# fnVolume: The file names of tomograms
fnVolume = {'../../../reconstructed_tomogram/Xen_D_tomo3_rec.mrc'}

# fnModParticle: The file names of IMOD models for each tomogram.
fnModParticle = {'Xen_D_MT26_PtsAdded_Twisted.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 reference 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 = {'Xen_D_MT26_PtsAddedRefP90_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 = {'../Xen_D_tomo3_mask.mrc'}

# dPhi: dPhi: angular search range around the particle Y axis.
dPhi = {-6.9:4.6:6.9, -3.5:2.3:3.5, -1.7:1.2:1.7, -1:1:1}

# dTheta: dTheta: angular search range around the particle Z axis.
dTheta = {-6.9:4.6:6.9, -3.5:2.3:3.5, -1.7:1.2:1.7, -1:1:1}

# dPsi: dPsi: angular search range around the paricle X axis.
dPsi = {-6.9:4.6:6.9, -3.5:2.3:3.5, -1.7:1.2:1.7, -1:1:1}

# 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 = {[6], [4], [2], [1]}

# 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 = {[0.1, 0.05], [0.1, 0.05], [0.1, 0.05], [0.1, 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 = {[0.1, 0.05], [0.1, 0.05], [0.1, 0.05], [0.1, 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 = {130, 130, 130, 130}

# 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, 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, 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 = [1, 90]

# fnOutput: The base name to use in constructing output filenames.
fnOutput = 'Xen_D_MT26'

# szVol: The size of the volume to be averaged in voxels.
szVol = [54, 54, 54]

# 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 <fnOutput>_AvgVol_<iterNum>P<navg>.mrc
lstThresholds = [165:165:165]

# 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 = 1

# 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 = 1

# 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.
# 3: user-defined Y axes.
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 = 'cylinder'

# 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 = 4

# outsideMaskRadius: = radius in pixels. 
# Voxels at larger radii will be masked out.
outsideMaskRadius = 24

# 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 = 1

# 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 = 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 = 54

# 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 = 2

# 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