xmipp3.protocols.protocol_eliminate_empty_images module

class xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase(**args)[source]

Bases: 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)[source]

createOutputStep()[source]

createOutputs()[source]: To be implemented by child. (create, fill and close the outputSet)

eliminationStep(stepId)[source]: Common code for particles and classes/averages

getInput()[source]: Get the input as it is in the form

prepareImages()[source]: 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)[source]: To be implemented by child. Must set self.check and inSet.close()

class xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses(**args)[source]

Bases: 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)[source]

createOutputs()[source]: To be implemented by child. (create, fill and close the outputSet)

getInput()[source]: Get the input as it is in the form

prepareImages()[source]: 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)[source]

specialBehavoir(partSet)[source]: To be implemented by child. Must set self.check and inSet.close()

class xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyParticles(**args)[source]

Bases: 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()[source]: To be implemented by child. (create, fill and close the outputSet)

getInput()[source]: Get the input as it is in the form

prepareImages()[source]: 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)[source]: Just setting the self.check