added extra help documentation

braindynamicslab · Dec 18, 2021 · cebc899 · cebc899
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diff --git a/code/neumapper/find_cluster_cutoff.m b/code/neumapper/find_cluster_cutoff.m
@@ -1,4 +1,22 @@
 function [Z, cutoff] = find_cluster_cutoff(distMat, num_bins_clustering, linkage_method)
+% Function find_cluster_cutoff
+% 
+% Helper function used internally for get_cluster_bins.m
+% 
+% Inputs:
+% distMat               : distance matrix restricted to the elements of a
+%                           cover bin
+% num_bins_clustering   : Positive integer used to define the histogram. 
+%                           Default = 10 when used in neumapper 
+% linkage_method        : Type of hierarchical clustering. 
+%                           Default = 'single'
+% 
+% Outputs:
+% Z         : output of linkage function
+% cutoff    : threshold value used for subdividing cover bin into cluster
+%               bins
+% 
+
    Z = linkage(distMat(tril(true(length(distMat)),-1))', linkage_method);
 
    lkg_vals = unique(Z(:,3));

diff --git a/code/tools/constructNPYheader.m b/code/tools/constructNPYheader.m
@@ -1,7 +1,35 @@
-
-
-
 function header = constructNPYheader(dataType, shape, varargin)
+% Original repository: https://github.com/kwikteam/npy-matlab
+% Please see below for details, and credit the original authors if you use
+% this file.
+% 
+% BSD 2-Clause License
+% 
+% Copyright (c) 2015, npy-matlab developers
+% All rights reserved.
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions are met:
+% 
+% 1. Redistributions of source code must retain the above copyright notice, this
+%    list of conditions and the following disclaimer.
+% 
+% 2. Redistributions in binary form must reproduce the above copyright notice,
+%    this list of conditions and the following disclaimer in the documentation
+%    and/or other materials provided with the distribution.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+% DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+% FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+% SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+% OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+% OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+
 
 	if ~isempty(varargin)
 		fortranOrder = varargin{1}; % must be true/false

diff --git a/code/tools/datToNPY.m b/code/tools/datToNPY.m
@@ -1,6 +1,9 @@
-
-
 function datToNPY(inFilename, outFilename, dataType, shape, varargin)
+% Original repository: https://github.com/kwikteam/npy-matlab
+% Please see below for details, and credit the original authors if you use
+% this file.
+% 
+% 
 % function datToNPY(inFilename, outFilename, shape, dataType, [fortranOrder, littleEndian])
 %
 % make a NPY file from a flat binary file, given that you know the shape,
@@ -10,7 +13,33 @@ function datToNPY(inFilename, outFilename, dataType, shape, varargin)
 % existing binary file - instead you can just create the appropriate header
 % and then concatenate it with the data. 
 %
-% ** completely untested
+% BSD 2-Clause License
+% 
+% Copyright (c) 2015, npy-matlab developers
+% All rights reserved.
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions are met:
+% 
+% 1. Redistributions of source code must retain the above copyright notice, this
+%    list of conditions and the following disclaimer.
+% 
+% 2. Redistributions in binary form must reproduce the above copyright notice,
+%    this list of conditions and the following disclaimer in the documentation
+%    and/or other materials provided with the distribution.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+% DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+% FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+% SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+% OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+% OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+
 
 if ~isempty(varargin)
     fortranOrder = varargin{1}; % must be true/false
@@ -22,9 +51,6 @@ function datToNPY(inFilename, outFilename, dataType, shape, varargin)
 
 header = constructNPYheader(dataType, shape, fortranOrder, littleEndian);
 
-% ** TODO: need to put the header into a temp file instead, in case the
-% outFilename is the same as the inFilename (and then delete the temp file
-% later)
 fid = fopen(tempFilename, 'w');
 fwrite(fid, header, 'uint8');
 fclose(fid)

diff --git a/code/tools/px_maxmin.m b/code/tools/px_maxmin.m
@@ -1,5 +1,9 @@
 function [L, DL, R] = px_maxmin(varargin)
-
+% Function px_maxmin used for farthest point sampling
+% Original authors: Vin de Silva, Patrick Perry, and collaborators from the
+% Computational Topology working group at Stanford University. Please see
+% below for details, and credit the original authors if you use this code.
+% 
 %PX_MAXMIN -- select landmark points by greedy optimisation
 %
 % Given a set of N points, PX_MAXMIN selects a subset of n points called

diff --git a/code/tools/readNPY.m b/code/tools/readNPY.m
@@ -1,11 +1,40 @@
-
-
 function data = readNPY(filename)
 % Function to read NPY files into matlab.
+% 
+% Original repository: https://github.com/kwikteam/npy-matlab
+% Please see below for details, and credit the original authors if you use
+% this file.
+% 
 % *** Only reads a subset of all possible NPY files, specifically N-D arrays of certain data types.
 % See https://github.com/kwikteam/npy-matlab/blob/master/tests/npy.ipynb for
 % more.
 %
+% BSD 2-Clause License
+% 
+% Copyright (c) 2015, npy-matlab developers
+% All rights reserved.
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions are met:
+% 
+% 1. Redistributions of source code must retain the above copyright notice, this
+%    list of conditions and the following disclaimer.
+% 
+% 2. Redistributions in binary form must reproduce the above copyright notice,
+%    this list of conditions and the following disclaimer in the documentation
+%    and/or other materials provided with the distribution.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+% DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+% FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+% SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+% OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+% OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
 
 [shape, dataType, fortranOrder, littleEndian, totalHeaderLength, ~] = readNPYheader(filename);
 

diff --git a/code/tools/readNPYheader.m b/code/tools/readNPYheader.m
@@ -1,14 +1,43 @@
-
-
 function [arrayShape, dataType, fortranOrder, littleEndian, totalHeaderLength, npyVersion] = readNPYheader(filename)
+% Original repository: https://github.com/kwikteam/npy-matlab
+% Please see below for details, and credit the original authors if you use
+% this file.
+% 
 % function [arrayShape, dataType, fortranOrder, littleEndian, ...
 %       totalHeaderLength, npyVersion] = readNPYheader(filename)
 %
 % parse the header of a .npy file and return all the info contained
 % therein.
+% 
 %
 % Based on spec at http://docs.scipy.org/doc/numpy-dev/neps/npy-format.html
-
+%
+% BSD 2-Clause License
+% 
+% Copyright (c) 2015, npy-matlab developers
+% All rights reserved.
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions are met:
+% 
+% 1. Redistributions of source code must retain the above copyright notice, this
+%    list of conditions and the following disclaimer.
+% 
+% 2. Redistributions in binary form must reproduce the above copyright notice,
+%    this list of conditions and the following disclaimer in the documentation
+%    and/or other materials provided with the distribution.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+% DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+% FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+% SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+% OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+% OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
 fid = fopen(filename);
 
 % verify that the file exists

diff --git a/code/tools/writeNPY.m b/code/tools/writeNPY.m
@@ -1,14 +1,42 @@
-
-
 function writeNPY(var, filename)
 % function writeNPY(var, filename)
 %
+% Original repository: https://github.com/kwikteam/npy-matlab
+% Please see below for details, and credit the original authors if you use
+% this file.
+% 
 % Only writes little endian, fortran (column-major) ordering; only writes
 % with NPY version number 1.0.
 %
 % Always outputs a shape according to matlab's convention, e.g. (10, 1)
 % rather than (10,).
-
+%
+% BSD 2-Clause License
+% 
+% Copyright (c) 2015, npy-matlab developers
+% All rights reserved.
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions are met:
+% 
+% 1. Redistributions of source code must retain the above copyright notice, this
+%    list of conditions and the following disclaimer.
+% 
+% 2. Redistributions in binary form must reproduce the above copyright notice,
+%    this list of conditions and the following disclaimer in the documentation
+%    and/or other materials provided with the distribution.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+% DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+% FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+% SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+% OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+% OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
 
 shape = size(var);
 dataType = class(var);