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Contents.m
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% CODE
%
% Files
% addpathdir - add folders of filenames using addpath() and dir()
% allcomb - All combinations (Cartesian Product)
% axpolytope - Indices of a polytope with vertices on every axis and every intersection of every plane formed by axes.
% axpolytope_test - generate vertices on the axes of a polytope in n-D
% chebycenter - Compute Chebyshev center of polytope Ax <= b.
% constant_colorbar - script to generate a colorbar with constant limits
% constructGBMatrices - Make Olmsted GB matrices for GB5DOF using labframe quaternion/normal inputs
% correctdis - convert to disorientation (for plotting)
% cprnd - Draw from the uniform distribution over a convex polytope.
% datagen - generate octonion data for various literature datasets (or
% datagen_setup - setup for generating octonion data (random or from literature)
% datagen_test - test generation of octonion data
% degdelaunayn - compute delaunay triangulation of d-1 hyperplane in d-dimensions
% disorientation - determines the unique misorientation between two adjacent
% DisplayRequiredFunctions - List required files and toolboxes. Displays them in the command window or console window (if deployed).
% dynamicCellExample - Dynamically creating a nested cell structure (unfinished/deprecated)
% facet_subdiv - Project a facet from n-dimensional space to a simplex in n-1
% facet_subdiv_test - SUBDIV_TEST e.g. subdivide a d-1 or d-2 simplex (e.g. triangle or line in 3D Cartesian coordinates) and plot
% findgeometry - FINDGEOMETRY: Output the misorientation FZ geometry of a point given a quaternion (e.g. 'OAB').
% findgeometry_test - test findgeometry for 'OAB', 'OBCE', 'OADE', etc. of misorientation FZ
% fz_inserter - Compute misorientations in the fundamental zone for two lists of orientations
% GB5DOF - computes the energy of an arbitrary boundary in FCC metals (BRK energy function)
% GB5DOF_setup - Compute 5DOF GB energy from BRK function
% GB5DOF_setup_test - GB5DOF_setup test
% GBdist2 - troubleshooting for GBdist() (deprecated)
% GBdist3 - troubleshooting for GBdist() (deprecated)
% GBdist4 - modified version of GBdist function by CMU group. Keeps o1 constant.
% GBdist4_r2018a - arguments
% GBdistdis - modified version of GBdist() (deprecated)
% GBdistEucl - modified version of GBdist() for Euclidean distances (deprecated)
% GBlab2oct - convert lab coordinate grain boundareis to octonions
% GBlab2oct_test - Test from GB Octonion Tutorial script
% GBoct2five - (incorrect, derivation error, 2020-11-03) Inverse operation of GBfive2oct.m (GB_octonion_code), output "five" struct
% GBoct2five_r2018a - arguments
% GBoct2five_test -
% GBoct2five_test2 -
% GBpair - (deprecated) Method 1: Find o3 that has the minimum summed distances, o1-->o3, and o2-->o3.
% GBpair2 - deprecated
% GBpair_r2018a - arguments
% GBpair_test - test
% gcfpos - get current figure position and copy to clipboard
% get_cubo - get n quaternions from randomly or uniformly sampled cubochoric points
% get_cubo_r2018a - arguments
% get_errmetrics - get various error metrics for measured data relative to
% get_failed - find failed jobs (under construction)
% get_failed_test - test getfailed.m
% get_fname - Get a filename to load or save (deprecated, specific to old naming scheme)
% get_interp - Interpolate query point values based on spherical or planar barycentric coords in a mesh
% get_octpairs - Get a set of octonions that are symmetrized with respect to a fixed reference GB (rng seed == 10)
% get_octpairs2 - deprecated version of get_octpairs()
% get_octpairs_r2018a - arguments
% get_octpairs_test - get_octpairs test
% get_ocubo - get octonions formed by pairs of quaternions from randomly or uniformly sampled cubochoric points.
% get_ocubo_r2018a - arguments
% get_ocubo_test - get_ocubo test
% get_omega - calculate octonion distance
% get_omega_r2018a - arguments
% get_repsets - Find sets of points with at least a degeneracy of n
% get_repsets_test - nonunique test
% get_sympairs - get all combinations (pairs) of operators for a point group
% get_sympairs_r2018a - arguments
% hsphext_subdiv - Hypersphere exterior hull subdivision.
% hsphext_subdiv_test - hypersphere exterior hull subdivision test
% hypercube - Calculate vertices and convex hull triangulation of a hypercube
% hypercube_test - hypercube test
% hyperquadrant - Generate n-dimensional Ellipsoid or Sphere
% hypersphere - Generate n-dimensional Ellipsoid or Sphere
% hypersphere_subdiv - Subdivide a "spherical" convex hull and collapse the triangulation.
% hypersphere_subdiv_test -
% hypersphereSetup - wrapper function for hypersphere.m, includes 'orthant' option
% inBPFZ - return logical of which boundary plane normals are in BP fundamental zone
% InCubicFZ - Test whether or not a set of rodrigues vectors is within the cubic misorientation fundamental zone.
% inhull - tests if a set of points are inside a convex hull
% inhull_setup - wrapper function for inhull (deprecated)
% inmisFZ - check which rodrigues vectors fall inside the misorientation fundamental zone via vert2con (FEX)
% inmisFZ_test - inmisFZ test
% insertrows - Insert rows into a matrix at specific locations
% interp5DOF - Convert misorientation and boundary plane normal 5DOF input
% interp5DOF_setup - setup for interpolating five-degree-of-freedom property
% interp5DOF_test - interp5DOF test
% interpplot - Create parity plot with 5DOF plots on side (deprecated)
% intersect_facet - Find intersection of ray with facet using barycentric coordinates.
% intersect_facet_test - intersect facet test
% ismembc_test - ismembc vs. ismember test
% knninterp - compute linear interpolation using hyperplane fitted to k-nearest neighbors
% knninterp_test - knninterp test
% mesh5DOF - generate "five" and "o" for a five degree-of-freedom fundamental zone (deprecated)
% meshBP - generate boundary plane (BP) fundamental zone mesh for a
% meshBP_test - test meshBP
% meshFZ - mesh the misorientation fundamental zone (issues with tetgen)
% meshgen - generate octonions randomly or from literature (deprecated)
% meshgen_test -
% misFZcon - get constraints for misorientation fundamental zone (misFZ)
% misFZcon_test - misFZcon test
% mustBeSqrt2Norm - check that first octonion in list has norm == sqrt(2) and each quaternion has norm == 1
% mustContainFields - check fieldnames(S) and make sure every checkname exists
% myismember - do an ismembertol by rows with set precision and tolerance
% n2c - t = num2cell(pts,1)
% n2cplot - convert rows of points to cells of points, convenient for plotting.
% normr - normalizes vectors row-by-row. Outputs zero vector if zero vector input (shadowed by Computer Vision Toolbox)
% numStabBary - a numerically stable barycentric approach in high dimensions
% numStabBary_example -
% numSubplots - Calculate how many rows and columns of sub-plots are needed to neatly display n subplots
% Oh_pg - Oh point group load/testing function
% optimize_zeta - Minimize the pairwise distance matrix of a set of GBs w.r.t. zeta (twist angle via U(1) symmetry)
% optimize_zeta_r2018a - arguments
% optimize_zeta_test - optimize_zeta test
% optimize_zeta_test_r2018a - optimize_zeta test
% orthoplex - Find indices and convex hull triangulation of an orthoplex
% orthoplex_test - orthoplex test
% OSLERP_setup - script to call OSLERP (deprecated)
% OSLERP_setup2 - another script to call OSLERP (deprecated)
% osymset - get symmetrically equivalent octonions
% osymset_r2018a - arguments
% osymsets - Get symmetrically equivalent octonions (osymsets) for each octonion in a list of octonions
% osymsets_r2018a - arguments
% parityplot - Create a parity plot and pass options to (scatter() or hexscatter()) and refline().
% parseReqFiles - parse required files & products using fileseparator sep
% parseReqFiles_test - parseMyFiles_test
% pd_sse - get the error of a pairwise distance matrix relative to the true pairwise distance matrix
% pd_sse_r2018a - arguments
% plot5DOF - plotting five degree-of-freedom parameters in misorientation and boundary plane spaces
% plotFZrodriguez - define the FZ vertices
% plotFZrodriguez_test - PLOTFZRODRIGUEZ_TEST
% plotFZrodriguez_vtx - plotFZrodriguez with 'A','B','C','D','E','O' vertices
% proj_down - project down by removing null dimensions (i.e. a rotation and translation) via singular value decomposition
% proj_down_r2018a - arguments
% proj_down_test -
% proj_up - project up (restore null dimensions) using "USV" struct from proj_down.m
% projfacet2hyperplane - project facet vertices onto a hyperplane defined by nvec
% projfacet2hyperplane_test - project facet to hyperplane test
% projray2hyperplane - Project ray (pt) from unit hypersphere to tangent hyperplane at another point (nvec)
% projray2hyperplane_test - project ray to hyperplane test
% projray2hypersphere - project ray to hypersphere, compute barycentric coordinates, compute intersecting facet
% projray2hypersphere_test - project ray to hypersphere test
% randOctParityData - submit sets of jobs to supercomputer or run locally for interp5DOF()
% readNODE - Read vertex positions from .node file, .node files are used by Stellar and Triangle
% rescale_test - rescale test (test of built-in function)
% rotationmat3D - creates a rotation matrix based on axis and angle
% RotMatrix - N-dimensional Rotation matrix
% roundp - rounds values in x to n digits past the decimal sign.
% run - run - Run MATLAB script
% run2 - run test
% sbatch_setup - setup for SLURM sbatch submissions (deprecated)
% simplex_subdiv - Compute the subdivision cartesian coordinates of a simplex
% slightRot - rotate points slightly in every dimension
% slightRot_test - slight rotation matrix test
% sphbary - compute spherical barycentric coordinates of a facet or simplex [1]
% sphbary_setup - sphbary coords and intersections for points
% sphbary_test - spherical barycentric coordinates test
% sphconvhulln - Compute the "convex hull" on a spherical surface
% sphconvhulln_test - spherical convhulln test
% sphere_stereograph - compute the stereographic image of points on a sphere.
% sphere_stereograph_inverse - compute stereographic preimages of points.
% sphere_stereograph_test - sphere stereograph test
% sphere_stereographic_inverse_test - sphere stereographic inverse test
% sphtri_subdiv - Subdivision scheme that segments the triangle formed by vertices of a spherical triangle
% sphtri_subdiv_test -
% sqrt2norm - take a set of octonions and give each row norm == sqrt(2) if (norm == 1) || (norm == sqrt(2))
% sqrt2norm_r2018a - arguments
% symaxis - Return the symmetry axes (if multiple) and the geometry given a quaternion
% symaxis_test - {
% tblvertcat - vertically catenate tables with different variables, filling in dummy values as needed
% tblvertcat_test - tblvertcat_test
% testForGBFZSymmetryPlot -
% toBPFZ - Rotate an arbitrary boundary plane normal for quaternion into standard boundary plane fundamental zone
% tofiveFZ - Take 5DOF data and rotate it into misorientation and boundary plane fundamental zones.
% tricollapse - collapse triangulation of points (i.e. a triangulation involving repeat points).
% vecpair2rmat - Compute a (non-unique) rotation matrix to go from v1 to v2.
% vert2con - convert a set of points to the set of inequality constraints
% vert2lcon - An extension of Michael Kleder's vert2con function, handles degeneracy
% write_video - write a set of images to a video named movname with some defaults
% write_video_test -
% zeta_min2 - ZETA_MIN Alternative version of CMU group function zeta_min(), vectorized by Sterling Baird
% zeta_min2_r2018a - arguments
% GBoct2mat - convertion grain boundary octonions to orientation matrices (**unfinished**)
% Kim2oct - load Kim2011 dataset, convert to norm-symmetrized octonions
% avgrepeats - average values for duplicate points, remove all but one from degenerate set
% avgrepeats_test - avgrepeats test
% bugtest - checking a "bug" (turns out actually intended) with arguments..end syntax
% el2po - elevation angles to polar angles
% el2po_test - po2el_test
% get_alen - get arclength of sphere (acos of dot product)
% get_charlbl - get character labels, e.g. '(a)', '(b)', ... for figures.
% get_five - generate random cubochoric misorientation and random boundary plane normal pairs
% get_knn - k-nearest neighbor points, distances, mean, and std
% get_walltimefn - get a function handle for computing interp5DOF SLURM walltimes (e.g. 'gpr')
% hexscatter - A scatter-plot substitute - generate a density plot using hexagonal patches.
% idw - inverse-distance weighting interpolation
% idw_tovar - Original inverse distance weight function by Andrew Tovar
% multiparity - create tiled parity plots using cell parity data
% multixyplots - create tiled xy-plots from variables in a table
% nnhist - nearest neighbor distance histogram
% nnhist_test - nnhist test
% padcat - concatenate vectors with different lengths by padding with NaN
% paperfigure - call figure in centimeters and with appropriate size
% papertext - do a text() command for the figure labels '(a)', '(b)', etc. for num == 1, 2, etc.
% plotting - plotting script for interp5DOF paper
% po2el - convert polar angles to elevation angles
% qlab2qm - Convert lab/sample frame quaternions of grain A and grain B and
% qmA2nA - QLAB2FIVE Convert lab/sample frame quaternions of grain A and grain B and
% quivplot - plot three quivers in the x-hat, y-hat, and z-hat directions
% savefigpng - save a figure and print the figure as 300 DPI .png
% sphplot - plot a simple sphere for visualization purposes
% tblfilt - filter a table based on a struct of parameters (deprecated, see built-in findgroups() and splitapply())
% tblfilt_test - parfilter_test
% test_voronoisphere - Script to test voronoisphere (modified from original (Bruno Luong) by Sterling Baird)
% toBPFZ_test -
% vcell_solidangle - Compute the solid angles of All voronoi cell
% voronoisphere - Compute the voronoi's diagram of points on the spheres S^2
% xyplot - make an errorbar xyplot using a table (tbl) and output (G) from findgroups()
% xyplots - plot multiple datasets on the same axes using a "master" table and findgroups()