xmipp3.protocols.protocol_reconstruct_swarm module

class xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm(**kwargs)[source]

Bases: ProtRefine3D

This is a 3D refinement protocol whose main input is a set of volumes and a set of particles. The set of particles has to be at full size (the finer sampling rate available), but the rest of inputs (reference volume and masks) can be at any downsampling factor. The protocol scales the input images and volumes to a size that depends on the target resolution.

The input set of volumes is considered to be a swarm of volumes and they try to optimize the correlation between the volumes and the set of particles. This is an stochastic maximization and only a fraction of the particles are used to update the volumes and evaluate them.

calculateAverage(iteration)[source]

cleanVolume(fnVol)[source]

convertInputStep(inputParticlesId)[source]

convertInputVolume(imgHandler, obj, fnIn, fnOut, TsCurrent, newXdim)[source]

createOutput()[source]

evaluateIndividuals(iteration)[source]

postProcessing(iteration)[source]

readInfoField(fnDir, block, label)[source]

reconstructNewVolumes(iteration)[source]

updateVolumes(iteration)[source]

writeInfoField(fnDir, block, label, value)[source]