cistem.protocols.program_ctffind module

class cistem.protocols.program_ctffind.ProgramCtffind(protocol)[source]

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 it is related, since it can be used from protocols that perform CTF estimation.

classmethod defineInputParams(form)[source]

Define input parameters from this program into the given form.

classmethod defineProcessParams(form)[source]
getCommand(**kwargs)[source]

Return the program and arguments to be run. The input keywords argument should contain key-values for one micrograph or group of micrographs.

parseOutput(filename)[source]

Retrieve defocus U, V and angle from the output file of the program execution.

parseOutputAsCtf(filename, psdFile=None)[source]

Parse the output file and build the CTFModel object with the values.