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removeDuplicates - remove duplicate particles  


removeDuplicates filename iterationNumber
removeDuplicates filename iterationNumber classID
removeDuplicates filename iterationNumber classID flgShuffle
removeDuplicates filename iterationNumber classID flgShuffle onlyTomNum  


Alignment can result in multiple model particles pointing to essentially the same location and orientation, especially when the search range is comparable to or larger than the spacing between particles. If flgRemoveDuplicates is set to 1 in parameter file 'filename', removeDuplicates will identify such duplicates in the motive list(s), and will remove them from further consideration by assigning them to the duplicate class (ID = -9999). Particle class is stored in column 20 of the motive list, with a default of 0. If a particle is marked as a duplicate, previous particle class will be preserved in column 16 of the motive list. All particles are always restored to their previous class before search for duplicates. RemoveDuplicates should be run immediately following mergeEm. Programs averageAll, calcFSC, and calcSSNR ignore members of the duplicate class unless -9999 has been explicitly added to selectClassID.

Conflicts between 'duplicates' can be resolved in multiple ways. RemoveDuplicates chooses a particular solution using hueristics which try to minimize the number of particles removed while preserving particles having high cross-correlation scores with the reference.

At iterations after the first, removeDuplicates restores the original particle class before performing a fresh search for duplicates. This allows particles which were removed as duplicates to potentially be restored at later iterations, e.g. if duplicateShiftTolerances become tighter.

Normally, tomograms are processed independently except that multiple tomograms refering to the same volume (e.g. when using duplication to enforce symmetry) are processed together. The test for identity currently relies on string comparison of the literal paths, however, so, recognized as pointing to the same volume.

The file name of the parameter file. See PEET(1) man page for descriptions of applicable parameter file settings. A sample parameter file, with parameter descriptions, is available at $PARTICLE/templates/master.prm. RemoveDuplicates uses the following parameters: debugLevel, duplicateShiftTolerance, duplicateAngularTolerance, flgRemoveDuplicates, fnModParticle, and fnOutput
iterationNumber (optional)
An integer specifying the alignment iteration whose output is to be processed. The name of the corresponding motive list file will contain iterationNumber + 1, since it refers to the iteration for which the file will serve as input.
classID (optional)
An integer specifying the class ID to be used for duplicate particles. (Default = -9999).
If non-zero, different initialization of the pseudo-random number generator will be used at each invocation. (Default = 0).
If non-zero, duplicate removal, if enabled, will be done on multiple volume table entries in parallel, yielding faster execution. This option should be disabled if there are volume table entries with unique names but which point to the same volume (e.g. via hard or symbolic links). (Default = 0).
If greater than 0 specifies the number of the volume to process; if omitted or less than or equal to 0, all tomograms will be processed together.


John Heumann  


PEET(1), prepareEM(1), prepareRef(1), mergeEM(1), alignSubset(1), averageAll(1), calcFSC(1), and calcSSNR(1)




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Time: 18:16:05 GMT, January 11, 2021