spider.protocols.protocol_classify_base module

class spider.protocols.protocol_classify_base.DendroNode(index, height)[source]

Bases: pyworkflow.utils.graph.Node

Special type of Node to store dendrogram values.

addImage(*images)[source]

Add some images to this node.

extendImageList(imageList)[source]
getChilds()[source]
getSize()[source]

Return the number of images assigned to this class.

class spider.protocols.protocol_classify_base.SpiderProtClassify(script, classDir, **kwargs)[source]

Bases: pwem.protocols.protocol_2d.ProtClassify2D, spider.protocols.protocol_base.SpiderProtocol

Base protocol for SPIDER classifications.

classifyStep(imcFile, numberOfFactors, numberOfClasses)[source]

Apply the selected filter to particles. Create the set of particles.

getClassDir()[source]
getNumberOfClasses()[source]
class spider.protocols.protocol_classify_base.SpiderProtClassifyCluster(script, classDir, **kwargs)[source]

Bases: spider.protocols.protocol_classify_base.SpiderProtClassify

Base for Clustering Spider classification protocols.

addChildNode(node, leftIndex, rightIndex, index, writeAverages, level, searchStop)[source]
buildDendrogram(writeAverages=False)[source]

Parse Spider docfile with the information to build the dendrogram. Params:

writeAverages: whether to write class averages or not.
createOutputStep()[source]
getImage(particleNumber)[source]