xmipp3.protocols.protocol_extract_particles module

class xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles(**kwargs)[source]

Bases: ProtExtractParticles, XmippProtocol

Extracts particle images from micrographs based on provided coordinates. This essential step prepares particle stacks for further processing such as classification and reconstruction.

RESIZE_DIMENSIONS = 1

RESIZE_FACTOR = 0

RESIZE_SAMPLINGRATE = 2

createParticles(item, row)[source]

getBoxScale()[source]: Computing the sampling factor between input and output. We should take into account the differences in sampling rate between micrographs used for picking and the ones used for extraction. The downsampling factor could also affect the resulting scale.

getBoxSize()[source]

getCoordSampling()[source]

getCoords()[source]

getEven(boxSize)[source]

getInputMicrographs()[source]: Return the micrographs associated to the SetOfCoordinates or Other micrographs.

getMicSampling()[source]

getOutput()[source]

notOne(value)[source]

readPartsFromMics(micList, outputParts)[source]: Read the particles extract for the given list of micrographs and update the outputParts set with new items.