cistem.protocols.program_ctffind module

class cistem.protocols.program_ctffind.ProgramCtffind(protocol)

Bases: object

Wrapper of Ctffind4 program that will handle parameters definition and also execution of the program with the proper arguments. This class is not a Protocol, but somewhat related, since it can be used from protocols that perform CTF estimation.

classmethod defineInputParams(form)

Define input/common parameters.

classmethod defineProcessParams(form)

Define specific parameters.

getCommand(**kwargs)

Parameters

kwargs – The input keywords argument should contain key-values

for one micrograph or group of micrographs. :return: the program and arguments to be run

parseOutput(filename)

Retrieve defocus U, V and angle from the output file of the program execution. :param filename: input file to parse :return: a tuple of CTF values

parseOutputAsCtf(filename, psdFile=None)

Parse the output file and build the CTFModel object with the values. :param filename: input file to parse :param psdFile: if defined, set PSD for the CTF model