# fnVolume: The file names of tomograms fnVolume = {'../odd/bpv_AvgVol_4P66.mrc', '../even/bpv_AvgVol_4P66.mrc'} # fnModParticle: The file names of IMOD models corresponding to each tomogram. fnModParticle = {'center.mod', 'center.mod'} # initMOTL: A code specifying how to construct the initial motive list: # 0: Set all rotational values to zero # # 1: Use the particle model and reference index to # initialize theta (rotation around the z axis), be sure # the points are sorted along a direction of interest # # 2: Use the particle model and reference index to initialize # theta and psi (rotation around the z axis and x axis) # # 3: Uniform random rotations. # # 4: Random axial rotations. # # or a string array to specify the filenames to load, must end in 1.em initMOTL = 0 # tiltRange: The tilt range used to acquire the tilt series [min max]. # This will compenstate for the missing wedge in generating # the alignment and the averages. A empty array, [] or {}, specifies # not to account for the missing wedge (and use more efficient # space domain averaging). tiltRange = {'../odd/wedgeWeightBinary_P66.mrc', '../even/wedgeWeightBinary_P66.mrc'} # dPhi: Phi is the rotation around the Y-axis specified above by the parameter "yaxis". # From this Y-axis, the corresponding X-axis and Z-axis are deduced. dPhi = {-36:9:36, -12:4:12, -6:2:6} # dTheta: Theta is around the corresponding Z-axis. dTheta is the increment. dTheta = {-36:9:36, -12:4:12, -6:2:6} # dPsi: Psi is around the corresponding X-axis. dPsi is the increment. dPsi = {-36:9:36, -12:4:12, -6:2:6} # searchRadius: The number of pixels to search in each dimension # searchRadius={4, 5} is equivalent to searchRadius={[4 4 4],[5 5 5]} searchRadius = {[4], [3], [2]} # lowCutoff: The frequency domain cutoff parameters for prefiltering the # particles and reference lowCutoff =< 0 prevents low frequency # filtering, hiCutoff >= 0.866 prevents high 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 lowCutoff =< 0 prevents low frequency # filtering, hiCutoff >= 0.866 prevents high frequency filtering. # An optional second parameter defines the transition width. hiCutoff = {[0.3, 0.05], [0.3, 0.05], [0.3, 0.05]} # refThreshold: The threshold to generate the reference particle at each stage # If this is less than 1 it specifies a cross correlation # coefficient threshold, if it is greater than 1 it specfies the # number of particles to use refThreshold = {1, 1, 1} # duplicateShiftTolerance: An arry of integers giving the maximum distance in pixels at # which particles can be considered duplicates at each iteration. Applied # separately to each dimension, so the region defined is a cube rather # than a sphere. duplicateShiftTolerance = [NaN, NaN, NaN] duplicateAngularTolerance = [NaN, NaN, NaN] # reference: If it is a string it should specify the name of an MRC file containing # the reference volume. If it is [i j]. It specifies the reference to be the # jth particle of the ith tomogram. reference = [1, 1] # fnOutput: The base name of the output files for the average volumes, the # reference volumes, and the transformation parameters fnOutput = 'bpv' # szVol: The size of the volume around each particle to average # if reference is filename, this parameter is ignored. the reference size dictates "szVol". szVol = [52, 52, 52] # CCMode: The cross correlation measure to use. # 0: Local energy normalized cross correlation (default) # 1: True local correlation coefficient CCMode = 1 # alignedBaseName: The basename for the aligned particle MRC files (default: ''). alignedBaseName = 'aligned' # debugLevel: How much debugging info to print {0|1|2|3} debugLevel = 3 # lstThresholds: The list of thresholds to use for computing the final volumes. # An average volume is generated for each value in this vector. # The format of the average volume file name is # fnOutout_AvgVol_navg_thresh_iteration.mrc lstThresholds = [2] # refFlagAllTom: 1: use particles with best correlation scores among all particles of all tomos; # 0: prefer equal number of particles from each tomo; refFlagAllTom = 1 # lstFlagAllTom: 1: use particles with best correlation scores among all particles of all tomos; # 0: prefer equal number of particles from each tomo; lstFlagAllTom = 1 # particlePerCPU: Specify how to distribute workload among all CPUs. # of particles per CPU for each # run. particlePerCPU = 1 # yaxisType: 0: use the volume's Y axis as the particle's Y axis. # 1: use the vector between neighboring model points as the Y axis. # 2: use end points of the contour specified by the "yaxisContour" parameter # as the Y axis. yaxisType = 0 # yaxisObjectNum: An integer specifying the index of the model object used for Y axis determination when yaxisType is 2. yaxisObjectNum = NaN # yaxisContourNum: An integer specifying the index of the contour in object "yaxisObjecNum" whose endpoints will determine the Y axis for the associated volume when when yaxisType is 2. yaxisContourNum = NaN # flgWedgeWeight: Apply missing wedge compensation to the alignment search flgWedgeWeight = 1 # sampleSphere: If This is set to 'full' or 'half', for the fisrt iteration, dTheta and dPsi will be ignored and # 'dPhi' and 'sampleInterval' will be used. # if it does not exist or is set to 'none', it will search over the range specified by dPhi, dTheta, dPsi. sampleSphere = 'none' # sampleInterval: The interval in degrees at which the spherical surface is sampled. sampleInterval = 9 # maskType: If it is set to 'sphere' or 'cylinder', it will use 'insideMaskRadius' and # 'outsideMaskRadius' to create a mask. # If it is set to a string other than 'sphere', 'cylinder', or 'none', the # string is assumed to be a filename of a stack whose voxels of zero value # specify voxels that will be masked out, whose voxels of nonzero value # specify voxels that will be included. # If it does not exist or is set to 'none', there will be no masking. maskType = 'sphere' # maskModelPts: It specifies which model and which point of that model will be used to create a # 'cylinder' mask. The format is [i j]. # It specifies the jth point of the ith model will be used. # It is used only when reference is specified as a filename and # maskType='cylinder'. # When reference is specified as [ii jj], the [ii jj] will be used. maskModelPts = [] # insideMaskRadius: radius in pixels. Voxels residing inside this radius is masked out; # for .77 virus tomo; insideMaskRadius = 10 # outsideMaskRadius: radius in pixels. Voxels residing outside this radius is masked out; outsideMaskRadius = 22 # flgRemoveDuplicates: If non-zero, search for and mark duplicate particles after # each alignment iteration. Particles marked as duplicates will be # excluded from averages and resolution estimates. flgRemoveDuplicates = 0 # flgAlignAverages: If non-zero, and if "yaxisType" is also non-zero, rotate average # volumes to have the particle's Y axes approximately vertical. flgAlignAverages = 0 #fnWedgeWeight = 'ww' # nWeightGroup: Disable (0) or enable (> 0) equalization of cross-correlations # between groups based on missing wedge orientation. If enabled, equalization # will be applied to minimize missing wedge bias during averaging and new # reference generation. NOTE: as of PEET 1.8.0 this parameter is an on / off # flag; the number of groups is no longer under direct user control. nWeightGroup = 8 # 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 be 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 = 1 # 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 = 1 # 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 = 1 # flgVolNamesAreTemplates: If 1 (default = 0), file names in the volume table (i.e. # volume, model, initial motive list, and wedge mask files 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