EMAN2 Reconstructor Manual

Last modified on Sat, 07 Nov 2009 02:18:53 CST
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Reconstructor Name Parameters Description

back_projection int size: Necessary. The x and y dimensions of the input images.
string sym: Optional. The symmetry to impose on the final reconstruction. Default is c1
float weight: Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1.
int zsample: Optional. The z dimensions of the reconstructed volume.
Simple (unfiltered) back-projection reconstruction. Weighting by contributing particles in the class average is optional and default behaviour

baldwinwoolford bool 3damp: this doesn't work, fixme dsaw
float hard: Optional. The quality metric threshold. Default is 0 (off).
int maskwidth: The width of the Fourier space kernel used to interpolate data to grid points
int mode: Optional. Fourier pixel insertion mode [1-8] - mode 2 is default.
bool postmultiply: A flag that controls whether or not the reconstructed volume is post multiplied in real space by the IFT of the weighting function. Default is on
bool quiet: Optional. Toggles writing useful information to standard out. Default is false.
string sym: Optional. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1
int x_in: Necessary. The x dimension of the input images.
int xsample: Optional. The x dimension (Fourier sampling) of the reconstructed volume, works for general volumes. Not commonly specified.
int y_in: Necessary. The y dimension of the input images.
int ysample: Optional. The y dimension (Fourier sampling) of the reconstructed volume, works for general volumes. Not commonly specified.
int zsample: Optional. The z dimension (Fourier sampling) of the reconstructed volume, very useful for tomographic reconstruction. Works for general volumes.
Reconstruction via direct Fourier inversion using gridding and delta function based weights

fourier bool 3damp: Optional. Toggles writing the 3D FFT amplitude image. Default is false.
float hard: Optional. The quality metric threshold. Default is 0 (off).
int mode: Optional. Fourier pixel insertion mode [1-8] - mode 2 is default.
bool quiet: Optional. Toggles writing useful information to standard out. Default is false.
emdata start_model: Start model
float start_model_weight: start_model_weight
string sym: Optional. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1
float weight: Weight of the slice that is being inserted. Default is 1.0.
int x_in: Necessary. The x dimension of the input images.
int xsample: Optional. The x dimension (Fourier sampling) of the reconstructed volume, works for general volumes. Not commonly specified.
int y_in: Necessary. The y dimension of the input images.
int ysample: Optional. The y dimension (Fourier sampling) of the reconstructed volume, works for general volumes. Not commonly specified.
int zsample: Optional. The z dimension (Fourier sampling) of the reconstructed volume, very useful for tomographic reconstruction. Works for general volumes.
Reconstruction via direct Fourier methods using a combination of nearest neighbour and Gaussian kernels

fouriersimple2D int nx: Necessary. The x dimension of the input images.
performs 2D reconstruction

nn4 emdata fftvol:
int ndim:
int npad:
int sign:
int size:
float snr:
string symmetry:
emdata weight:
int weighting:
Direct Fourier inversion routine

nn4_ctf emdata fftvol:
int npad:
int sign:
int size:
float snr:
string symmetry:
int varsnr:
emdata weight:
int weighting:
Direct Fourier inversion reconstruction routine

nnSSNR emdata SSNR:
emdata fftvol:
int npad:
int size:
string symmetry:
float w:
emdata weight:
emdata weight2:
Reconstruction by nearest neighbor with 3D SSNR

nnSSNR_ctf emdata SSNR:
emdata fftvol:
emdata fftwvol:
int npad:
int sign:
int size:
float snr:
string symmetry:
float w:
emdata weight:
emdata weight2:
emdata weight3:
Reconstruction by nearest neighbor with 3D SSNR with CTF

wiener_fourier bool dlog:
int mode:
float padratio:
int size:
floatarray snr:
bool use_weights:
float weight:
Experimental - Direct Fourier reconstruction taking into account the Wiener filtration of the individual images.

Reconstructor Name	Parameters	Description
back_projection	int size: Necessary. The x and y dimensions of the input images. string sym: Optional. The symmetry to impose on the final reconstruction. Default is c1 float weight: Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1. int zsample: Optional. The z dimensions of the reconstructed volume.	Simple (unfiltered) back-projection reconstruction. Weighting by contributing particles in the class average is optional and default behaviour
baldwinwoolford	bool 3damp: this doesn't work, fixme dsaw float hard: Optional. The quality metric threshold. Default is 0 (off). int maskwidth: The width of the Fourier space kernel used to interpolate data to grid points int mode: Optional. Fourier pixel insertion mode [1-8] - mode 2 is default. bool postmultiply: A flag that controls whether or not the reconstructed volume is post multiplied in real space by the IFT of the weighting function. Default is on bool quiet: Optional. Toggles writing useful information to standard out. Default is false. string sym: Optional. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1 int x_in: Necessary. The x dimension of the input images. int xsample: Optional. The x dimension (Fourier sampling) of the reconstructed volume, works for general volumes. Not commonly specified. int y_in: Necessary. The y dimension of the input images. int ysample: Optional. The y dimension (Fourier sampling) of the reconstructed volume, works for general volumes. Not commonly specified. int zsample: Optional. The z dimension (Fourier sampling) of the reconstructed volume, very useful for tomographic reconstruction. Works for general volumes.	Reconstruction via direct Fourier inversion using gridding and delta function based weights
fourier	bool 3damp: Optional. Toggles writing the 3D FFT amplitude image. Default is false. float hard: Optional. The quality metric threshold. Default is 0 (off). int mode: Optional. Fourier pixel insertion mode [1-8] - mode 2 is default. bool quiet: Optional. Toggles writing useful information to standard out. Default is false. emdata start_model: Start model float start_model_weight: start_model_weight string sym: Optional. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1 float weight: Weight of the slice that is being inserted. Default is 1.0. int x_in: Necessary. The x dimension of the input images. int xsample: Optional. The x dimension (Fourier sampling) of the reconstructed volume, works for general volumes. Not commonly specified. int y_in: Necessary. The y dimension of the input images. int ysample: Optional. The y dimension (Fourier sampling) of the reconstructed volume, works for general volumes. Not commonly specified. int zsample: Optional. The z dimension (Fourier sampling) of the reconstructed volume, very useful for tomographic reconstruction. Works for general volumes.	Reconstruction via direct Fourier methods using a combination of nearest neighbour and Gaussian kernels
fouriersimple2D	int nx: Necessary. The x dimension of the input images.	performs 2D reconstruction
nn4	emdata fftvol: int ndim: int npad: int sign: int size: float snr: string symmetry: emdata weight: int weighting:	Direct Fourier inversion routine
nn4_ctf	emdata fftvol: int npad: int sign: int size: float snr: string symmetry: int varsnr: emdata weight: int weighting:	Direct Fourier inversion reconstruction routine
nnSSNR	emdata SSNR: emdata fftvol: int npad: int size: string symmetry: float w: emdata weight: emdata weight2:	Reconstruction by nearest neighbor with 3D SSNR
nnSSNR_ctf	emdata SSNR: emdata fftvol: emdata fftwvol: int npad: int sign: int size: float snr: string symmetry: float w: emdata weight: emdata weight2: emdata weight3:	Reconstruction by nearest neighbor with 3D SSNR with CTF
wiener_fourier	bool dlog: int mode: float padratio: int size: floatarray snr: bool use_weights: float weight:	Experimental - Direct Fourier reconstruction taking into account the Wiener filtration of the individual images.