topaz.protocols.protocol_training module

class topaz.protocols.protocol_training.TopazProtTraining(**args)[source]

Bases: pwem.protocols.protocol_particles_picking.ProtParticlePickingAuto

Train the Topaz parameters for a picking

convertInputStep(inputCoordinates, scale, kfold)[source]

Converts a set of coordinates to box files and binaries to mrc if needed. It generates 2 folders 1 for the box files and another for the mrc files.

denoiseStep(modelNoise, extra)[source]
getDenoiseArgs(inputDir, outDir)[source]
getPickingFileName(micList, key)[source]
getPreprocessArgs(inputDir, outDir)[source]
preprocessStep(scale, extra)[source]

Downsamples the micrographs with a factor determined by the scale parameter and normalize them with the per-micrograph scaled Gaussian mixture model

readCoordsFromMics(outputDir, micDoneList, outputCoords)[source]

Read the coordinates from a given list of micrographs

trainingStep(radius, enc, numEpochs, modelFit, method, numParts, extra)[source]

Train the model with the provided parameters and the previously preprocessed micrograph images and the provided input coordinates.