# fnVolume: The file names of tomograms fnVolume = {'../../6E6.rec'} # fnModParticle: The file names of IMOD models for each tomogram. fnModParticle = {'../../6E6.mod'} # initMOTL: A code specifying how to construct the initial motive list: # 0: Set all rotational values to zero # # 1: Use the particle and reference model points to initialize # rotation around the particle z axis # # 2: Use the particle and refernce model points to initialize # rotation around the particle x and z axes # # 3: Uniform random rotations # # 4: Random axial rotations # # or a cell array of strings specify the filenames to load initMOTL = {'../../6E6_InitMotl.csv'} # tiltRange: The tilt angles used to acquire the tilt series [min max]. # Used to compensate for the missing wedge during alignment and # averaging. An empty array, [] or {}, disables this compensation # (and uses more efficient but less accurate real-space averaging). # For use with dual or multiple axes, tiltRange can also be a (cell) array # of strings, with each string specifying the path to an appropriate # binary mask. tiltRange = {[-62.79, 65]} # dPhi: dPhi: angular search range around the particle Y axis. dPhi = {-9:3:9, -4.5:1.5:4.5, -2.25:0.75:2.25} # dTheta: dTheta: angular search range around the particle Z axis. dTheta = {-9:3:9, -4.5:1.5:4.5, -2.25:0.75:2.25} # dPsi: dPsi: angular search range around the paricle X axis. dPsi = {-9:3:9, -4.5:1.5:4.5, -2.25:0.75:2.25} # searchRadius: Search radii in tomogram pixels for each iteration. # A single integer specifies the same radius for X, Y, and Z, while # a vector of 3 integers gives X, Y, and Z radii separately. E.g. # searchRadius={4, 5} is equivalent to searchRadius={[4 4 4], [5 5 5]}. searchRadius = {[2], [2], [2]} # lowCutoff: The frequency domain cutoff parameters for prefiltering the # particles and reference. lowCutoff =< 0 prevents low frequency # filtering. An optional second parameter defines the transition width. lowCutoff = {[0, 0.05], [0, 0.05], [0, 0.05]} # hiCutoff: The frequency domain cutoff parameters for prefiltering the # particles and reference. hiCutoff >= 0.866 prevents high frequency # filtering. An optional second parameter defines the transition width. hiCutoff = {[0.35, 0.05], [0.35, 0.05], [0.35, 0.05]} # refThreshold: Controls reference generation at each iteration. If less # than or equal 1, it specifies the minimum cross-correlation threshold. # If greater than 1, it is the number of particles to use. refThreshold = {100, 100, 100} # duplicateShiftTolerance: an integer array giving the maximum distances # in pixels at which particles can be considered duplicates at each # iteration. As for searchRadius, X, Y and Z distances may be specified # individually or a single number can be given for all 3. duplicateShiftTolerance = [NaN, NaN, NaN] # duplicateAngularTolerance: an array giving the maximum angle (in degrees) # between orientations at which particles can be considered duplicates at # each iteration. duplicateAngularTolerance = [NaN, NaN, NaN] # reference: If flgFairReference = 1, an integer k specifying that a # binary search using k levels will be used to generate a multiparticle # reference containing 2^k particles. Otherwise, if a string, the name # of an MRC file containing the reference volume, or if [i j], # specifies the jth particle of ^the ith volume as the reference. reference = '../../InitialRef.mrc' # fnOutput: The base name to use in constructing output filenames. fnOutput = '6E6' # szVol: The size of the volume to be averaged in voxels. szVol = [50, 50, 50] # alignedBaseName: The basename for writing invididual aligned particles. # (default = '' or missing means do not create these files). alignedBaseName = '' # debugLevel: How much debugging info to print < 0 | 1 | 2 | 3 > debugLevel = 3 # lstThresholds: Numbers of particles to use for computing the final averages. # A volume will generated for each value in this vector. The # corresponding files will be named _AvgVol_P.mrc lstThresholds = [162] # refFlagAllTom: Controls particle selection during reference generation. # 1: use particles with the best correlation scores among all # particles of all tomos when creating new references. # 0: prefer equal numbers of particles from each tomogram # when creating new references. refFlagAllTom = 0 # lstFlagAllTom: Controls particle selection during final averaging. # 1: use particles with best correlation scores among all particles # of all tomos when creating final averages. # 0: prefer equal number of particles from each tomo when creating # final averages. lstFlagAllTom = 0 # particlePerCPU: The maximum number of particles distributed simultaneously to # a single cpu during parallel processing. particlePerCPU = 5 # yaxisType: specifies the particle's Y axis. # 0: use the volume's Y axis as the particle's Y axis. # 1: particle model points determine the particle Y axis. # 2: end points of the contour containing the particle determine the # particle Y axis. yaxisType = 1 # yaxisObjectNum: OBSOLETE. No longer supported. yaxisObjectNum = NaN # yaxisContourNum: OBSOLETE. No longer supported. yaxisContourNum = NaN # flgWedgeWeight: Apply missing wedge compensation during alignment? flgWedgeWeight = 1 # sampleSphere: If set to 'full' or 'half', speed up full- or half- # spherical searches at the first iteration by automatically choosing # appropriate angular sampling intervals for Theta and Psi based on # sampleInterval. If missing or set to 'none', do a full grid search # based on dPhi, dTheta, and dPsi. sampleSphere = 'none' # sampleInterval: during spherical sampling, the minimum interval in # degrees at which Theta and Psi will be sampled. This sampling interval # will be used at the equator, with larger intervals nearer the poles. sampleInterval = NaN # maskType: Controls optional masking of the reference. # If 'sphere' or 'cylinder", generate a spherical or cylindrical mask # based on 'insideMaskRadius' and ^'outsideMaskRadius'. The axis of the # cylindrical mask will default to the particle Y axis, but can be # overridden using MaskModelPts, below. If a string other than than 'sphere', # 'cylinder', or 'none', the filename of an MRC image containing the mask, # with non-zero values indicating voxels to be included. If missing, or set # to 'none', there will be no masking. maskType = 'none' # maskModelPts: Manually specify cylindrical mask orientation. # If not empty, determines the axis of the cylindrical mask. # The format is [Z Y], where Z and Y are Slicer angles specifying rotations # in integer degrees around the tomogram Z and Y axes. These rotations # (first Z, then Y) will be applied to an initial vector along the Y axis. # If empty, PEET will attempt to choose an appropriate axis automatically. maskModelPts = [] # insideMaskRadius: radius in pixels. # Voxels at smaller radii will be masked out. insideMaskRadius = 0 # outsideMaskRadius: = radius in pixels. # Voxels at larger radii will be masked out. outsideMaskRadius = NaN # nWeightGroup: number of groups to use for equalizing cross-correlation # between groups with different orientations during averaging. nWeightGroup = 8 # flgRemoveDuplicates: If non-zero, duplicate particles will be removed from # further consideration after each round of alignment by assigning them # to the duplicate class ID (-9999). AverageAll and calcSSNR ignore # members of this class when flgRemoveDuplicates is 1. calcFSC does also # unless -9999 is explicitly added to selectClassID. flgRemoveDuplicates = 0 # flgAlignAverages: If non-zero, align particles to have their Y axes # approximately vertical in the final average. flgAlignAverages = 0 # flgFairReference: If 1, create a multiparticle reference. Otherwise, # choose a single particle reference or use the user-specified volume. flgFairReference = 0 # flgAbsValue: If 1 (default), maximize the absolute value of the # cross-correlation during alignment, rather than the raw # cross-correlation. Use of the absolute value reduces the chance of # pure noise reinforcing to match the reference, but can prevent # proper alignment of some highly repetitive patterns (e.g. # checkerboard or zebra stripe patterns) in which in which in- and # out-of-phase alignments become indistinguishable. flgAbsValue = 1 # flgStrictSearchLimits: If 0 (default) or missing, radial and # angular search limits will be2 applied independently at each iteration. # If 1, the overall change for any parameter will be limited to the largest # change specified at any single iteration. flgStrictSearchLimits = 0 # edgeShift: The number of pixels to shift the edge of the wedge mask to # ensure that all of the frequency info is included. edgeShift = 0 # flgNoReferenceRefinement: If 1, use the initial reference at all # iterations. If 0 (the default), a refined estimate of the reference # will be generated at each iteration. flgNoReferenceRefinement = 0 # flgRandomize: If 1 (default = 0), select particles for averaging randomly, # rather than by cross-correlation. flgRandomize = 0 # cylinderHeight: The height in voxels of the cylindrical mask. Blank or NaN # will be treated as infinity, and the cylinder will span the entire volume. cylinderHeight = NaN # maskBlurStdDev: Blur the mask by convolution with a Gaussian having this # standard deviation (in voxels). If omitted or NaN (the default), the # mask will be binary. After blurring, the mask edge will be spread # over approximately 2.5 standard deviations on either side of # the original edge location. maskBlurStdDev = NaN # flgVolNamesAreTemplates: If 1 (default = 0), file names in the volume # table (i.e. volume, model, initial motive list, and wedge mask file # names) may be templates to be expanded rather than individual # filenames. For example, "vol1-10.mrc", would be expanded by PEET to # [vol1.mrc, vol2.mrc, ... vol10.mrc]. Any filename ending in 2 numbers # separated by a dash ('-') and, optionally, follwed by a suffix, will # be considered a template. flgVolNamesAreTemplates = 0 # The following were added manually for clustering/classification #pcaFnParticleMask = '../../RS2MaskLong.mrc'