spider.protocols.protocol_custommask module

class spider.protocols.protocol_custommask.SpiderProtCustomMask(**kwargs)[source]

Bases: pwem.protocols.protocol_2d.ProtCreateMask2D, spider.protocols.protocol_base.SpiderProtocol

This protocol creates a 2D mask using SPIDER.

In the step following this one, dimension-reduction, the covariance of the pixels in all images will be computed. Only pixels under a given mask will be analyzed. If this step is performed, a mask that follows closely the contour the particle of interest will be used. Absent a custom-made mask, a circular mask will be used. For non-globular structures, this customized mask will reduce computational demand and the likelihood of numerical inaccuracy in the next dimension-reduction step. On the other hand, given the power of modern computers, this step may be unnecessary.

convertInputStep(inputLoc, outputFn)[source]

Convert the input image to a Spider (with stk extension).

createMaskStep(filterRadius1, sdFactor, filterRadius2, maskThreshold)[source]

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