We manifestly assume no zero-padding here, just the 
00193                 // necessary extension along x for the fft
00194                 if (!f->is_real()) nx = (nx - 2 + (f->is_fftodd() ? 1 : 0)); 
00195 
00196                 // these are padded dimensions
00197                 const int nxp = npad*nx;
00198                 const int nyp = (ny > 1) ? npad*ny : 1; // don't pad y for 1-d image
00199                 const int nzp = (nz > 1) ? npad*nz : 1; // don't pad z for 2-d image
00200 
00201                 // now one half of the padded, fft-extended size along x
00202                 const int lsd2 = (nxp + 2 - nxp%2) / 2; 
00203                 // The [padded] fft-extended fourier version of f is fp.
00204 
00205                 EMData* fp = NULL;
00206                 if (f->is_complex()) { 
00207                         // If f is already a fourier object then fp is a copy of f.
00208                         // (The fp workspace is modified, so we copy f to keep f pristine.)
00209                         fp=f->copy();
00210                 } else {
00211                         //  [normalize] [pad] compute fft
00212                         fp = f->norm_pad(donorm, npad);
00213                         fp->do_fft_inplace();
00214                 }
00215                 // The [padded] fft-extended version of g is gp.
00216                 EMData* gp = NULL;
00217                 if(f==g) {
00218                         // g is an alias for f, so gp should be an alias for fp
00219                         gp=fp;
00220                 } else if (g->is_complex()) {
00221                         // g is already a Fourier object, so gp is just an alias for g
00222                         // (The gp workspace is not modified, so we don't need a copy.)
00223                         gp = g;
00224                 } else {
00225                         // normal case: g is real and different from f, so compute gp
00226                         gp = g->norm_pad(donorm, npad);
00227                         gp->do_fft_inplace();
00228                 }
00229                 // Get complex matrix views of fp and gp; matrices start from 1 (not 0)
00230                 fp->set_array_offsets(1,1,1);
00231                 gp->set_array_offsets(1,1,1);
00232                 
00233                 // If the center flag is true, put the center of the correlation in the middle
00234                 // If it is false, put it in (0,0), this approach saves time, but it is diffcult to manage the result
00235                 if (center) {
00236                         //  Multiply two functions (the real work of this routine)
00237                         int itmp = nx/2;
00238                         //float sx  = float(-twopi*float(itmp)/float(nxp));
00239                         float sxn = 2*float(itmp)/float(nxp);
00240                         float sx = -M_PI*sxn;
00241                         itmp = ny/2;
00242                         //float sy  = float(-twopi*float(itmp)/float(nyp));
00243                         float syn = 2*float(itmp)/float(nyp);
00244                         float sy = -M_PI*syn;
00245                         itmp = nz/2;
00246                         //float sz  = float(-twopi*float(itmp)/float(nzp));
00247                         float szn = 2*float(itmp)/float(nzp);
00248                         float sz = -M_PI*szn;
00249                         if ( nx%2==0 && (ny%2==0 || ny==1 ) && (nz%2==0 || nz==1 ) ) {
00250                                 switch (ptype) {
00251                                         case AUTOCORRELATION:
00252                                         // fpmat := |fpmat|^2
00253                                         // Note nxp are padded dimensions
00254                                                 for (int iz = 1; iz <= nzp; iz++) {
00255                                                         for (int iy = 1; iy <= nyp; iy++) {
00256                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00257                                                                         float fpr = real(fp->cmplx(ix,iy,iz));
00258                                                                         float fpi = imag(fp->cmplx(ix,iy,iz));
00259                                                                         fp->cmplx(ix,iy,iz) = complex<float>(fpr*fpr+fpi*fpi, 0.0f);
00260                                                                 }
00261                                                         }
00262                                                 }
00263                                                 break;
00264                                         case SELF_CORRELATION:
00265                                         // fpmat:=|fpmat|
00266                                         // Note nxp are padded dimensions
00267                                                 for (int iz = 1; iz <= nzp; iz++) {
00268                                                         for (int iy = 1; iy <= nyp; iy++) {
00269                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00270                                                                         fp->cmplx(ix,iy,iz) = complex<float>(abs(fp->cmplx(ix,iy,iz)), 0.0f);
00271                                                                 }
00272                                                         }
00273                                                 }
00274                                                 break;
00275                                         case CORRELATION:
00276                                         // fpmat:=fpmat*conjg(gpmat)
00277                                         // Note nxp are padded dimensions
00278                                                 for (int iz = 1; iz <= nzp; iz++) {
00279                                                         for (int iy = 1; iy <= nyp; iy++) {
00280                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00281                                                                         fp->cmplx(ix,iy,iz) *= conj(gp->cmplx(ix,iy,iz));
00282                                                                 }
00283                                                         }
00284                                                 }
00285                                         break;
00286                                         case CONVOLUTION:
00287                                         // fpmat:=fpmat*gpmat
00288                                         // Note nxp are padded dimensions
00289                                                 for (int iz = 1; iz <= nzp; iz++) {
00290                                                         for (int iy = 1; iy <= nyp; iy++) {
00291                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00292                                                                         fp->cmplx(ix,iy,iz) *= gp->cmplx(ix,iy,iz);
00293                                                                 }
00294                                                         }
00295                                                 }
00296                                                 break;
00297                                         default:
00298                                                 LOGERR("Illegal option in Fourier Product");
00299                                                 throw InvalidValueException(ptype, "Illegal option in Fourier Product");
00300                                 }                                       
00301                                 for (int iz = 1; iz <= nzp; iz++) {
00302                                         for (int iy = 1; iy <= nyp; iy++) {
00303                                                 for (int ix = (iz+iy+1)%2+1; ix <= lsd2; ix+=2) {
00304                                                         fp->cmplx(ix,iy,iz) = -fp->cmplx(ix,iy,iz);
00305                                                 }
00306                                         }
00307                                 }
00308                         } else {                        
00309                                 switch (ptype) {
00310                                         case AUTOCORRELATION:
00311                                         // fpmat := |fpmat|^2
00312                                         // Note nxp are padded dimensions
00313                                                 for (int iz = 1; iz <= nzp; iz++) {
00314                                                 int jz=iz-1; if(jz>nzp/2) jz=jz-nzp; float argz=sz*jz;
00315                                                         for (int iy = 1; iy <= nyp; iy++) {
00316                                                         int jy=iy-1; if(jy>nyp/2) jy=jy-nyp; float argy=sy*jy+argz;
00317                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00318                                                                         int jx=ix-1; float arg=sx*jx+argy;
00319                                                                         float fpr = real(fp->cmplx(ix,iy,iz));
00320                                                                         float fpi = imag(fp->cmplx(ix,iy,iz));
00321                                                                         fp->cmplx(ix,iy,iz)= (fpr*fpr + fpi*fpi) *std::complex<float>(cos(arg),sin(arg));
00322                                                                 }
00323                                                         }
00324                                                 }
00325                                                 break;
00326                                         case SELF_CORRELATION:
00327                                         // fpmat:=|fpmat|
00328                                         // Note nxp are padded dimensions
00329                                                 for (int iz = 1; iz <= nzp; iz++) {
00330                                                 int jz=iz-1; if(jz>nzp/2) jz=jz-nzp; float argz=sz*jz;
00331                                                         for (int iy = 1; iy <= nyp; iy++) {
00332                                                         int jy=iy-1; if(jy>nyp/2) jy=jy-nyp; float argy=sy*jy+argz;
00333                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00334                                                                         int jx=ix-1; float arg=sx*jx+argy;
00335                                                                         fp->cmplx(ix,iy,iz) = abs(fp->cmplx(ix,iy,iz)) *std::complex<float>(cos(arg),sin(arg));
00336                                                                 }
00337                                                         }
00338                                                 }
00339                                                 break;
00340                                         case CORRELATION:
00341                                         // fpmat:=fpmat*conjg(gpmat)
00342                                         // Note nxp are padded dimensions
00343                                                 for (int iz = 1; iz <= nzp; iz++) {
00344                                                 int jz=iz-1; if(jz>nzp/2) jz=jz-nzp; float argz=sz*jz;
00345                                                         for (int iy = 1; iy <= nyp; iy++) {
00346                                                         int jy=iy-1; if(jy>nyp/2) jy=jy-nyp; float argy=sy*jy+argz;
00347                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00348                                                                         int jx=ix-1; float arg=sx*jx+argy;
00349                                                                         fp->cmplx(ix,iy,iz) *= conj(gp->cmplx(ix,iy,iz)) *std::complex<float>(cos(arg),sin(arg));
00350                                                                 }
00351                                                         }
00352                                                 }
00353                                         break;
00354                                         case CONVOLUTION:
00355                                         // fpmat:=fpmat*gpmat
00356                                         // Note nxp are padded dimensions
00357                                                 if(npad == 1) {
00358                                                         sx -= 4*(nx%2)/float(nx);
00359                                                         sy -= 4*(ny%2)/float(ny);
00360                                                         sz -= 4*(nz%2)/float(nz);
00361                                                 }
00362                                                 for (int iz = 1; iz <= nzp; iz++) {
00363                                                         int jz=iz-1; if(jz>nzp/2) jz=jz-nzp; float argz=sz*jz;
00364                                                         for (int iy = 1; iy <= nyp; iy++) {
00365                                                                 int jy=iy-1; if(jy>nyp/2) jy=jy-nyp; float argy=sy*jy+argz;
00366                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00367                                                                         int jx=ix-1; float arg=sx*jx+argy;
00368                                                                         fp->cmplx(ix,iy,iz) *= gp->cmplx(ix,iy,iz) *std::complex<float>(cos(arg),sin(arg));
00369                                                                 }
00370                                                         }
00371                                                 }
00372                                                 break;
00373                                         default:
00374                                                 LOGERR("Illegal option in Fourier Product");
00375                                                 throw InvalidValueException(ptype, "Illegal option in Fourier Product");
00376                                 }
00377                         }
00378                 } else {
00379                         // If the center flag is false, then just do basic multiplication
00380                         switch (ptype) {
00381                                 case AUTOCORRELATION:
00382                                         for (int iz = 1; iz <= nzp; iz++) {
00383                                                 for (int iy = 1; iy <= nyp; iy++) {
00384                                                         for (int ix = 1; ix <= lsd2; ix++) {
00385                                                                 float fpr = real(fp->cmplx(ix,iy,iz));
00386                                                                 float fpi = imag(fp->cmplx(ix,iy,iz));
00387                                                                 fp->cmplx(ix,iy,iz) = complex<float>(fpr*fpr+fpi*fpi, 0.0f);
00388                                                         }
00389                                                 }
00390                                         }
00391                                         break;
00392                                 case SELF_CORRELATION:
00393                                         for (int iz = 1; iz <= nzp; iz++) {
00394                                                 for (int iy = 1; iy <= nyp; iy++) {
00395                                                         for (int ix = 1; ix <= lsd2; ix++) {
00396                                                                 fp->cmplx(ix,iy,iz) = complex<float>(abs(fp->cmplx(ix,iy,iz)), 0.0f);
00397                                                         }
00398                                                 }
00399                                         }
00400                                         break;
00401                                 case CORRELATION:
00402                                         //phase_mult = 1;
00403                                         for (int iz = 1; iz <= nzp; iz++) {
00404                                                 for (int iy = 1; iy <= nyp; iy++) {
00405                                                         for (int ix = 1; ix <= lsd2; ix++) {
00406                                                                 fp->cmplx(ix,iy,iz)*= conj(gp->cmplx(ix,iy,iz));
00407                                                         }
00408                                                 }
00409                                         }
00410                                         break;
00411                                 case CONVOLUTION:
00412                                         if(npad == 1) {
00413                                                 float sx = -M_PI*2*(nx%2)/float(nx);
00414                                                 float sy = -M_PI*2*(ny%2)/float(ny);
00415                                                 float sz = -M_PI*2*(nz%2)/float(nz);
00416                                                 for (int iz = 1; iz <= nzp; iz++) {
00417                                                         int jz=iz-1; if(jz>nzp/2) jz=jz-nzp; float argz=sz*jz;
00418                                                         for (int iy = 1; iy <= nyp; iy++) {
00419                                                                 int jy=iy-1; if(jy>nyp/2) jy=jy-nyp; float argy=sy*jy+argz;
00420                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00421                                                                         int jx=ix-1; float arg=sx*jx+argy;
00422                                                                         fp->cmplx(ix,iy,iz) *= gp->cmplx(ix,iy,iz) *std::complex<float>(cos(arg),sin(arg));
00423                                                                 }
00424                                                         }
00425                                                 }
00426                                         } else {
00427                                                 for (int iz = 1; iz <= nzp; iz++) {
00428                                                         for (int iy = 1; iy <= nyp; iy++) {
00429                                                                 for (int ix = 1; ix <= lsd2; ix++) {
00430                                                                         fp->cmplx(ix,iy,iz)*= gp->cmplx(ix,iy,iz);
00431                                                                 }
00432                                                         }
00433                                                 }
00434                                         }
00435                                         break;
00436                                 default:
00437                                         LOGERR("Illegal option in Fourier Product");
00438                                         throw InvalidValueException(ptype, "Illegal option in Fourier Product");
00439                         }
00440                 }
00441                 // Now done w/ gp, so let's get rid of it (if it's not an alias of fp or simply g was complex on input);
00442                 if (gexists && (f != g) && (!g->is_complex())) {
00443                         if( gp ) {
00444                                 delete gp;
00445                                 gp = 0;
00446                         }
00447                 }
00448                 // back transform
00449                 fp->do_ift_inplace();
00450                 if(center && npad ==2)  fp->depad();
00451                 else                    fp->depad_corner();
00452 
00453                 //vector<int> saved_offsets = fp->get_array_offsets();  I do not know what the meaning of it was, did not work anyway PAP
00454                 fp->set_array_offsets(1,1,1);
00455 
00456                 normfact = (nxp/nx)*(nyp/ny)*(nzp/nz);  // Normalization factor for the padded operations
00457                 if(normfact>1) {
00458                         for (int iz = 1; iz <= nz; iz++) for (int iy = 1; iy <= ny; iy++) for (int ix = 1; ix <= nx; ix++) (*fp)(ix,iy,iz) *= normfact;
00459                 }
00460                 // Lag normalization
00461                 if(flag>4)  {
00462                         normfact = nx*ny*nz;  // Normalization factor
00463                         int nxc=nx/2+1, nyc=ny/2+1, nzc=nz/2+1;
00464                         for (int iz = 1; iz <= nz; iz++) {
00465                                 float lagz=float(normfact/(nz-abs(iz-nzc)));
00466                                 for (int iy = 1; iy <= ny; iy++) {
00467                                         float lagyz=lagz/(ny-abs(iy-nyc));
00468                                         for (int ix = 1; ix <= nx; ix++) {
00469                                                 (*fp)(ix,iy,iz) *= lagyz/(nx-abs(ix-nxc));
00470                                         }
00471                                 }
00472                         }       
00473                 }
00474                 //OVER AND OUT
00475                 //fp->set_array_offsets(saved_offsets);  This was strange and did not work, PAP
00476                 fp->set_array_offsets(0,0,0);
00477                 fp->update();
00478                 return fp;
00479         }

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

Definition at line 9742 of file processor.cpp.

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

09743 {
09744         map<string, vector<string> > processor_groups;
09745 
09746         vector <string> processornames = Factory<Processor>::get_list();
09747 
09748         for (size_t i = 0; i < processornames.size(); i++) {
09749                 Processor * f = Factory<Processor>::get(processornames[i]);
09750                 if (dynamic_cast<RealPixelProcessor*>(f) != 0) {
09751                         processor_groups["RealPixelProcessor"].push_back(f->get_name());
09752                 }
09753                 else if (dynamic_cast<BoxStatProcessor*>(f)  != 0) {
09754                         processor_groups["BoxStatProcessor"].push_back(f->get_name());
09755                 }
09756                 else if (dynamic_cast<ComplexPixelProcessor*>(f)  != 0) {
09757                         processor_groups["ComplexPixelProcessor"].push_back(f->get_name());
09758                 }
09759                 else if (dynamic_cast<CoordinateProcessor*>(f)  != 0) {
09760                         processor_groups["CoordinateProcessor"].push_back(f->get_name());
09761                 }
09762                 else if (dynamic_cast<FourierProcessor*>(f)  != 0) {
09763                         processor_groups["FourierProcessor"].push_back(f->get_name());
09764                 }
09765                 else if (dynamic_cast<NewFourierProcessor*>(f)  != 0) {
09766                         processor_groups["FourierProcessor"].push_back(f->get_name());
09767                 }
09768                 else if (dynamic_cast<NormalizeProcessor*>(f)  != 0) {
09769                         processor_groups["NormalizeProcessor"].push_back(f->get_name());
09770                 }
09771                 else {
09772                         processor_groups["Others"].push_back(f->get_name());
09773                 }
09774         }
09775 
09776         return processor_groups;
09777 }

bool isZero double  in_d,
double  in_dEps = 1e-16
[inline]
 

Definition at line 48 of file vecmath.h.

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

00049         { 
00050             return (in_d < in_dEps && in_d > -in_dEps)? true : false; 
00051         }

double length const Vector4 &  v  )  [inline]
 

Definition at line 688 of file vecmath.h.

References EMAN::Vector4::length(), and v.

Referenced by EMAN::Vector4::normalize(), EMAN::Vec2< Type >::normalize(), and EMAN::Vec3< int >::normalize().

00688 { return v.length(); }

double length const Vector3 &  v  )  [inline]
 

Definition at line 317 of file vecmath.h.

References EMAN::Vector3::length(), and v.

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

00317 { return v.length(); }

Point3 lerp const Point3 &  p0,
const Point3 &  p1,
double  dT
[inline]
 

Definition at line 406 of file vecmath.h.

00407         {
00408             const double dTMinus = 1.0 - dT;
00409             return Point3( dTMinus * p0[0] + dT * p1[0], dTMinus * p0[1] + dT * p1[1], dTMinus * p0[2] + dT * p1[2] ); 
00410         }

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

Definition at line 8115 of file processor.cpp.

References Assert, and EMAN::EMData::process_inplace().

08116 {
08117         Assert(image != 0);
08118         Assert(processornames.size() > 0);
08119 
08120         for (size_t i = 0; i < processornames.size(); i++) {
08121                 image->process_inplace(processornames[i]);
08122         }
08123         return 0;
08124 }

Vector4 operator * const double  s,
const Vector4 &  v
[inline]
 

Definition at line 684 of file vecmath.h.

References v.

00684                                                                      {
00685             return Vector4( v[0] * s, v[1] * s, v[2] * s, v[3] * s );
00686         }

Point3 operator * const Point3 &  p,
const Matrix3 &  m
[inline]
 

Definition at line 578 of file vecmath.h.

00578                                                                    {
00579             return Point3(m(0,0) * p[0] + m(1,0) * p[1] + m(2,0) * p[2],
00580                           m(0,1) * p[0] + m(1,1) * p[1] + m(2,1) * p[2],
00581                           m(0,2) * p[0] + m(1,2) * p[1] + m(2,2) * p[2]);
00582         }

Vector3 operator * const Vector3 &  v,
const Matrix3 &  m
[inline]
 

Definition at line 571 of file vecmath.h.

References v.

00571                                                                      {
00572             return Vector3(m(0,0) * v[0] + m(1,0) * v[1] + m(2,0) * v[2],
00573                            m(0,1) * v[0] + m(1,1) * v[1] + m(2,1) * v[2],
00574                            m(0,2) * v[0] + m(1,2) * v[1] + m(2,2) * v[2]);
00575         }

Vector3 operator * const double  s,
const Vector3 &  v
[inline]
 

Definition at line 305 of file vecmath.h.

References v.

00305                                                                      {
00306             return Vector3( v[0] * s, v[1] * s, v[2] * s );
00307         }

ScreenVector operator * const double  s,
const ScreenVector &  v
[inline]
 

Definition at line 133 of file vecmath.h.

References v.

00133                                                                                {
00134             return ScreenVector( (int)(v[0] * s), (int)(v[1] * s) );
00135         }

template<typename Type, typename Type2>
Vec2<Type> operator * const Vec2< Type > &  v,
const Type2 &  d
[inline]
 

Definition at line 826 of file vec3.h.

References v.

00826                                                                           {
00827         // Preserve the vector type
00828                 Vec2<Type> v1(v);
00829                 v1 *= d;
00830                 return v1;
00831         }

template<typename Type, typename Type2>
Vec2<Type2> operator * const Type &  d,
const Vec2< Type2 > &  v
[inline]
 

Definition at line 817 of file vec3.h.

References v.

00818         {
00819                 // Preserve the vector type
00820                 Vec2<Type2> v1(v);
00821                 v1 *= d;
00822                 return v1;
00823         }

template<typename Type, typename Type2>
Type operator * const Vec2< Type > &  v1,
const Vec2< Type2 > &  v2
[inline]
 

Definition at line 811 of file vec3.h.

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

00812         {
00813                 return v1.dot(v2);
00814         }

template<typename Type, typename Type2>
Vec3<Type> operator * const Vec3< Type > &  v,
const Type2 &  d
[inline]
 

Definition at line 448 of file vec3.h.

References v.

00448                                                                           {
00449                 // Preserve the vector type
00450                 Vec3<Type> v1(v);
00451                 v1 *= d;
00452                 return v1;
00453         }

template<typename Type, typename Type2>
Vec3<Type2> operator * const Type &  d,
const Vec3< Type2 > &  v
[inline]
 

Definition at line 439 of file vec3.h.

References v.

00440         {
00441                 // Preserve the vector type
00442                 Vec3<Type2> v1(v);
00443                 v1 *= d;
00444                 return v1;
00445         }

template<typename Type, typename Type2>
Type operator * const Vec3< Type > &  v1,
const Vec3< Type2 > &  v2
[inline]
 

Definition at line 433 of file vec3.h.

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

00434         {
00435                 return v1.dot(v2);
00436         }

template<typename Type>
Vec2f operator * const Transform3D &  M,
const Vec2< Type > &  v
 

Definition at line 899 of file transform.h.

References v, Vec2f, x, and y.

00900         {
00901 //      This is the  left multiplication of a vector, v by a matrix M
00902                 float x = M[0][0] * v[0] + M[0][1] * v[1] + M[0][3] ;
00903                 float y = M[1][0] * v[0] + M[1][1] * v[1] + M[1][3];
00904                 return Vec2f(x, y);
00905         }

template<typename Type>
Vec3f operator * const Transform3D &  M,
const Vec3< Type > &  v
 

Definition at line 888 of file transform.h.

References v, Vec3f, x, and y.

00889         {
00890 //      This is the  left multiplication of a vector, v by a matrix M
00891                 float x = M[0][0] * v[0] + M[0][1] * v[1] + M[0][2] * v[2] + M[0][3];
00892                 float y = M[1][0] * v[0] + M[1][1] * v[1] + M[1][2] * v[2] + M[1][3];
00893                 float z = M[2][0] * v[0] + M[2][1] * v[1] + M[2][2] * v[2] + M[2][3];
00894                 return Vec3f(x, y, z);
00895         }

template<typename Type>
Vec3f operator * const Vec3< Type > &  v,
const Transform3D &  M
 

Definition at line 878 of file transform.h.

References v, Vec3f, x, and y.

00879         {
00880 //               This is the right multiplication of a row vector, v by a transform3D matrix M
00881                 float x = v[0] * M[0][0] + v[1] * M[1][0] + v[2] * M[2][0] ;
00882                 float y = v[0] * M[0][1] + v[1] * M[1][1] + v[2] * M[2][1];
00883                 float z = v[0] * M[0][2] + v[1] * M[1][2] + v[2] * M[2][2];
00884                 return Vec3f(x, y, z);
00885         }

Transform3D EMAN::operator * const Transform3D M1,
const Transform3D M2
 

Definition at line 1532 of file transform.cpp.

01533 {
01534 //       This is the  left multiplication of a matrix M1 by a matrix M2; that is M2*M1
01535 //       It returns a new matrix
01536         Transform3D resultant;
01537         for (int i=0; i<3; i++) {
01538                 for (int j=0; j<4; j++) {
01539                         resultant[i][j] = M2[i][0] * M1[0][j] +  M2[i][1] * M1[1][j] + M2[i][2] * M1[2][j];
01540                 }
01541                 resultant[i][3] += M2[i][3];  // add on the new translation (not included above)
01542         }
01543 
01544         for (int j=0; j<3; j++) {
01545                 resultant[3][j] = M2[3][j];
01546         }
01547 
01548         return resultant; // This will have the post_trans of M2
01549 }

template<typename Type>
Vec3f 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 473 of file transform.h.

References v, Vec3f, x, and y.

00474         {
00475                 float x = v[0] * M[0][0] + v[1] * M[1][0] + v[2] * M[2][0] ;
00476                 float y = v[0] * M[0][1] + v[1] * M[1][1] + v[2] * M[2][1];
00477                 float z = v[0] * M[0][2] + v[1] * M[1][2] + v[2] * M[2][2];
00478                 return Vec3f(x, y, z);
00479         }

template<typename Type>
Vec2f operator * const Transform &  M,
const Vec2< Type > &  v
 

Matrix times Vector, a pure mathematical operation.

Definition at line 464 of file transform.h.

References EMAN::Transform::transform(), v, and Vec2f.

00465         {
00466                 return M.transform(v);
00467         }

template<typename Type>
Vec3f operator * const Transform &  M,
const Vec3< Type > &  v
 

Matrix times Vector, a pure mathematical operation.

Definition at line 457 of file transform.h.

References EMAN::Transform::transform(), v, and Vec3f.

00458         {
00459                 return M.transform(v);
00460         }

Transform EMAN::operator * const Transform M2,
const Transform M1
 

Matrix times Matrix, a pure mathematical operation.

Definition at line 1149 of file transform.cpp.

01150 {
01151         Transform result;
01152         for (int i=0; i<3; i++) {
01153                 for (int j=0; j<4; j++) {
01154                         result[i][j] = M2[i][0] * M1[0][j] +  M2[i][1] * M1[1][j] + M2[i][2] * M1[2][j];
01155                 }
01156                 result[i][3] += M2[i][3];
01157         }
01158 
01159         return result;
01160 }

Quaternion EMAN::operator * float  s,
const Quaternion q
 

Definition at line 337 of file quaternion.cpp.

00338 {
00339         Quaternion q1 = q;
00340         q1 *= s;
00341         return q1;
00342 }

Quaternion EMAN::operator * const Quaternion q,
float  s
 

Definition at line 330 of file quaternion.cpp.

00331 {
00332         Quaternion q1 = q;
00333         q1 *= s;
00334         return q1;
00335 }

Quaternion EMAN::operator * const Quaternion q1,
const Quaternion q2
 

Definition at line 323 of file quaternion.cpp.

References q.

00324 {
00325         Quaternion q = q1;
00326         q *= q2;
00327         return q;
00328 }

EMData * EMAN::operator * const EMData a,
const EMData b
 

Definition at line 2852 of file emdata.cpp.

References b, EMAN::EMData::copy(), and EMAN::EMData::mult().

02853 {
02854         EMData * r = a.copy();
02855         r->mult(b);
02856         return r;
02857 }

EMData * EMAN::operator * float  n,
const EMData em
 

Definition at line 2811 of file emdata.cpp.

References EMAN::EMData::copy(), and EMAN::EMData::mult().

02812 {
02813         EMData * r = em.copy();
02814         r->mult(n);
02815         return r;
02816 }

EMData * EMAN::operator * const EMData em,
float  n
 

Definition at line 2781 of file emdata.cpp.

References EMAN::EMData::copy(), and EMAN::EMData::mult().

02782 {
02783         EMData* r = em.copy();
02784         r ->mult(n);
02785         return r;
02786 }

template<typename Type, typename Type2>
bool operator!= const Vec2< Type > &  v1,
const Vec2< Type2 > &  v2
[inline]
 

Definition at line 859 of file vec3.h.

00859                                                                              {
00860                 if (v1[0] != v2[0] || v1[1] != v2[1] ) {
00861                         return true;
00862                 }
00863                 return false;
00864         }

template<typename Type, typename Type2>
bool operator!= const Vec3< Type > &  v1,
const Vec3< Type2 > &  v2
[inline]
 

Definition at line 481 of file vec3.h.

00481                                                                              {
00482                 if (v1[0] != v2[0] || v1[1] != v2[1] || v1[2] != v2[2]) {
00483                         return true;
00484                 }
00485                 return false;
00486         }

bool EMAN::operator!= const Quaternion q1,
const Quaternion q2
 

Definition at line 370 of file quaternion.cpp.

00371 {
00372         return (!(q1 == q2));
00373 }

bool EMAN::operator!= const Pixel p1,
const Pixel p2
 

Definition at line 62 of file geometry.cpp.

00063 {
00064         return !(p1 == p2);
00065 }

bool EMAN::operator!= const Dict d1,
const Dict d2
 

Definition at line 903 of file emobject.cpp.

00904 {
00905         return !(d1 == d2);
00906 }

bool EMAN::operator!= const EMObject e1,
const EMObject e2
 

Definition at line 759 of file emobject.cpp.

00760 {
00761         return !(e1 == e2);
00762 }

template<typename Type, typename Type2>
Vec2<Type> operator+ const Vec2< Type > &  v,
const Type2 &  n
[inline]
 

Definition at line 782 of file vec3.h.

References v.

00783         {
00784                 Vec2<Type> v1(v);
00785                 v1 += n;
00786                 return v1;
00787         }

template<typename Type, typename Type2>
Vec2<Type> operator+ const Vec2< Type > &  v1,
const Vec2< Type2 > &  v2
[inline]
 

Definition at line 776 of file vec3.h.

00777         {
00778                 return Vec2<Type>(static_cast<Type>(v1[0] + v2[0]), static_cast<Type>(v1[1] + v2[1]));;
00779         }

template<typename Type, typename Type2>
Vec3<Type> operator+ const Vec3< Type > &  v,
const Type2 &  n
[inline]
 

Definition at line 388 of file vec3.h.

References v.

00389         {
00390                 Vec3<Type> v1(v);
00391                 v1 += n;
00392                 return v1;
00393         }

template<typename Type, typename Type2>
Vec3<Type> operator+ const Vec3< Type > &  v1,
const Vec3< Type2 > &  v2
[inline]
 

Definition at line 381 of file vec3.h.

00382         {
00383 
00384                 return Vec3<Type>(static_cast<Type>(v1[0] + v2[0]), static_cast<Type>(v1[1] + v2[1]),static_cast<Type>(v1[2] + v2[2]));;
00385         }

Quaternion EMAN::operator+ const Quaternion q1,
const Quaternion q2
 

Definition at line 308 of file quaternion.cpp.

References q.

00309 {
00310         Quaternion q = q1;
00311         q += q2;
00312         return q;
00313 }

EMData * EMAN::operator+ const EMData a,
const EMData b
 

Definition at line 2838 of file emdata.cpp.

References EMAN::EMData::add(), b, and EMAN::EMData::copy().

02839 {
02840         EMData * r = a.copy();
02841         r->add(b);
02842         return r;
02843 }

EMData * EMAN::operator+ float  n,
const EMData em
 

Definition at line 2796 of file emdata.cpp.

References EMAN::EMData::add(), and EMAN::EMData::copy().

02797 {
02798         EMData * r = em.copy();
02799         r->add(n);
02800         return r;
02801 }

EMData * EMAN::operator+ const EMData em,
float  n
 

Definition at line 2767 of file emdata.cpp.

References EMAN::EMData::add(), and EMAN::EMData::copy().

02768 {
02769         EMData * r = em.copy();
02770         r->add(n);
02771         return r;
02772 }

template<typename Type>
Vec2<Type> operator- const Vec2< Type > &  v  )  [inline]
 

Definition at line 804 of file vec3.h.

References v.

00805         {
00806                 return Vec2<Type>(-v[0],-v[1]);
00807         }

template<typename Type, typename Type2>
Vec2<Type> operator- const Vec2< Type > &  v,
const Type2 &  n
[inline]
 

Definition at line 796 of file vec3.h.

References v.

00797         {
00798                 Vec2<Type> v1(v);
00799                 v1 -= n;
00800                 return v1;
00801         }

template<typename Type, typename Type2>
Vec2<Type> operator- const Vec2< Type > &  v1,
const Vec2< Type2 > &  v2
[inline]
 

Definition at line 790 of file vec3.h.

00791         {
00792                 return Vec2<Type>(static_cast<Type>(v1[0] - v2[0]),     static_cast<Type>(v1[1] - v2[1]));
00793         }

template<typename Type>
Vec3<Type> operator- const Vec3< Type > &  v  )  [inline]
 

Definition at line 419 of file vec3.h.

References v.

00420         {
00421                 return Vec3<Type>(-v[0],-v[1],-v[2]);
00422         }

template<typename Type, typename Type2>
Vec3<Type> operator- const Vec3< Type > &  v,
const Type2 &  n
[inline]
 

Definition at line 412 of file vec3.h.

References v.

00413         {
00414                 Vec3<Type> v1(v);
00415                 v1 -= n;
00416                 return v1;
00417         }

template<typename Type, typename Type2>
Vec3<Type> operator- const Vec3< Type > &  v1,
const Vec3< Type2 > &  v2
[inline]
 

Definition at line 404 of file vec3.h.

00405         {
00406                 return Vec3<Type>(static_cast<Type>(v1[0] - v2[0]),
00407                                                   static_cast<Type>(v1[1] - v2[1]),
00408                                                   static_cast<Type>(v1[2] - v2[2]));
00409         }

Quaternion EMAN::operator- const Quaternion q1,
const Quaternion q2
 

Definition at line 315 of file quaternion.cpp.

References q.

00316 {
00317         Quaternion q = q1;
00318         q -= q2;
00319         return q;
00320 }

IntPoint EMAN::operator- const IntPoint p  ) 
 

Definition at line 41 of file geometry.cpp.

00042 {
00043         return IntPoint(-p[0],-p[1],-p[2]);
00044 }

EMData * EMAN::operator- const EMData a,
const EMData b
 

Definition at line 2845 of file emdata.cpp.

References b, EMAN::EMData::copy(), and EMAN::EMData::sub().

02846 {
02847         EMData * r = a.copy();
02848         r->sub(b);
02849         return r;
02850 }

EMData * EMAN::operator- float  n,
const EMData em
 

Definition at line 2803 of file emdata.cpp.

References EMAN::EMData::add(), EMAN::EMData::copy(), and EMAN::EMData::mult().

02804 {
02805         EMData * r = em.copy();
02806         r->mult(-1.0f);
02807         r->add(n);
02808         return r;
02809 }

EMData * EMAN::operator- const EMData em,
float  n
 

Definition at line 2774 of file emdata.cpp.

References EMAN::EMData::copy(), and EMAN::EMData::sub().

Referenced by rsub().

02775 {
02776         EMData* r = em.copy();
02777         r->sub(n);
02778         return r;
02779 }

template<typename Type, typename Type2>
Vec2<Type> operator/ const Vec2< Type > &  v,
const Type2 &  d
[inline]
 

Definition at line 843 of file vec3.h.

References v.

00843                                                                           {
00844                 // Preserve the vector type
00845                 Vec2<Type> v1(v);
00846                 v1 /= d;
00847                 return v1;
00848         }

template<typename Type, typename Type2>
Vec2<Type2> operator/ const Type &  d,
const Vec2< Type2 > &  v
[inline]
 

Definition at line 834 of file vec3.h.

References v.

00835         {
00836         // Preserve the vector type
00837                 Vec2<Type2> v1(v);
00838                 v1 /= d;
00839                 return v1;
00840         }

template<typename Type, typename Type2>
Vec3<Type> operator/ const Vec3< Type > &  v,
const Type2 &  d
[inline]
 

Definition at line 465 of file vec3.h.

References v.

00465                                                                           {
00466                 // Preserve the vector type
00467                 Vec3<Type> v1(v);
00468                 v1 /= d;
00469                 return v1;
00470         }

template<typename Type, typename Type2>
Vec3<Type2> operator/ const Type &  d,
const Vec3< Type2 > &  v
[inline]
 

Definition at line 456 of file vec3.h.

References v.

00457         {
00458                 // Preserve the vector type
00459                 Vec3<Type2> v1(v);
00460                 v1 /= d;
00461                 return v1;
00462         }

Quaternion EMAN::operator/ const Quaternion q1,
const Quaternion q2
 

Definition at line 344 of file quaternion.cpp.

References q.

00345 {
00346         Quaternion q = q1;
00347         q /= q2;
00348         return q;
00349 }

EMData * EMAN::operator/ const EMData a,
const EMData b
 

Definition at line 2859 of file emdata.cpp.

References b, EMAN::EMData::copy(), and EMAN::EMData::div().

02860 {
02861         EMData * r = a.copy();
02862         r->div(b);
02863         return r;
02864 }

EMData * EMAN::operator/ float  n,
const EMData em
 

Definition at line 2818 of file emdata.cpp.

References EMAN::EMData::copy(), EMAN::EMData::div(), EMAN::EMData::mult(), and EMAN::EMData::to_one().

02819 {
02820         EMData * r = em.copy();
02821         r->to_one();
02822         r->mult(n);
02823         r->div(em);
02824 
02825         return r;
02826 }

EMData * EMAN::operator/ const EMData em,
float  n
 

Definition at line 2788 of file emdata.cpp.

References EMAN::EMData::copy(), and EMAN::EMData::div().

Referenced by rdiv().

02789 {
02790         EMData * r = em.copy();
02791         r->div(n);
02792         return r;
02793 }

bool EMAN::operator< const Pixel p1,
const Pixel p2
 

Definition at line 46 of file geometry.cpp.

References EMAN::Pixel::value.

00047 {
00048         if (p1.value < p2.value) {
00049                 return true;
00050         }
00051         return false;
00052 }

std::ostream& operator<< std::ostream &  os,
const Matrix4 &  m
[inline]
 

Definition at line 952 of file vecmath.h.

References EMAN::Matrix4::row().

00952                                                                         {
00953             os << m.row(0) << std::endl;
00954             os << m.row(1) << std::endl;
00955             os << m.row(2) << std::endl;
00956             os << m.row(3) << std::endl;
00957             return os;
00958         }

std::ostream& operator<< std::ostream &  os,
const Vector4 &  v
[inline]
 

Definition at line 690 of file vecmath.h.

References v.

00690                                                                         {
00691             os << "(" << v[0] << ", " << v[1] << ", " << v[2] << ", " << v[3] << ")";
00692             return os;
00693         }

std::ostream& operator<< std::ostream &  os,
const Matrix3 &  m
[inline]
 

Definition at line 584 of file vecmath.h.

References EMAN::Matrix3::row().

00584                                                                         {
00585             os << m.row(0) << std::endl;
00586             os << m.row(1) << std::endl;
00587             os << m.row(2) << std::endl;
00588             return os;
00589         }

std::ostream& operator<< std::ostream &  os,
const Point3 &  p
[inline]
 

Definition at line 412 of file vecmath.h.

00412                                                                        {
00413             os << "(" << p[0] << ", " << p[1] << ", " << p[2] << ")";
00414             return os;
00415         }

std::ostream& operator<< std::ostream &  os,
const Vector3 &  v
[inline]
 

Definition at line 320 of file vecmath.h.

References v.

00320                                                                         {
00321             os << "(" << v[0] << ", " << v[1] << ", " << v[2] << ")";
00322             return os;
00323         }

std::ostream& operator<< std::ostream &  os,
const ScreenPoint &  p
[inline]
 

Definition at line 200 of file vecmath.h.

00200                                                                             {
00201             os << "(" << p[0] << ", " << p[1] << ")";
00202             return os;
00203         }

std::ostream& operator<< std::ostream &  os,
const ScreenVector &  v
[inline]
 

Definition at line 137 of file vecmath.h.

References v.

00137                                                                              {
00138             os << "(" << v[0] << ", " << v[1] << ")";
00139             return os;
00140         }

template<typename Type, typename Type2>
bool operator== const Vec2< Type > &  v1,
const Vec2< Type2 > &  v2
[inline]
 

Definition at line 851 of file vec3.h.

00851                                                                              {
00852                 if (v1[0] == v2[0] && v1[1] == v2[1] ) {
00853                         return true;
00854                 }
00855                 return false;
00856         }

template<typename Type, typename Type2>
bool operator== const Vec3< Type > &  v1,
const Vec3< Type2 > &  v2
[inline]
 

Definition at line 473 of file vec3.h.

00473                                                                              {
00474                 if (v1[0] == v2[0] && v1[1] == v2[1] && v1[2] == v2[2]) {
00475                         return true;
00476                 }
00477                 return false;
00478         }

bool EMAN::operator== const Quaternion q1,
const Quaternion q2
 

Definition at line 352 of file quaternion.cpp.

References EMAN::Quaternion::as_list().

00353 {
00354         bool result = true;
00355         const float err_limit = 0.00001f;
00356         
00357         vector < float >v1 = q1.as_list();
00358         vector < float >v2 = q2.as_list();
00359 
00360         for (size_t i = 0; i < v1.size(); i++) {
00361                 if (fabs(v1[i] - v2[i]) > err_limit) {
00362                         result = false;
00363                         break;
00364                 }
00365         }
00366 
00367         return result;
00368 }

bool EMAN::operator== const Pixel p1,
const Pixel p2
 

Definition at line 54 of file geometry.cpp.

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

00055 {
00056         if (p1.x == p2.x && p1.y == p2.y && p1.z == p2.z && p1.value == p2.value) {
00057                 return true;
00058         }
00059         return false;
00060 }

bool EMAN::operator== const Dict d1,
const Dict d2
 

Definition at line 897 of file emobject.cpp.

References EMAN::Dict::dict.

00898 {
00899         // Just make use of map's version of operator==
00900         return (d1.dict == d2.dict);
00901 }

bool EMAN::operator== const EMObject e1,
const EMObject e2
 

Definition at line 668 of file emobject.cpp.

References EMAN::EMObject::b, EMAN::EMObject::d, EMAN::EMObject::emdata, EMAN::EMObject::f, EMAN::EMObject::farray, EMAN::EMObject::fp, EMAN::EMObject::iarray, EMAN::EMObject::ip, EMAN::EMObject::n, EMAN::EMObject::str, EMAN::EMObject::strarray, EMAN::EMObject::type, EMAN::EMObject::ui, EMAN::EMObject::vp, and EMAN::EMObject::xydata.

00669 {
00670 
00671         if (e1.type != e2.type) {
00672                 return false;
00673         }
00674 
00675         switch (e1.type) {
00676         case  EMObject::BOOL:
00677                 return (e1.b == e2.b);
00678         break;
00679         case  EMObject::INT:
00680                 return (e1.n == e2.n);
00681         break;
00682         case  EMObject::UNSIGNEDINT:
00683                 return (e1.ui == e2.ui);
00684         break;
00685         case  EMObject::FLOAT:
00686                 return (e1.f == e2.f);
00687         break;
00688         case  EMObject::DOUBLE:
00689                 return (e1.d == e2.d);
00690         break;
00691         case EMObject::CTF:
00692         case  EMObject::STRING:
00693                 return (e1.str == e2.str);
00694         break;
00695         case  EMObject::FLOAT_POINTER:
00696                 return (e1.fp == e2.fp);
00697         break;
00698         case  EMObject::INT_POINTER:
00699                 return (e1.ip == e2.ip);
00700         break;
00701         case  EMObject::VOID_POINTER:
00702                 return (e1.vp == e2.vp);
00703         break;
00704         case  EMObject::EMDATA:
00705                 return (e1.emdata == e2.emdata);
00706         break;
00707         case  EMObject::XYDATA:
00708                 return (e1.xydata == e2.xydata);
00709         break;
00710         case  EMObject::TRANSFORM:
00711         case  EMObject::FLOATARRAY:
00712                 if (e1.farray.size() == e2.farray.size()) {
00713                         for (size_t i = 0; i < e1.farray.size(); i++) {
00714                                 if (e1.farray[i] != e2.farray[i]) {
00715                                         return false;
00716                                 }
00717                         }
00718                         return true;
00719                 }
00720                 else {
00721                         return false;
00722                 }
00723         break;
00724         case  EMObject::INTARRAY:
00725                 if (e1.iarray.size() == e2.iarray.size()) {
00726                         for (size_t i = 0; i < e1.iarray.size(); i++) {
00727                                 if (e1.iarray[i] != e2.iarray[i]) {
00728                                         return false;
00729                                 }
00730                         }
00731                         return true;
00732                 }
00733         break;
00734         case  EMObject::STRINGARRAY:
00735                 if (e1.strarray.size() == e2.strarray.size()) {
00736                         for (size_t i = 0; i < e1.strarray.size(); i++) {
00737                                 if (e1.strarray[i] != e2.strarray[i]) {
00738                                         return false;
00739                                 }
00740                         }
00741                         return true;
00742                 }
00743                 else {
00744                         return false;
00745                 }
00746         break;
00747         case  EMObject::UNKNOWN:
00748                 // UNKNOWN really means "no type" and if two objects both have
00749                 // type UNKNOWN they really are the same
00750                 return (e1.type == e2.type);
00751         break;
00752         default:
00753                 return false;
00754         break;
00755         }
00756         return false;
00757 }

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

Direct Fourier inversion Reconstructor.

Definition at line 1949 of file reconstructor.cpp.

References Assert, EMAN::EMData::average_circ_sub(), EMAN::EMData::center_origin_fft(), checked_delete(), EMAN::EMData::do_fft_inplace(), EMAN::EMData::get_attr_default(), EMAN::Transform::get_trans_2d(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::norm_pad(), nx, ny, EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), t, and Vec2f.

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

01950 {
01951         int nx = slice->get_xsize();
01952         int ny = slice->get_ysize();
01953         int ndim = (ny==1) ? 1 : 2;
01954 
01955         if( ndim==2 && nx!=ny )
01956         {
01957                 // FIXME: What kind of exception should we throw here?
01958                 throw std::runtime_error("Tried to padfft a 2D slice which is not square.");
01959         }
01960 
01961         // process 2D slice or 1D line -- subtract the average outside of the circle, zero-pad, fft extend, and fft
01962         EMData* temp = slice->average_circ_sub();
01963 
01964         Assert( temp != NULL );
01965         EMData* zeropadded = temp->norm_pad( false, npad );
01966         Assert( zeropadded != NULL );
01967         checked_delete( temp );
01968 
01969         zeropadded->do_fft_inplace();
01970         EMData* padfftslice = zeropadded;
01971 
01972         // shift the projection
01973         Vec2f trans = t.get_trans_2d();
01974         float sx = -trans[0];
01975         float sy = -trans[1];
01976         if(sx != 0.0f || sy != 0.0)
01977                 padfftslice->process_inplace("filter.shift", Dict("x_shift", sx, "y_shift", sy, "z_shift", 0.0f));
01978 
01979         int remove = slice->get_attr_default("remove", 0);
01980         padfftslice->set_attr( "remove", remove );
01981 
01982 
01983 
01984         padfftslice->center_origin_fft();
01985         return padfftslice;
01986 }

EMData * EMAN::periodogram EMData f  ) 
 

Definition at line 40 of file fundamentals.cpp.

References EMAN::EMData::cmplx(), EMAN::EMData::copy(), EMAN::EMData::do_fft_inplace(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), imag(), EMAN::EMData::is_complex(), EMAN::EMData::is_fftodd(), EMAN::EMData::norm_pad(), nx, ny, power(), real(), EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::update().

00040                        {
00041         // These are actual dimensions
00042         int nx  = f->get_xsize();
00043         int ny  = f->get_ysize();
00044         int nz  = f->get_zsize();
00045                 // We manifestly assume no zero-padding here, just the 
00046                 // necessary extension along x for the fft
00047 
00048         if (f->is_complex()) nx = (nx - 2 + f->is_fftodd()); // nx is the real-space size of the input image
00049         int lsd2 = (nx + 2 - nx%2) / 2; // Extended x-dimension of the complex image
00050 
00051 //  Process f if real
00052         EMData* fp = NULL;
00053         if(f->is_complex()) fp = f->copy(); // we need to make a full copy so that we don't damage the original
00054         else {
00055                 fp = f->norm_pad(false, 1); // Extend and do the FFT if f is real
00056                 fp->do_fft_inplace();
00057         }
00058         fp->set_array_offsets(1,1,1);
00059 
00060         //  Periodogram: fp:=|fp|**2
00061         for (int iz = 1; iz <= nz; iz++) {
00062                 for (int iy = 1; iy <= ny; iy++) {
00063                         for (int ix = 1; ix <= lsd2; ix++) {
00064                                 float fpr = real(fp->cmplx(ix,iy,iz));
00065                                 float fpi = imag(fp->cmplx(ix,iy,iz));
00066                                 fp->cmplx(ix,iy,iz) = fpr*fpr + fpi*fpi;
00067                         }
00068                 }
00069         }
00070         //  Create power as a 3D array (-n/2:n/2+n%2-1)
00071         int nyt, nzt;
00072         int nx2 = nx/2;
00073         int ny2 = ny/2; if(ny2 == 0) nyt =0; else nyt=ny;
00074         int nz2 = nz/2; if(nz2 == 0) nzt =0; else nzt=nz;
00075         int nx2p = nx2+nx%2;
00076         int ny2p = ny2+ny%2;
00077         int nz2p = nz2+nz%2;
00078         EMData& power = *(new EMData()); // output image
00079         power.set_size(nx, ny, nz);
00080         power.set_array_offsets(-nx2,-ny2,-nz2);
00081 //If instead of preservation of the norm one would prefer to have peak of a PW of a single sine wave equal one
00082 //                             multiply power by the scale below, or the other way around.
00083         float scale = 4.0f/float (nx*nx)/float (ny*ny)/float (nz*nz);
00084         for (int iz = 1; iz <= nz; iz++) {
00085                 int jz=iz-1; 
00086                 if(jz>=nz2p) jz=jz-nzt;
00087                 for (int iy = 1; iy <= ny; iy++) {
00088                         int jy=iy-1; 
00089                         if(jy>=ny2p) jy=jy-nyt;
00090                         for (int ix = 1; ix <= lsd2; ix++) {
00091                                 int jx=ix-1; 
00092                                 if(jx>=nx2p) jx=jx-nx;
00093                                 power(jx,jy,jz) = real(fp->cmplx(ix,iy,iz)) * scale;
00094                         }
00095                 }
00096         }
00097 
00098 //  Create the Friedel related half
00099         int  nzb, nze, nyb, nye, nxb, nxe;
00100         nxb =-nx2+(nx+1)%2;
00101         nxe = nx2-(nx+1)%2;
00102         if(ny2 == 0) {nyb =0; nye = 0;} else {nyb =-ny2+(ny+1)%2; nye = ny2-(ny+1)%2;}
00103         if(nz2 == 0) {nzb =0; nze = 0;} else {nzb =-nz2+(nz+1)%2; nze = nz2-(nz+1)%2;}
00104         for (int iz = nzb; iz <= nze; iz++) {
00105                 for (int iy = nyb; iy <= nye; iy++) {
00106                         for (int ix = 1; ix <= nxe; ix++) { // Note this loop begins with 1 - FFT should create correct Friedel related 0 plane
00107                                 power(-ix,-iy,-iz) = power(ix,iy,iz);
00108                         }
00109                 }
00110         }
00111         if(ny2 != 0)  {
00112                 if(nz2 != 0)  {
00113                         if(nz%2 == 0) {  //if nz even, fix the first slice
00114                                 for (int iy = nyb; iy <= nye; iy++) {
00115                                         for (int ix = nxb; ix <= -1; ix++) { 
00116                                                 power(ix,iy,-nz2) = power(-ix,-iy,-nz2);
00117                                         }
00118                                 }
00119                                 if(ny%2 == 0) {  //if ny even, fix the first line
00120                                         for (int ix = nxb; ix <= -1; ix++) { 
00121                                                 power(ix,-ny2,-nz2) = power(-ix,-ny2,-nz2);
00122                                         }
00123                                 }
00124                         }
00125                 }
00126                 if(ny%2 == 0) {  //if ny even, fix the first column
00127                         for (int iz = nzb; iz <= nze; iz++) {
00128                                 for (int ix = nxb; ix <= -1; ix++) {
00129                                         power(ix,-ny2,-iz) = power(-ix,-ny2,iz);
00130                                 }
00131                         }
00132                 }
00133                 
00134         }
00135                 
00136         if( fp ) {
00137                 delete fp; // avoid a memory leak!
00138                 fp = 0;
00139         }
00140         //power[0][0][0]=power[1][0][0];  //Steve requested the original origin.
00141 
00142         power.update();
00143         power.set_array_offsets(0,0,0);
00144         return &power;
00145 //OVER AND OUT
00146 }

EMData * EMAN::rdiv const EMData em,
float  n
 

Definition at line 2833 of file emdata.cpp.

References operator/().

02834 {
02835         return EMAN::operator/(n, em);
02836 }

EMData * EMAN::rsconvolution EMData f,
EMData K
 

Real-space convolution of two images.

Purpose: Calculate the convolution of two 1-, 2-,
or 3-dimensional images.
Parameters:
[in] f First real-space image object. Image may be 1-, 2-, or 3-dimensional. Image f is not changed.
[in] K Second real-space image object (the convolution Kernel). Image may be 1-, 2-, or 3-dimensional. Image K is not changed.
Returns:
Real-space convolution image.

Definition at line 249 of file rsconvolution.cpp.

References EMAN::EMData::get_array_offsets(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, mult_circ(), mult_internal(), EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), EMAN::EMData::to_zero(), and EMAN::EMData::update().

00249                                                 {//Does not work properly in 3D, corners are not done, PAP 07/16/09
00250                 // Kernel should be the smaller image
00251                 int nxf=f->get_xsize(); int nyf=f->get_ysize(); int nzf=f->get_zsize();
00252                 int nxK=K->get_xsize(); int nyK=K->get_ysize(); int nzK=K->get_zsize();
00253                 if ((nxf<nxK)&&(nyf<nyK)&&(nzf<nzK)) {
00254                         // whoops, f smaller than K
00255                         swap(f,K); swap(nxf,nxK); swap(nyf,nyK); swap(nzf,nzK);
00256                 } else if ((nxK<=nxf)&&(nyK<=nyf)&&(nzK<=nzf)) {
00257                         // that's what it should be, so do nothing
00258                         ;
00259                 } else {
00260                         // incommensurate sizes
00261                         throw ImageDimensionException("input images are incommensurate");
00262                 }
00263                 // Kernel needs to be _odd_ in size
00264                 if ((nxK % 2 != 1) || (nyK % 2 != 1) || (nzK % 2 != 1))
00265                         throw ImageDimensionException("Real-space convolution kernel"
00266                                 " must have odd nx,ny,nz (so the center is well-defined).");
00267                 EMData* result = new EMData();
00268                 result->set_size(nxf, nyf, nzf);
00269                 result->to_zero();
00270                 // kernel corners, need to check for degenerate case
00271                 int kxmin = -nxK/2; int kymin = -nyK/2; int kzmin = -nzK/2;
00272                 int kxmax = (1 == nxK % 2) ? -kxmin : -kxmin - 1;
00273                 int kymax = (1 == nyK % 2) ? -kymin : -kymin - 1;
00274                 int kzmax = (1 == nzK % 2) ? -kzmin : -kzmin - 1;
00275                 vector<int> K_saved_offsets = K->get_array_offsets();
00276                 K->set_array_offsets(kxmin,kymin,kzmin);
00277                 // interior boundaries, need to check for degenerate cases
00278                 int izmin = 0, izmax = 0, iymin = 0, iymax = 0, ixmin = 0, ixmax = 0;
00279                 if (1 != nzf) {
00280                         izmin = -kzmin;
00281                         izmax = nzf - 1 - kzmax;
00282                 }
00283                 if (1 != nyf) {
00284                         iymin = -kymin;
00285                         iymax = nyf - 1 - kymax;
00286                 }
00287                 if (1 != nxf) {
00288                         ixmin = -kxmin;
00289                         ixmax = nxf - 1 - kxmax;
00290                 }
00291                 // interior (no boundary condition issues here)
00292                 for (int iz = izmin; iz <= izmax; iz++) {
00293                         for (int iy = iymin; iy <= iymax; iy++) {
00294                                 for (int ix = ixmin; ix <= ixmax; ix++) {
00295                                         (*result)(ix,iy,iz) =
00296                                                 mult_internal(*K, *f, 
00297                                                                       kzmin, kzmax, kymin, kymax, kxmin, kxmax,
00298                                                                           iz, iy, ix);
00299                                 }
00300                         }
00301                 }
00302                 // corners
00303                 // corner sizes, with checking for degenerate cases
00304                 int sz = (1 == nzK) ? 1 : -kzmin + kzmax;
00305                 int sy = (1 == nyK) ? 1 : -kymin + kymax;
00306                 int sx = (1 == nxK) ? 1 : -kxmin + kxmax;
00307                 // corner starting locations, with checking for degenerate cases
00308                 int zstart = (0 == izmin) ? 0 : izmin - 1;
00309                 int ystart = (0 == iymin) ? 0 : iymin - 1;
00310                 int xstart = (0 == ixmin) ? 0 : ixmin - 1;
00311                 // corners
00312                 for (int cz = 0; cz < sz; cz++) {
00313                         int iz = (zstart - cz) % nzf;
00314                         if (iz < 0) iz += nzf;
00315                         for (int cy = 0; cy < sy; cy++) {
00316                                 int iy = (ystart - cy) % nyf;
00317                                 if (iy < 0) iy += nyf;
00318                                 for (int cx=0; cx < sx; cx++) {
00319                                         int ix = (xstart - cx) % nxf;
00320                                         if (ix < 0) ix += nxf;
00321                                         (*result)(ix,iy,iz) =
00322                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, 
00323                                                                  kymax, kxmin, kxmax,
00324                                                                  nzf, nyf, nxf, iz, iy, ix);
00325                                 }
00326                         }
00327                 }
00328                 // remaining stripes -- should use a more elegant (non-3D-specific) method here
00329                 // ix < ixmin
00330                 for (int ix = 0; ix < ixmin; ix++) {
00331                         for (int iy = iymin; iy <= iymax; iy++) {
00332                                 for (int iz = izmin; iz <= izmax; iz++) {
00333                                         (*result)(ix,iy,iz) =
00334                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00335                                                                  kxmin, kxmax,
00336                                                                  nzf, nyf, nxf, iz, iy, ix);
00337                                 }
00338                         }
00339                 }
00340                 // ix > ixmax
00341                 for (int ix = ixmax+1; ix < nxf; ix++) {
00342                         for (int iy = iymin; iy <= iymax; iy++) {
00343                                 for (int iz = izmin; iz <= izmax; iz++) {
00344                                         (*result)(ix,iy,iz) =
00345                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00346                                                                  kxmin, kxmax,
00347                                                                  nzf, nyf, nxf, iz, iy, ix);
00348                                 }
00349                         }
00350                 }
00351                 // iy < iymin
00352                 for (int iy = 0; iy < iymin; iy++) {
00353                         for (int ix = ixmin; ix <= ixmax; ix++) {
00354                                 for (int iz = izmin; iz <= izmax; iz++) {
00355                                         (*result)(ix,iy,iz) =
00356                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00357                                                                  kxmin, kxmax,
00358                                                                  nzf, nyf, nxf, iz, iy, ix);
00359                                 }
00360                         }
00361                 }
00362                 // iy > iymax
00363                 for (int iy = iymax+1; iy < nyf; iy++) {
00364                         for (int ix = ixmin; ix <= ixmax; ix++) {
00365                                 for (int iz = izmin; iz <= izmax; iz++) {
00366                                         (*result)(ix,iy,iz) =
00367                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00368                                                                  kxmin, kxmax,
00369                                                                  nzf, nyf, nxf, iz, iy, ix);
00370                                 }
00371                         }
00372                 }
00373                 // iz < izmin
00374                 for (int iz = 0; iz < izmin; iz++) {
00375                         for (int ix = ixmin; ix <= ixmax; ix++) {
00376                                 for (int iy = iymin; iy <= iymax; iy++) {
00377                                         (*result)(ix,iy,iz) =
00378                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00379                                                                  kxmin, kxmax,
00380                                                                  nzf, nyf, nxf, iz, iy, ix);
00381                                 }
00382                         }
00383                 }
00384                 // iz > izmax
00385                 for (int iz = izmax+1; iz < nzf; iz++) {
00386                         for (int ix = ixmin; ix <= ixmax; ix++) {
00387                                 for (int iy = iymin; iy <= iymax; iy++) {
00388                                         (*result)(ix,iy,iz) =
00389                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00390                                                                  kxmin, kxmax,
00391                                                                  nzf, nyf, nxf, iz, iy, ix);
00392                                 }
00393                         }
00394                 }
00395                 
00396                 
00397                 // ix < ixmin, iy < iymin
00398                 for (int ix = 0; ix < ixmin; ix++) {
00399                         for (int iy = 0; iy < iymin; iy++) {
00400                                 for (int iz = izmin; iz <= izmax; iz++) {
00401                                         (*result)(ix,iy,iz) =
00402                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00403                                                                  kxmin, kxmax,
00404                                                                  nzf, nyf, nxf, iz, iy, ix);
00405                                 }
00406                         }
00407                 }
00408                 
00409                 // ix < ixmin, iy > iymax
00410                 for (int ix = 0; ix < ixmin; ix++) {
00411                         for (int iy = iymax+1; iy < nyf; iy++) {
00412                                 for (int iz = izmin; iz <= izmax; iz++) {
00413                                         (*result)(ix,iy,iz) =
00414                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00415                                                                  kxmin, kxmax,
00416                                                                  nzf, nyf, nxf, iz, iy, ix);
00417                                 }
00418                         }
00419                 }
00420 
00421         // ix > ixmax, iy < iymin
00422                 for (int ix = ixmax+1; ix < nxf; ix++) {
00423                         for (int iy = 0; iy < iymin; iy++) {
00424                                 for (int iz = izmin; iz <= izmax; iz++) {
00425                                         (*result)(ix,iy,iz) =
00426                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00427                                                                  kxmin, kxmax,
00428                                                                  nzf, nyf, nxf, iz, iy, ix);
00429                                 }
00430                         }
00431                 }
00432                 
00433                 // ix > ixmax, iy > iymax
00434                 for (int ix = ixmax+1; ix < nxf; ix++) {
00435                         for (int iy = iymax+1; iy < nyf; iy++) {
00436                                 for (int iz = izmin; iz <= izmax; iz++) {
00437                                         (*result)(ix,iy,iz) =
00438                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00439                                                                  kxmin, kxmax,
00440                                                                  nzf, nyf, nxf, iz, iy, ix);
00441                                 }
00442                         }
00443                 }
00444 
00445 
00446                 
00447         // ix < ixmin, iz < izmin
00448                 for (int ix = 0; ix < ixmin; ix++) {
00449                         for (int iy = iymin; iy <= iymax; iy++) {
00450                                 for (int iz = 0; iz < izmin; iz++) {
00451                                         (*result)(ix,iy,iz) =
00452                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00453                                                                  kxmin, kxmax,
00454                                                                  nzf, nyf, nxf, iz, iy, ix);
00455                                 }
00456                         }
00457                 }
00458                 
00459                  // ix < ixmin, iz > izmax
00460                 for (int ix = 0; ix < ixmin; ix++) {
00461                         for (int iy = iymin; iy <= iymax; iy++) {
00462                                 for (int iz = izmax+1; iz < nzf; iz++) {
00463                                         (*result)(ix,iy,iz) =
00464                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00465                                                                  kxmin, kxmax,
00466                                                                  nzf, nyf, nxf, iz, iy, ix);
00467                                 }
00468                         }
00469                 }
00470 
00471 
00472          // ix > ixmin, iz < izmin
00473                 for (int ix = ixmax+1; ix < nxf; ix++) {
00474                         for (int iy = iymin; iy <= iymax; iy++) {
00475                                 for (int iz = 0; iz < izmin; iz++) {
00476                                         (*result)(ix,iy,iz) =
00477                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00478                                                                  kxmin, kxmax,
00479                                                                  nzf, nyf, nxf, iz, iy, ix);
00480                                 }
00481                         }
00482                 }
00483                 
00484                  // ix > ixmin, iz > izmax
00485                 for (int ix = ixmax+1; ix < nxf; ix++) {
00486                         for (int iy = iymin; iy <= iymax; iy++) {
00487                                 for (int iz = izmax+1; iz < nzf; iz++) {
00488                                         (*result)(ix,iy,iz) =
00489                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00490                                                                  kxmin, kxmax,
00491                                                                  nzf, nyf, nxf, iz, iy, ix);
00492                                 }
00493                         }
00494                 }
00495 
00496                 
00497 
00498        // iy < iymin, iz < izmin
00499            
00500            for (int iz = 0; iz < izmin; iz++) {
00501                         for (int ix = ixmin; ix <= ixmax; ix++) {
00502                                 for (int iy = 0; iy < iymin; iy++) {
00503                                         (*result)(ix,iy,iz) =
00504                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00505                                                                  kxmin, kxmax,
00506                                                                  nzf, nyf, nxf, iz, iy, ix);
00507                                 }
00508                         }
00509                 }
00510 
00511 
00512        // iy < iymin, iz > izmax
00513            
00514            for (int iz = izmax+1; iz < nzf; iz++) {
00515                         for (int ix = ixmin; ix <= ixmax; ix++) {
00516                                 for (int iy = 0; iy < iymin; iy++) {
00517                                         (*result)(ix,iy,iz) =
00518                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00519                                                                  kxmin, kxmax,
00520                                                                  nzf, nyf, nxf, iz, iy, ix);
00521                                 }
00522                         }
00523                 }
00524                 
00525                 
00526                 // iy > iymax, iz < izmin
00527            
00528            for (int iz = 0; iz < izmin; iz++) {
00529                         for (int ix = ixmin; ix <= ixmax; ix++) {
00530                                 for (int iy = iymax+1; iy < nyf; iy++) {
00531                                         (*result)(ix,iy,iz) =
00532                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00533                                                                  kxmin, kxmax,
00534                                                                  nzf, nyf, nxf, iz, iy, ix);
00535                                 }
00536                         }
00537                 }
00538 
00539 
00540        // iy > iymax, iz > izmax
00541            
00542            for (int iz = izmax+1; iz < nzf; iz++) {
00543                         for (int ix = ixmin; ix <= ixmax; ix++) {
00544                                 for (int iy = iymax+1; iy < nyf; iy++) {
00545                                         (*result)(ix,iy,iz) =
00546                                                 mult_circ(*K, *f, kzmin, kzmax, kymin, kymax, 
00547                                                                  kxmin, kxmax,
00548                                                                  nzf, nyf, nxf, iz, iy, ix);
00549                                 }
00550                         }
00551                 }
00552 
00553                 
00554                 K->set_array_offsets(K_saved_offsets);
00555                 result->update();
00556                 return result;
00557         }

EMData* rscp EMData *  f  ) 
 

Real-space convolution with the K-B window.

Purpose: Calculate the convolution with the K-B window.
Parameters:
[in] f First real-space image object. Image may be 1-, 2-, or 3-dimensional. Image f is not changed.
Returns:
Real-space convolution image.

EMData * EMAN::rsub const EMData em,
float  n
 

Definition at line 2828 of file emdata.cpp.

References operator-().

Referenced by main().

02829 {
02830         return EMAN::operator-(n, em);
02831 }

EMData* self_correlation EMData *  f,
fp_flag  myflag,
bool  center
[inline]
 

Image self-correlation.

Purpose: Calculate the self-correlation of a 1-, 2-,
or 3-dimensional image.
Method: This function calls fourierproduct.
This function actually calls fourierproduct.

Parameters:
[in] f Image object, either a real-space image or a Fourier image. Image may be 1-, 2-, or 3-dimensional. Image f is not changed.
[in] myflag Processing flag (see above).
[in] center 
Returns:
Real-space self-correlation image.

Definition at line 211 of file fundamentals.h.

References fourierproduct(), and SELF_CORRELATION.

00211                                                                                 {
00212                 return fourierproduct(f, NULL, myflag, SELF_CORRELATION, center);
00213         }

Vector4 unit const Vector4 &  v  )  [inline]
 

Definition at line 689 of file vecmath.h.

References EMAN::Vector4::length(), and v.

00689 { const double len = v.length(); return v / len; }

Vector3 unit const Vector3 &  v  )  [inline]
 

Definition at line 318 of file vecmath.h.

References EMAN::Vector3::length(), and v.

00318 { const double len = v.length(); return v / len; }


Variable Documentation

const int EMAN::MAXFFT = 32768 [static]
 

Definition at line 49 of file polardata.h.


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