continuousflex.protocols.protocol_subtomogram_refine_alignment module

class continuousflex.protocols.protocol_subtomogram_refine_alignment.FlexProtRefineSubtomoAlign(**kwargs)

Bases: pwem.protocols.protocol_3d.ProtAnalysis3D

Protocol for refining subtomogram alignment and filling the missing wedge based on optical flow and Fast Rotational Matching (FRM). The protocol takes as input a set of subtomograms, with their subtomogram averaging protocol. It uses this global subtomogrm average to fill the missing wedge in Fourier space (the missing wedge is replaced by the corresponding region from the global average). Optical flow is used to match the global average with each of the missing wedge filled and aligned subtomograms (matched subtomograms are generated). Rigid-body alignment is performed using FRM from the matched subtomogram, and the rigid-body alignment for the input subtomograms is updated. Few iterations are usually sufficient (1-5), and the rigid-body alignment will be refined

applyAlignment(num)

calculateNewAverage(num)

calculateOpticalFlows(num)

combineRefinedAlignment(num)

convertInputStep()

createOutputStep(num=0)

fillMissingWedge(num)

getAngleY()

getVolumeDimesion()

prepareMetaData()

read_optical_flow(path_flowx, path_flowy, path_flowz)

read_optical_flow_by_number(num, op_path=None)

refineAlignment(num)

warpByFlow(num)