xmipp3.protocols.protocol_projmatch.projmatch_steps module

Since the Projection Matching protocol of Xmipp 3 has a very large form definition, we have separated in this sub-module.

xmipp3.protocols.protocol_projmatch.projmatch_steps.getProjectionMatchingArgs(self, iterN)

Get the arguments for the projection matching program that does not vary with the CTF groups.

xmipp3.protocols.protocol_projmatch.projmatch_steps.insertAngularClassAverageStep(self, iterN, refN, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.insertAngularProjectLibraryStep(self, iterN, refN, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.insertComputeResolutionStep(self, iterN, refN, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.insertFilterVolumeStep(self, iterN, refN, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.insertMaskReferenceStep(self, iterN, refN, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.insertReconstructionStep(self, iterN, refN, suffix='', **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.runAngularProjectLibraryStep(self, iterN, refN, args, stepParams, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.runAssignImagesToReferences(self, iterN, **kwargs)

assign the images to the different references based on the crosscorrelation coeficient #if only one reference it just copy the docfile generated in the previous step

xmipp3.protocols.protocol_projmatch.projmatch_steps.runCalculateFscStep(self, iterN, refN, args, constantToAdd, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.runCreateOutputStep(self)

Create standard output results_images, result_classes

xmipp3.protocols.protocol_projmatch.projmatch_steps.runExecuteCtfGroupsStep(self, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.runFilterVolumeStep(self, iterN, refN, constantToAddToFiltration)

xmipp3.protocols.protocol_projmatch.projmatch_steps.runInitAngularReferenceFileStep(self)

Create Initial angular file. Either fill it with zeros or copy input

xmipp3.protocols.protocol_projmatch.projmatch_steps.runProjectionMatching(self, iterN, refN, args, **kwargs)

Loop over all CTF groups and launch a projection matching for each one. Note: Iterate ctf groups in reverse order to have same order as

in add_to docfiles from angular_class_average. #FIXME: check why reverse order is needed

xmipp3.protocols.protocol_projmatch.projmatch_steps.runReconstructionStep(self, iterN, refN, program, method, args, suffix, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.runStoreResolutionStep(self, resolIterMd, resolIterMaxMd, sampling)

xmipp3.protocols.protocol_projmatch.projmatch_steps.runTransformMaskStep(self, program, args, **kwargs)

xmipp3.protocols.protocol_projmatch.projmatch_steps.runVolumeConvertStep(self, reconstructedFilteredVolume, maskedFileName)