jjsoft.protocols.protocol_align_ts module

class jjsoft.protocols.protocol_align_ts.ProtJjsoftAlignTs(**args)[source]

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

Aligning the tilt series using the fiducial positions and motion compensation with tomowarpalign. Software from : https://sites.google.com/site/3demimageprocessing/ Returns the set of aligned tilt series

alignTsStep()[source]
computeInterpolatedStackStep()[source]
convertInputStep()[source]
createOutputStep()[source]
getOutputInterpolatedSetOfTiltSeries()[source]
get_IMOD_files(prevwFolder, ts_folder, TsId)[source]

Returns the path of the Tilt Serie and the angles files

make_aligncom(ts_folder, TsId)[source]

Writes an artificial align.com file

make_newstcom(ts_folder, TsId)[source]

Writes an artifitial newst.com file

make_resid_file(prevprefix, prefix)[source]

Creates the resid file in the correct format from a sfid text file

write_prexg_identity(ts, prexgPath)[source]

Creates the prexg file as a identity matrix