gctf.convert.convert module

This module contains converter functions that will serve to: 1. Write from base classes to Gctf specific files 2. Read from Gctf files to base classes

class gctf.convert.convert.CoordinatesWriter(filename)[source]

Bases: object

Simple class to write coordinates (in star file as in Relion).

HEADER = '\ndata_\n\nloop_\n_rlnCoordinateX #1\n_rlnCoordinateY #2\n'
close()[source]
writeCoord(x, y)[source]
gctf.convert.convert.geometryFromMatrix(matrix, inverseTransform)[source]
gctf.convert.convert.getShifts(transform, alignType)[source]
is2D == True-> matrix is 2D (2D images alignment)
otherwise matrix is 3D (3D volume alignment or projection)
invTransform == True -> for xmipp implies projection
-> for xmipp implies alignment
gctf.convert.convert.parseGctfOutput(filename)[source]

Retrieve defocus U, V, angle, crossCorrelation and ctfResolution from the output file of the Gctf execution.

gctf.convert.convert.readCtfModel(ctfModel, filename)[source]
gctf.convert.convert.rowToCtfModel(ctfRow, ctfModel)[source]

Create a CTFModel from a row of a meta

gctf.convert.convert.setWrongDefocus(ctfModel)[source]