xmipp3.protocols.protocol_eliminate_empty_images module

class xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase(**args)

Bases: pwem.protocols.protocol_2d.ProtClassify2D

Base to eliminate images using statistical methods (variance of variances of sub-parts of input image) eliminates those samples, where there is no object/particle (only noise is presented there). Threshold parameter can be used for fine-tuning the algorithm for type of data.

addAdvancedParams(form)

createOutputStep()

createOutputs()

To be implemented by child. (create, fill and close the outputSet)

eliminationStep(stepId)

Common code for particles and classes/averages

getInput()

Get the input as it is in the form

prepareImages()

Must set: - self.inputImages: Images to process in a SetOfImages. - self.streamClosed: Streaming state of the input. - self.lenPartsSet: Size of the input set.

specialBehavoir(inSet)

To be implemented by child. Must set self.check and inSet.close()

class xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses(**args)

Bases: xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase

Takes a set of classes (or averages) and using statistical methods (variances of sub-parts of input image) eliminates those samples, where there is no object/particle (only noise is presented there). Threshold parameter can be used for fine-tuning the algorithm for type of data. Also discards classes with less population than a given percentage.

createOutputClasses(suffix, streamingState, enableDict)

createOutputs()

To be implemented by child. (create, fill and close the outputSet)

getInput()

Get the input as it is in the form

prepareImages()

Must set: - self.inputImages: Images to process in a SetOfImages. - self.streamClosed: Streaming state of the input. - self.lenPartsSet: Size of the input set.

rejectByPopulation(ids)

specialBehavoir(partSet)

To be implemented by child. Must set self.check and inSet.close()

class xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyParticles(**args)

Bases: xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase

Takes a set of particles and using statistical methods (variance of variances of sub-parts of input image) eliminates those samples, where there is no object/particle (only noise is presented there). Threshold parameter can be used for fine-tuning the algorithm for type of data.

createOutputs()

To be implemented by child. (create, fill and close the outputSet)

getInput()

Get the input as it is in the form

prepareImages()

Must set: - self.inputImages: Images to process in a SetOfImages. - self.streamClosed: Streaming state of the input. - self.lenPartsSet: Size of the input set.

specialBehavoir(partsSet)

Just setting the self.check