pwem.protocols.protocol_extract_coordinates module

class pwem.protocols.protocol_extract_coordinates.ProtExtractCoords(**kwargs)[source]

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()[source]
extractCoordinates(partsIds=None)[source]
extractCoordsStep(partsIds)[source]
geometryFromMatrix(matrix, inverseTransform)[source]
getInputParticles()[source]
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
getSuffix(suffix)[source]
getTmpOutputPath(suffix)[source]
loadInputs()[source]