Content-type: text/html Manpage of averageAll


Section: User Commands (1)
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averageAll - compute reference and/or average volumes  


averageAll filename iterationNumber desiredOutput tomNum
averageAll filename iterationNumber desiredOutput
averageAll filename iterationNumber
averageAll filename  


If averageAll is called with only a single parameter file name, it computes average volumes according to an initial motive list (initMOTL) and other settings specified in parameter file 'filename'. If called with two arguments, it computes averages using the output of the specified alignment iteration. If called with 3 arguments, it computes the either reference or average volumes or both, as requested, again using the alignment from iteration 'iterationNumber'. When iterationNumber is specified, filename should be the name of the the parameter file used to perform the alignment. When only filename is specified, it should be the name of a parameter file edited specifically to reflect the positions and orientations of particles to be averaged, plus any optional settings, described below.

An optional 4th argument containing a tomogram number can also be supplied to compute and save a partial average from the tomogram specified in an internal format. Specifying a negative tomogram number then causes all previously computed partial averages to be combined into final average(s). PEET uses this optional 4th argument to compute partial averages in parallel, when appropriate, speeding up the overall process. Sample parameter files are available at $PARTICLE/templates.

The file name of the parameter file. See PEET man page and below for descriptions of applicable parameter file settings.
iterationNumber (optional)
An integer specifying the alignment iteration whose output will determine the rotations and translations used to compute the reference and/or average volumes. If omitted, the initial motive list specified by the parameter file will be used.
desiredOutput (optional)
A string specifying the desired output type. May be one of 'average', 'both', or 'reference'. For historical reasons, 'T' and 'F' will also be accepted as synonyms for 'both' and 'reference', respectively; 'averages' will also be accepted in place of 'average'. If omitted, defaults to 'average'. AverageAll supports the alignedBaseName, cylinderHeight, debugLevel, edgeShift, flgMeanFill, flgNormalize, flgVolNamesAreTemplates, flgRandomize, flgWedgeWeight, fnModParticle, fnOutput, fnVolume, initMOTL, lstFlagAllTom, lstThresholds, maskType, nWeightGroup, reference, refFlagAllTom, szVol, tiltRange, yaxisType, yaxisObjectNum, and yaxisContourNum parameter file settings, described in the PEET man page. It also supports the following additional options:
includeList = integer vector
A list of indices of particles to be included in computing averages and references.
excludeList = integer vector
A list of indices of particles to be ignored in computing averages and references.
selectClassID = integer vector
The class ID(s) of particles to be considered in computing averages and references. If not empty, all other particle classes will be excluded. By default, any particles flagged as duplicates (see the man page for removeDuplicates), will be ignored unless the duplicate class ID (-9999) is included in selectClassID. PEET stores particle class in column 20 of the motive list, with a default of 0. includeList is applied first, then excludeList, then selectClassID.
flgAlignAverages = < 0 | 1 > (default: 0)
If flgAlignAverages is 1, a final rotation will be applied to bring average volumes (but not references) to the desired orientation. The rotation can be specified manaully; see alignAveragesAngles, below. Alternatively, if yaxisType is non-zero and alignAverageAngles is empty or omitted, angles will be chosen automatically so as to make the particle y axes approximately vertical in the averages.
alignAveragesAngles = [rotX rotY rotZ]
Slicer angles in degrees specifying the rotation applied to align average volumes. If empty or omitted, these angles will be chosen automatically.
fnWedgeWeight = string
Base name of the files in which to store the missing wedge weights. By default, wedge weights are saved to files with a base name of 'wedgeWeight'. To save using a different base name, specify it here. To disable saving, set fnWedgeWeight=''.
wedgeThresholdFactor = float
A float that will be used to scale an empirical threshold. Fourier components contributed from fewer number of particles than the threhold will be ignored. The default scaling is 1.0. For noisy tomograms, increasing this scale may give better averages.
flgAllowParallelAveraging = < 0 | 1> (default: 1)
If 1, parallel averaging will be used whenever multiple volumes are to be processed, the total number of particles is greater than 100, and at least one volume contains more than 10 particles. Multiple entries eTomo's Volume Table (or equivalently in the parameter file's fnVolume array) are treated as multiple volumes, even if they all point to the same volume. Sample parameter files are available in $PARTICLE/templates.


Rick Gaudette
Quanren Xiong
John Heumann  


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




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Time: 21:10:05 GMT, March 20, 2017