EMAN2 Reconstructor Manual


Last modified on Fri, 30 Apr 2010 15:38:26 CDT
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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
fourier string mode: Optional. Fourier pixel insertion mode name. gauss_2 is the default.
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: 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 direct Fourier methods using one of a variety of different kernels, most of which are Gaussian based
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