jjsoft.protocols.protocol_motion_compensation module¶

class jjsoft.protocols.protocol_motion_compensation.ProtJjsoftAlignReconstructTomogram(**args)[source]¶

Bases: pwem.protocols.protocol.EMProtocol, tomo.protocols.protocol_base.ProtTomoBase

Reconstruct tomograms by aligning the tilt series using the fiducial positions with tomoalign and then reconstructs the tomogram with tomorec. Software from : https://sites.google.com/site/3demimageprocessing/ Returns the set of tomograms

alignTsStep()[source]¶

convertFiducialTextStep()[source]¶

convertInputStep()[source]¶

createOutputStep()[source]¶

get_Ts_files(ts_folder, TsId)[source]¶: Returns the path of the Tilt Serie and the angles files

parse_fid(scip_fid, out_fid)[source]¶: Converts the scipion fid format to JJ format needed

reconstructTomogramStep()[source]¶