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 Series and the angles files

static make_aligncom(ts_folder, TsId)[source]¶: Writes an artificial align.com file

make_newstcom(ts_folder, TsId)[source]¶: Writes an artifitial newst.com file

static make_resid_file(prevprefix, prefix)[source]¶: Creates the resid file in the correct format from a sfid text file

static write_prexg_identity(ts, prexgPath)[source]¶: Creates the prexg file as a identity matrix