EMAN2 Reconstructor Manual

Last modified on Tue, 05 Apr 2022 00:12:57 CDT
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Reconstructor Name Parameters Description

back_projection intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical.
string sym: Optional. The symmetry to impose on the final reconstruction. Default is c1
bool verbose: Optional. Toggles writing useful information to standard out. Default is false.
float weight: Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1.
Simple (unfiltered) back-projection reconstruction. Weighting by contributing particles in the class average is optional and default behaviour

fourier bool corners: Optional. If not set, then reconstruction will cover a spherical volume with a radius of nx/2. If set, the full Fourier volume will be reconstructed, but will be ~2x slower.
string mode: Optional. Fourier pixel insertion mode name (nearest_neighbor, gauss_2, gauss_3, gauss_5, gauss_5_slow, gypergeom_5, experimental) gauss_2 is the default.
emdata normout: Will write the normalization volume to the given EMData object file when finish() is called.
bool quiet: Optional. If false, print verbose information.
string savenorm: Debug. Will cause the normalization volume to be written directly to the specified file when finish() is called.
intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical.
bool sqrtnorm: Optional. When normalizing, additionally divides by the sqrt of the normalization factor to damp exaggerated features. Is this justifyable ? No idea (yet). Default is false.
intarray subvolume: Optional. (xorigin,yorigin,zorigin,xsize,ysize,zsize) all in Fourier pixels. Useful for parallelism.
string sym: Required. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1, ie - an asymmetric object
bool usessnr: Optional. Looks for and uses the class_ssnr header parameter from each slice to weight each voxel during insertion to the reconstruction.
bool verbose: Optional. Toggles writing useful information to standard out. Default is false.
Reconstruction via direct Fourier methods using one of a variety of different kernels, most of which are Gaussian based

fourier_iter intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical.
string sym: Optional. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1, ie - an asymmetric object
bool verbose: Optional. Toggles writing useful information to standard out. Default is false.
Reconstruction via Fourier interpolation using an iterative strategy to define the interpolation kernel

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

nn4_ctf_rect emdata fftvol:
int npad:
emdata refvol:
int sign:
int size:
float snr:
string symmetry:
int varsnr:
emdata weight:
int weighting:
Direct Fourier inversion reconstruction routine

nn4_ctfw int do_ctf:
emdata fftvol:
int npad:
emdata refvol:
int sign:
int size:
float snr:
string symmetry:
int varsnr:
emdata weight:
int weighting:
Direct Fourier inversion reconstruction routine

nn4_ctfws int do_ctf:
emdata fftvol:
int npad:
emdata refvol:
int sign:
int size:
float snr:
string symmetry:
int varsnr:
emdata weight:
int weighting:
Direct Fourier inversion reconstruction routine

nn4_rect emdata fftvol:
int ndim:
int npad:
int sign:
int sizeprojection:
int sizex:
int sizey:
int sizez:
float snr:
string symmetry:
emdata weight:
int weighting:
float xratio:
float yratio:
float zratio:
Direct Fourier inversion routine

nnSSNR emdata SSNR:
emdata fftvol:
int npad:
int size:
string symmetry:
emdata vol_ssnr:
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:
emdata vol_ssnr:
float w:
emdata weight:
emdata weight2:
emdata weight3:
Reconstruction by nearest neighbor with 3D SSNR with CTF

real_median int mode: Default is 0, median. 1 - compute estimated statistical mode.
intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical.
string sym: Optional. The symmetry to impose on the final reconstruction. Default is c1
int verbose: Optional. Toggles writing diagnostic information to standard out. Default is 0.
float weight: Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1.
A back projection reconstructor with alternative statistics. mode: 0 - median rather than mean per voxel (default) 1 - similar to a mode. progressive subdivision of numeric axis to find dense value cluster 2 - median with a bias towands zero (postive and negative) 3 - median with a bias towards the 1/2 of the values spanning a narrower range 4 - specifically for tomography, requires slices to be in order by tilt

wiener_fourier bool corners: Optional. If not set, then reconstruction will cover a spherical volume with a radius of nx/2. If set, the full Fourier volume will be reconstructed, but will be ~2x slower.
string mode: Optional. Fourier pixel insertion mode name (nearest_neighbor, gauss_2, gauss_3, gauss_5, gauss_5_slow, gypergeom_5, experimental) gauss_2 is the default.
emdata normout: Will write the normalization volume to the given EMData object file when finish() is called.
bool quiet: Optional. If false, print verbose information.
string savenorm: Debug. Will cause the normalization volume to be written directly to the specified file when finish() is called.
intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical.
bool sqrtnorm: Optional. When normalizing, additionally divides by the sqrt of the normalization factor to damp exaggerated features. Is this justifyable ? No idea (yet). Default is false.
intarray subvolume: Optional. (xorigin,yorigin,zorigin,xsize,ysize,zsize) all in Fourier pixels. Useful for parallelism.
string sym: Required. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1, ie - an asymmetric object
bool usessnr: Optional. Looks for and uses the class_ssnr header parameter from each slice to weight each voxel during insertion to the reconstruction.
bool verbose: Optional. Toggles writing useful information to standard out. Default is false.
Reconstruction via direct Fourier methods using one of a variety of different kernels, most of which are Gaussian based. This version also incorporates a nonisotropic Wiener filter based on SNR estimates stored in the class-average headers by the ctf.auto averager.

Reconstructor Name	Parameters	Description
back_projection	intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical. string sym: Optional. The symmetry to impose on the final reconstruction. Default is c1 bool verbose: Optional. Toggles writing useful information to standard out. Default is false. float weight: Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1.	Simple (unfiltered) back-projection reconstruction. Weighting by contributing particles in the class average is optional and default behaviour
fourier	bool corners: Optional. If not set, then reconstruction will cover a spherical volume with a radius of nx/2. If set, the full Fourier volume will be reconstructed, but will be ~2x slower. string mode: Optional. Fourier pixel insertion mode name (nearest_neighbor, gauss_2, gauss_3, gauss_5, gauss_5_slow, gypergeom_5, experimental) gauss_2 is the default. emdata normout: Will write the normalization volume to the given EMData object file when finish() is called. bool quiet: Optional. If false, print verbose information. string savenorm: Debug. Will cause the normalization volume to be written directly to the specified file when finish() is called. intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical. bool sqrtnorm: Optional. When normalizing, additionally divides by the sqrt of the normalization factor to damp exaggerated features. Is this justifyable ? No idea (yet). Default is false. intarray subvolume: Optional. (xorigin,yorigin,zorigin,xsize,ysize,zsize) all in Fourier pixels. Useful for parallelism. string sym: Required. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1, ie - an asymmetric object bool usessnr: Optional. Looks for and uses the class_ssnr header parameter from each slice to weight each voxel during insertion to the reconstruction. bool verbose: Optional. Toggles writing useful information to standard out. Default is false.	Reconstruction via direct Fourier methods using one of a variety of different kernels, most of which are Gaussian based
fourier_iter	intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical. string sym: Optional. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1, ie - an asymmetric object bool verbose: Optional. Toggles writing useful information to standard out. Default is false.	Reconstruction via Fourier interpolation using an iterative strategy to define the interpolation kernel
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
nn4_ctf_rect	emdata fftvol: int npad: emdata refvol: int sign: int size: float snr: string symmetry: int varsnr: emdata weight: int weighting:	Direct Fourier inversion reconstruction routine
nn4_ctfw	int do_ctf: emdata fftvol: int npad: emdata refvol: int sign: int size: float snr: string symmetry: int varsnr: emdata weight: int weighting:	Direct Fourier inversion reconstruction routine
nn4_ctfws	int do_ctf: emdata fftvol: int npad: emdata refvol: int sign: int size: float snr: string symmetry: int varsnr: emdata weight: int weighting:	Direct Fourier inversion reconstruction routine
nn4_rect	emdata fftvol: int ndim: int npad: int sign: int sizeprojection: int sizex: int sizey: int sizez: float snr: string symmetry: emdata weight: int weighting: float xratio: float yratio: float zratio:	Direct Fourier inversion routine
nnSSNR	emdata SSNR: emdata fftvol: int npad: int size: string symmetry: emdata vol_ssnr: 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: emdata vol_ssnr: float w: emdata weight: emdata weight2: emdata weight3:	Reconstruction by nearest neighbor with 3D SSNR with CTF
real_median	int mode: Default is 0, median. 1 - compute estimated statistical mode. intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical. string sym: Optional. The symmetry to impose on the final reconstruction. Default is c1 int verbose: Optional. Toggles writing diagnostic information to standard out. Default is 0. float weight: Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1.	A back projection reconstructor with alternative statistics. mode: 0 - median rather than mean per voxel (default) 1 - similar to a mode. progressive subdivision of numeric axis to find dense value cluster 2 - median with a bias towands zero (postive and negative) 3 - median with a bias towards the 1/2 of the values spanning a narrower range 4 - specifically for tomography, requires slices to be in order by tilt
wiener_fourier	bool corners: Optional. If not set, then reconstruction will cover a spherical volume with a radius of nx/2. If set, the full Fourier volume will be reconstructed, but will be ~2x slower. string mode: Optional. Fourier pixel insertion mode name (nearest_neighbor, gauss_2, gauss_3, gauss_5, gauss_5_slow, gypergeom_5, experimental) gauss_2 is the default. emdata normout: Will write the normalization volume to the given EMData object file when finish() is called. bool quiet: Optional. If false, print verbose information. string savenorm: Debug. Will cause the normalization volume to be written directly to the specified file when finish() is called. intarray size: Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical. bool sqrtnorm: Optional. When normalizing, additionally divides by the sqrt of the normalization factor to damp exaggerated features. Is this justifyable ? No idea (yet). Default is false. intarray subvolume: Optional. (xorigin,yorigin,zorigin,xsize,ysize,zsize) all in Fourier pixels. Useful for parallelism. string sym: Required. The symmetry of the reconstructed volume, c?, d?, oct, tet, icos, h?. Default is c1, ie - an asymmetric object bool usessnr: Optional. Looks for and uses the class_ssnr header parameter from each slice to weight each voxel during insertion to the reconstruction. bool verbose: Optional. Toggles writing useful information to standard out. Default is false.	Reconstruction via direct Fourier methods using one of a variety of different kernels, most of which are Gaussian based. This version also incorporates a nonisotropic Wiener filter based on SNR estimates stored in the class-average headers by the ctf.auto averager.