spider.protocols.protocol_ca_pca module

class spider.protocols.protocol_ca_pca.SpiderProtCAPCA(**kwargs)

Bases: spider.protocols.protocol_base.SpiderProtocol

Protocol for Correspondence Analysis (CA) or Principal Component Analysis (PCA).

CA is the preferred method of finding inter-image variations. PCA computes the distance between data vectors with Euclidean distances, while CA uses Chi-squared distance. CA is superior because it ignores differences in exposure between images, eliminating the need to rescale between images. In contrast, PCA seems to be more robust: less likely to be trapped in an infinite loop of numerical inaccuracy.

For more info see: [[http://spider.wadsworth.org/spider_doc/spider/docs/techs/classification/tutorial.html#CAPCA][SPIDER MDA documentation]]

capcaStep(analysisType, numberOfFactors, maskType)

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

convertMaskStep(maskType)

Convert the input mask if needed.

createOutputStep()