pwem.protocols.protocol_extract_coordinates module

class pwem.protocols.protocol_extract_coordinates.ProtExtractCoords(**kwargs)

Bases: pwem.protocols.protocol_particles_picking.ProtParticlePickingAuto

Extract the coordinates information from a set of particles.

This protocol is useful when we want to re-extract the particles (maybe resulting from classification and cleaning) with the original dimensions. It can be also handy to visualize the resulting particles in their location on micrographs.

createOutputStep()

extractCoordinates(partsIds=None)

extractCoordsStep(partsIds)

geometryFromMatrix(matrix, inverseTransform)

getInputParticles()

getShifts(transform, alignType)

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

getSuffix(suffix)

getTmpOutputPath(suffix)

loadInputs()