plateform stringclasses 1
value | repo_name stringlengths 13 113 | name stringlengths 3 74 | ext stringclasses 1
value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
|---|---|---|---|---|---|---|---|---|
github | xyza11808/MATLAB-master | squared_levenstein.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/squared_levenstein.m | 1,109 | utf_8 | 84456222699578d64124e96f1c94732c | function K = squared_levenstein(kern,dat1,dat2,ind1,ind2,kerParam)
%---calculating the distance matrix----
D= [];
Xf = get_x(dat1);
Xs = get_x(dat2);
X1 = {};
X2 = {};
for i = 1:size(Xf,1)
tmp = Xf(i,:);
X1{i} = tmp(tmp > 0);
end
for i = 1:size(Xs,1)
tmp = Xs(i,:);
X2{i} = tmp(tmp > 0);
end
D = zeros(length(in... |
github | xyza11808/MATLAB-master | symbol_string.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/symbol_string.m | 1,032 | utf_8 | 47615576056b2b8cce5fba0a9f138d74 | function K = symbol_string(kern,dat1,dat2,ind1,ind2,kerParam)
% --- conversion to sequences------------------
D= []; Xf = get_x(dat1); Xs = get_x(dat2); X1 = {}; X2 = {};
for i = 1:size(Xf,1), tmp = Xf(i,:); X1{i} = tmp(tmp > 0); end
for i = 1:size(Xs,1), tmp = Xs(i,:); X2{i} = tmp(tmp > 0);end
n = kerParam{1};
lam... |
github | xyza11808/MATLAB-master | triangle_levenstein.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/triangle_levenstein.m | 1,299 | utf_8 | b6ec92e672ffcfceff8bf7204954426f | function K = squared_levenstein(kern,dat1,dat2,ind1,ind2,kerParam)
%-------- convert matrix to cell array ----
D= [];
Xf = get_x(dat1);
Xs = get_x(dat2);
X1 = {};
X2 = {};
for i = 1:size(Xf,1)
tmp = Xf(i,:);
X1{i} = tmp(tmp > 0);
end
for i = 1:size(Xs,1)
tmp = Xs(i,:);
X2{i} = tmp(tmp > 0);
end
%----- get d... |
github | xyza11808/MATLAB-master | empirical_levenstein.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/empirical_levenstein.m | 1,111 | utf_8 | 8cf92e54279eb38ff7bc2d84c99d48ff | function K = empirical_levenstein(kern,dat1,dat2,ind1,ind2,kerParam)
%---calculating the distance matrix----
D= [];
Xf = get_x(dat1);
Xs = get_x(dat2);
X1 = {};
X2 = {};
for i = 1:size(Xf,1)
tmp = Xf(i,:);
X1{i} = tmp(tmp > 0);
end
for i = 1:size(Xs,1)
tmp = Xs(i,:);
X2{i} = tmp(tmp > 0);
end
D = zeros(length(... |
github | xyza11808/MATLAB-master | matching.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/matching.m | 1,966 | utf_8 | e473fac2e5fc05f63a32fae819314876 | function K = matching( k, d1, d2, ind1, ind2, par)
%
% Matching type similarity function (actually not a kernel) as described in the paper:
% "Recognition with local features: the kernel recipe"
% by C. Wallraven, B.Caputo and A.Graf
%
% takes 2 parameters: { minorKernelName, minorKernelParameter}
%
% implemented... |
github | xyza11808/MATLAB-master | kondor.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/kondor.m | 4,192 | utf_8 | 48340a77f793e03e46b4958284ba219f | function K = kondor( k, d1, d2, ind1, ind2, kpara)
%
% Set-Kernel as described in the paper:
% "Kernels between sets of vectors"
% by R.Kondor and T.Jebara
%
% takes 4 parameters: { eta (ridge), symmetryFlag, minorKernelName, minorKernelParameter}
%
% implemented minor kernel names are:
% 'linear', 'rbf' ....... |
github | xyza11808/MATLAB-master | string_subsequence.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/string_subsequence.m | 1,454 | utf_8 | 2247b85e3375c6ce58c3c7ac994ddc48 | function K = string_subsequence(kern,dat1,dat2,ind1,ind2,kerParam)
% --- conversion to sequences------------------
D= []; X1 = get_x(dat1); X2 = get_x(dat2);
% for i = 1:size(Xf,1), tmp = Xf(i,:); X1{i} = tmp(tmp > 0); end
% for i = 1:size(Xs,1), tmp = Xs(i,:); X2{i} = tmp(tmp > 0);end
n = kerParam{1};
lambda = ker... |
github | xyza11808/MATLAB-master | levenstein.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/levenstein.m | 1,267 | utf_8 | 00491c62cb54740ae520faed3e17b68c | function K = levenstein(kern,dat1,dat2,ind1,ind2,kerParam)
Xf = get_x(dat1);
Xs = get_x(dat2);
X1 = {};
X2 = {};
for i = 1:size(Xf,1)
tmp = Xf(i,:);
X1{i} = tmp(tmp > 0);
end
for i = 1:size(Xs,1)
tmp = Xs(i,:);
X2{i} = tmp(tmp > 0);
end
%---calculating the distance matrix----
D= [];
for i = 1:length(ind1)
... |
github | xyza11808/MATLAB-master | kpa.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@kernel/kpa.m | 2,958 | utf_8 | 9b643e3e350aeddd765332549e466668 | function K = kpa( k, d1, d2, ind1, ind2, par)
%
% Set-Kernel based on (K)ernel (P)rincipal (A)ngles
% as described in the paper:
% "Learning over Sets using Kernel Principal Angles", JMLR, page 921
% by L.Wolf and A.Shashua
%
% takes 4 parameters: {logScale, symmetryFlag, minorKernelName, minorKernelParameter}
... |
github | xyza11808/MATLAB-master | training.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@svm/training.m | 9,448 | utf_8 | fde8442e15d6ce99a6c9168cf454f6ec | function [retDat,algo] = training(algo,retDat)
if algo.algorithm.verbosity>0
disp(['training ' get_name(algo) '.... '])
end
opt=algo.optimizer;
if strcmp(algo.optimizer,'default')
len=length(retDat.Y);
if len<=200 %% <---if there are more then 200 eamples use svm_light
opt='andre';
else
... |
github | xyza11808/MATLAB-master | plot.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@svm/plot.m | 3,599 | utf_8 | 95a0968f1ec95c3db6534510e45ab93f |
function data_square_plot(a,d)
%
% Plots a surface plot of an svm which uses !_2_! dimensional inputs.
% Red decision line is drawn.
%
% Usage :
% plot(a)
%
% a -- The algorithm already trained
% The colormap can be changed afterwards.
%
% Example:
% d=gen(spiral({'n=1','m=50'}));
% [r s0]=train(svm... |
github | xyza11808/MATLAB-master | get_name.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@algorithm/get_name.m | 155 | utf_8 | e2e919fb4b93c6bee311bc867c8dc5af |
function nam = get_name(com,detailed)
nam = com.name;
%%%% SGE support
if isdeferred(com), nam = get_name(com.deferred, nam, com.is_data); end
%%%%
|
github | xyza11808/MATLAB-master | am_i_data.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@algorithm/am_i_data.m | 154 | utf_8 | 2f77ebbbea8c45db571542075050befc |
function b=am_i_data(dat)
%
% bool = am_i_dat(data)
%
% Returns true if this object is data, else it false is returned
b=dat.is_data; |
github | xyza11808/MATLAB-master | training.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@distance/training.m | 86 | utf_8 | e132f486701db8ae5d73564964f1682a |
function [d,a] = training(a,d)
a.dat=d;
d=set_x(d,feval('get_distance',a,d));
|
github | xyza11808/MATLAB-master | testing.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@distance/testing.m | 75 | utf_8 | 0a25e5b6c1c2d6a60c7d8d95019f7da9 |
function d = testing(a,d)
d=set_x(d,feval('get_kernel',a,d,a.dat));
|
github | xyza11808/MATLAB-master | training.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@loss/training.m | 79 | utf_8 | d6ab32fd3f6095ddbb0d6d52e7362f4e |
function [ret,algo] = training(algo,dat)
ret=feval(algo.type,algo,dat);
|
github | xyza11808/MATLAB-master | testing.m | .m | MATLAB-master/FSLib_v5_2_2017/lib/@loss/testing.m | 72 | utf_8 | 4eca2a3ec33408f03a262a6c3bc6da66 |
function ret = testing(algo,dat)
ret=feval(algo.type,algo,dat);
|
github | xyza11808/MATLAB-master | ILFS.m | .m | MATLAB-master/FSLib_v5_2_2017/methods/ILFS.m | 12,591 | utf_8 | 0b7cf0a2d04507ce3a0449537b510151 | function [RANKED, WEIGHT, SUBSET] = ILFS_auto(X, Y , TT, verbose )
% Infinite Latent Feature Selection - ICCV 2017
% Accepted at the IEEE International Conference on Computer Vision (ICCV), 2017, Venice. Preprint copy
% =========================================================================
% Reference : Infin... |
github | xyza11808/MATLAB-master | MCFS_p.m | .m | MATLAB-master/FSLib_v5_2_2017/methods/MCFS_p.m | 10,054 | utf_8 | e3d6b02ccef3ec5834ec9dc53934cd65 | function [FeaIndex,FeaNumCandi] = MCFS_p(fea,FeaNumCandi,options)
% MCFS: Feature Section for Multi Class/Cluster data
%
% FeaIndex = MCFS_p(data,FeaNumCandi,options)
%
% Input:
% fea - data matrix. Each row vector of data is a
% sample vector.
% FeaN... |
github | xyza11808/MATLAB-master | LaplacianScore.m | .m | MATLAB-master/FSLib_v5_2_2017/methods/LaplacianScore.m | 4,826 | utf_8 | ff75a470a0a9072f85f8d7e99c7acb31 | function [Y] = LaplacianScore(X, W)
% Usage:
% [Y] = LaplacianScore(X, W)
%
% X: Rows of vectors of data points
% W: The affinity matrix.
% Y: Vector of (1-LaplacianScore) for each feature.
% The features with larger y are more important.
%
% Examples:
%
% fea = rand(50,70);
% options = [];
% ... |
github | xyza11808/MATLAB-master | mRMR.m | .m | MATLAB-master/FSLib_v5_2_2017/methods/mRMR.m | 3,191 | utf_8 | e9021a94b8c41a44bb4ece8b445ee666 | function [fea, score] = mRMR(X_train, Y_train, K)
% Matlab Code-Library for Feature Selection
% Version 5.0 August 2017
% Support: Giorgio Roffo
% E-mail: giorgio.roffo@glasgow.ac.uk
% If you use our toolbox please cite our supporting papers:
%
% BibTex
% --------------------------------------------------------... |
github | xyza11808/MATLAB-master | uTest_Shuffle.m | .m | MATLAB-master/U3/uTest_Shuffle.m | 17,327 | utf_8 | 34f8bba147f0ea796e6c850c5907d329 | function uTest_Shuffle(doSpeed, doBias)
% Automatic test: Shuffle
% This is a routine for automatic testing. It is not needed for processing and
% can be deleted or moved to a folder, where it does not bother.
%
% uTest_Shuffle(doSpeed, doBias)
% INPUT:
% doSpeed: Optional logical flag to trigger time consuming speed... |
github | xyza11808/MATLAB-master | FM_marginalise.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_marginalise.m | 2,200 | utf_8 | 223599e8f751e18057488674a4231e1c | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_save_struct.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_save_struct.m | 1,488 | utf_8 | d1efeff852e8b06af71a5fdf6603e9d8 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_function_3.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_function_3.m | 5,096 | utf_8 | 5359fa5f35448b772073238b51841159 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_report_latex.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_report_latex.m | 23,136 | utf_8 | 100ff54b6e07c9649fa428891523b308 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_GUI.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_GUI.m | 103,578 | utf_8 | d3e075a382dea0ff12a93fdcd36c1330 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_GUI_colors.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_GUI_colors.m | 14,070 | utf_8 | d9c7c58cd3e4adc07c9cc8351685462b | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_covariance.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_covariance.m | 1,641 | utf_8 | fcbf9de59a15349fe885a0da1c0a7e7d | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_errorchecker.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_errorchecker.m | 7,457 | utf_8 | 12a73c11142ed5cc677c82c254bab5e9 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_report_text.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_report_text.m | 11,208 | utf_8 | 2dfcdd2f9ead3e23baa60c04f8e48d3a | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_output_fom.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_output_fom.m | 2,008 | utf_8 | e0c4cae7c0b0fc60cd39c65223e2b212 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_plot_likelihood.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_plot_likelihood.m | 3,208 | utf_8 | 6a6d5e93919b9503c3b43d67bd4ad0d8 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_analytic_deriv_2.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_analytic_deriv_2.m | 6,891 | utf_8 | ea7dcd5bb0be3672b42ac31d43c94b9c | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_function_1.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_function_1.m | 1,204 | utf_8 | db4301b733780392f64850d6ddf7767d | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | Seo_Eisenstein_2003.m | .m | MATLAB-master/Fisher4Cast_v2_2/Seo_Eisenstein_2003.m | 4,578 | utf_8 | 7bfe455abbe2baa4c0a4619998242bfd | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_num_deriv.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_num_deriv.m | 3,293 | utf_8 | 055486d08bc152fa08d60d1a6f9e5806 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_sum.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_sum.m | 1,480 | utf_8 | 1fd7973caff6b19a0efacf94c8e8ee30 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_plot_ellipse.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_plot_ellipse.m | 6,132 | utf_8 | d1a8d2b8c9829edb61c9d3bb04171943 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_process_numeric.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_process_numeric.m | 2,403 | utf_8 | 25d0f99f438d9888d01bd4ee484f013f | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | Cooray_et_al_2004.m | .m | MATLAB-master/Fisher4Cast_v2_2/Cooray_et_al_2004.m | 4,383 | utf_8 | e82ede1a085b2f3bd52e91d74ede25ac | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_generate_plot.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_generate_plot.m | 1,367 | utf_8 | 5cd68ea44c6f818fd436ea9f36596398 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_axis_specifications.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_axis_specifications.m | 2,469 | utf_8 | f90d3984164c0d3a9a2567d083743e72 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_process_analytic.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_process_analytic.m | 2,079 | utf_8 | 7cc6ad9255cff9a97a17fe60c3c31797 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_function_2.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_function_2.m | 1,747 | utf_8 | c1a90b0f9709d7ac1a5a852696876723 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_plot_specifications.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_plot_specifications.m | 3,039 | utf_8 | 5e277b0eb0bcc8c4a0ac31bc1128b9c1 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_matrix.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_matrix.m | 1,399 | utf_8 | 10b84a5ba897f418ececc04080207cac | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_analytic_deriv_1.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_analytic_deriv_1.m | 3,374 | utf_8 | 970ef06f8f3c66a24ea0e1646564395a | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | FM_run.m | .m | MATLAB-master/Fisher4Cast_v2_2/FM_run.m | 5,015 | utf_8 | c5534340815ae7266d7f3b307516e09a | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_SeoEisenstein2007_Main.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_SeoEisenstein2007/EXT_FF_SeoEisenstein2007_Main.m | 3,897 | utf_8 | e8e22bd04685cd7d9b377c8e453857b3 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_SeoEisenstein2007_LagrangianDisplacement.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_SeoEisenstein2007/EXT_FF_SeoEisenstein2007_LagrangianDisplacement.m | 2,138 | utf_8 | 2e7f6ac3e3062d76d8df24a48e70acf2 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_SeoEisenstein2007_Input.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_SeoEisenstein2007/EXT_FF_SeoEisenstein2007_Input.m | 2,550 | utf_8 | 243cc6100dde9bcaebc918a4dfcf99c1 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_SeoEisenstein2007_errFit.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_SeoEisenstein2007/EXT_FF_SeoEisenstein2007_errFit.m | 9,837 | utf_8 | bf6999ad46ab40fb046c525d845e1581 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_SeoEisenstein2007_sound_horizon.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_SeoEisenstein2007/EXT_FF_SeoEisenstein2007_sound_horizon.m | 2,100 | utf_8 | c730d1d179ba8a3014704b9148b7c882 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_cummean.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_cummean.m | 1,026 | utf_8 | 863796413e134f956dc9d7f199194d80 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_calculate_error.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_calculate_error.m | 3,708 | utf_8 | 937347a6b85d139736fd1112c8ce4e1a | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_fitting_formula.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_fitting_formula.m | 5,588 | utf_8 | df3367a646d65658cc49307d93f2b400 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_Main.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_Main.m | 6,476 | utf_8 | 202a6acb1e58f80165fa020033c93810 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_setsurvey.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_setsurvey.m | 1,538 | utf_8 | ed52358615ff864a41519bae2c24579e | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_com_volume.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_com_volume.m | 3,049 | utf_8 | da77cc11a775d7c2c02812a1bd2a1469 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_photo_params.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_photo_params.m | 1,322 | utf_8 | 42219827afbcec667e01e539a841148a | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_Input.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_Input.m | 2,272 | utf_8 | 2a06da3861a10c29a71a22324b797eb7 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_FF_Blake_etal2005_spectro_params.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_FF_Blake_etal2005/EXT_FF_Blake_etal2005_spectro_params.m | 1,791 | utf_8 | e7851dddd86f91039b6a15f27e16e7e9 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_fomswg_gui.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_fomswg/EXT_fomswg_gui.m | 17,370 | utf_8 | f54cf70bd1b48ca5f12e3dc7ee800629 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_fomswg_plot_ellipse.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_fomswg/EXT_fomswg_plot_ellipse.m | 1,823 | utf_8 | a977dfb79a3459adc98bd56cf014f1c3 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_fomswg.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_fomswg/EXT_fomswg.m | 25,714 | utf_8 | 159fb587d45b339d409add58ab4a78d5 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_fomswg_plot_specifications.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_fomswg/EXT_fomswg_plot_specifications.m | 4,400 | utf_8 | 0e6ca2c3245a20f546cbf7277152ef95 | % ------------------------------------------------------------------------
% Copyright (C) 2008-2009
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | EXT_fomswg_plot_PC.m | .m | MATLAB-master/Fisher4Cast_v2_2/EXT_fomswg/EXT_fomswg_plot_PC.m | 1,690 | utf_8 | 24229a9daca5e34e7820662d4a0552fc | % ------------------------------------------------------------------------
% Copyright (C) 2008-2010
% Bruce Bassett Yabebal Fantaye Renee Hlozek Jacques Kotze
%
%
%
% This file is part of Fisher4Cast.
%
% Fisher4Cast is free software: you can redistribute it and/or modify
% it under the terms of the Berkeley Softwar... |
github | xyza11808/MATLAB-master | constructNPYheader.m | .m | MATLAB-master/npy-matlab-master/npy-matlab/constructNPYheader.m | 2,844 | utf_8 | dc8486379b4b067036d2e8906ca6723b |
function header = constructNPYheader(dataType, shape, varargin)
if ~isempty(varargin)
fortranOrder = varargin{1}; % must be true/false
littleEndian = varargin{2}; % must be true/false
else
fortranOrder = true;
littleEndian = true;
end
dtypesMatlab = {'uint8','uint16','uint32','uint64','int8','int16'... |
github | xyza11808/MATLAB-master | datToNPY.m | .m | MATLAB-master/npy-matlab-master/npy-matlab/datToNPY.m | 1,490 | utf_8 | 83c9fc24b9fe87737ec384e8ea8a6a51 |
function datToNPY(inFilename, outFilename, dataType, shape, varargin)
% function datToNPY(inFilename, outFilename, shape, dataType, [fortranOrder, littleEndian])
%
% make a NPY file from a flat binary file, given that you know the shape,
% dataType, ordering, and endianness of the flat binary file.
%
% The point he... |
github | xyza11808/MATLAB-master | writeNPY.m | .m | MATLAB-master/npy-matlab-master/npy-matlab/writeNPY.m | 470 | utf_8 | 561adf7ce2f8b0bdf0e611a5b1aeabe1 |
function writeNPY(var, filename)
% function writeNPY(var, filename)
%
% 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,).
shape = size(var);
dataType = class(var);
hea... |
github | xyza11808/MATLAB-master | readNPYheader.m | .m | MATLAB-master/npy-matlab-master/npy-matlab/readNPYheader.m | 2,089 | utf_8 | b7f1965e929221519e65ec7b8e74ebde |
function [arrayShape, dataType, fortranOrder, littleEndian, totalHeaderLength, npyVersion] = readNPYheader(filename)
% function [arrayShape, dataType, fortranOrder, littleEndian, ...
% totalHeaderLength, npyVersion] = readNPYheader(filename)
%
% parse the header of a .npy file and return all the info contained
... |
github | xyza11808/MATLAB-master | readNPY.m | .m | MATLAB-master/npy-matlab-master/npy-matlab/readNPY.m | 878 | utf_8 | f674d6ff7e59396e231b3d2e93919f97 |
function data = readNPY(filename)
% Function to read NPY files into matlab.
% *** 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.
%
[shape, dataType, fortranOrder, littleEndian, totalHea... |
github | xyza11808/MATLAB-master | nnet_train_2.m | .m | MATLAB-master/DNN_Code-master/nnet_train_2.m | 44,163 | utf_8 | a458365f76630ba1c48dba9a27656140 | function paramsp = nnet_train_2( runName, runDesc, paramsp, Win, bin, resumeFile, maxepoch, indata, outdata, numchunks, intest, outtest, numchunks_test, layersizes, layertypes, mattype, rms, errtype, hybridmode, weightcost, decay, jacket)
%
% Demo code for the paper "Deep Learning via Hessian-free Optimization" by Jame... |
github | xyza11808/MATLAB-master | plotAVoverlay.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/plotAVoverlay.m | 725 | utf_8 | f67c81fbf6d8b49748f10db6746fca2a |
function overlayAxis = plotAVoverlay(avSlice, indices, tvAxis, varargin)
if ~isempty(varargin)
overlayAxis = varargin{1};
im = get(overlayAxis, 'Children');
else
overlayAxis = axes();
set(overlayAxis, 'Position', get(tvAxis, 'Position'));
im = imagesc(avSlice', 'Parent', overlayAxis);
set(gc... |
github | xyza11808/MATLAB-master | sanitizeStructureTree.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/sanitizeStructureTree.m | 787 | utf_8 | 8bace88acb4f45270ba14a50656f85f3 |
function sanitizeStructureTree(inFilename, outFilename)
% function sanitizeStructureTree(inFilename, outFilename)
%
% make the structure tree that you get from:
%
% into something that you can load into a table with loadStructureTree.m
%
% This means taking out all the commas within fields.
fid = fopen(inFilename,... |
github | xyza11808/MATLAB-master | selectStructure.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/selectStructure.m | 8,406 | utf_8 | 5003599517117c7d7a640352556900f8 | function [selection,value] = listdlg(varargin)
%LISTDLG List selection dialog box.
% [SELECTION,OK] = LISTDLG('ListString',S) creates a modal dialog box
% which allows you to select a string or multiple strings from a list.
% SELECTION is a vector of indices of the selected strings (length 1 in
% the single se... |
github | xyza11808/MATLAB-master | sliceByVector.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/sliceByVector.m | 2,050 | utf_8 | 2d4d0bca4e0f36969397881c826daa5b |
function thisSlice = sliceByVector(vol, v, vPerp, refPoint, sampPointsParallel, sampPointsPerp)
% function thisSlice = sliceByVector(vol, v, vPerp, refPoint, sampPointsParallel, sampPointsPerp)
%
% returns a 2d slice of the volume "vol". The slice is along vectors v and
% vPerp, starting at refPoint and extending sam... |
github | xyza11808/MATLAB-master | loadFPtable.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/loadFPtable.m | 389 | utf_8 | 72aefa986400b84220a6b916ae8b4d16 |
function FPtable = loadFPtable(fn)
% load the lookup table from CCF to FP slices
[~, fnBase] = fileparts(fn);
fid = fopen(fn, 'r');
titles = textscan(fid, '%s%s%s%s%s%s%s%s%s%s%s', 1, 'delimiter', ',');
titles = cellfun(@(x)x{1}, titles, 'uni', false);
data = textscan(fid, '%s%s%d%d%d%d%d%d%s%s%s', 'delimiter', ','... |
github | xyza11808/MATLAB-master | plotAVslice.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/plotAVslice.m | 320 | utf_8 | b5c4ff9d4803459c07ade6456816f34e |
function im = plotAVslice(thisSlice)
% function plotAVslice(thisSlice)
%
% useful way to plot a slice you get from sliceByVector, if the slice was
% made from the allen atlas ccf "template volume"
im = imagesc(thisSlice');
% set(gca, 'YDir','normal')
axis image
axis off
colormap(allen_ccf_colormap);
caxis([1 1305]); |
github | xyza11808/MATLAB-master | sliceBrowser.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/sliceBrowser.m | 5,552 | utf_8 | 174cfc92059dd6bc033a83b6ebb85e07 | function sliceBrowser(slice_figure, processed_images_folder, f, reference_size)
% -----------------------------------------------------------------
% browser to go through histology along with the reference browser
%-----------------------------------------------------------------
% initialize user data variables held... |
github | xyza11808/MATLAB-master | allenCCFbregma.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/allenCCFbregma.m | 295 | utf_8 | 2cc2c4a83f053fb7b9efd2244c064c65 |
function bregma = allenCCFbregma()
% function bregma = allenCCFbregma()
%
% Return coordinates of bregma in allen CCF 10um volume coordinates
% This is just an estimate by me, the only one that's definitely right is
% the third dimension which is the midline
bregma = [540 0 570]; % AP, DV, LR
|
github | xyza11808/MATLAB-master | sliceOutlineWithRegionVec.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/sliceOutlineWithRegionVec.m | 1,838 | utf_8 | 6a26a96fc3f8421a9f55a1b28c2a5d29 |
function [coords, coordsReg, h] = sliceOutlineWithRegionVec(avSlice, regInd, regColor, ax)
if nargin<2
regInd = [];
regColor = [];
end
if nargin<4
ax = [];
end
if ~isempty(regInd) % specified a region to highlight
% do this first so it's in the background of the outlines
c = contourc(double(isme... |
github | xyza11808/MATLAB-master | allenAtlasBrowser.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/allenAtlasBrowser.m | 28,287 | utf_8 | 8981e82af5e538340baab36ee58a0fb9 |
function f = allenAtlasBrowser(f, templateVolume, annotationVolume, structureTree, save_location, save_suffix, plane)
% Browser for the allen atlas ccf data in matlab.
%
% Inputs templateVolume, annotationVolume, and structureTree are the data describing the atlas.
% The annotation volume should be the "by_index" vers... |
github | xyza11808/MATLAB-master | plotAsProbe.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/plotAsProbe.m | 1,322 | utf_8 | 8827dd9b17c5d5e8d71ff7e5ac408365 |
function plotAsProbe(data, ann_percents, yc, cm, cm2, sqSizeY, active_site_start, rpl)
% data is vector, same lenght as xc and yc
% cm is colormap, size [n x 3]
%
% other usage: if data is empty and cm's first dimension is the same length
% as xc and yc, then use those colors literally
sqCoordsY = [sqSizeY/2 sqSizeY/... |
github | xyza11808/MATLAB-master | gridIn3D.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/gridIn3D.m | 2,584 | utf_8 | 8f5efa6bee95447e99a0af1a04dd69fc |
function contourHands = gridIn3D(volData, contourHeight, sliceSpacing, origin)
hold on;
% contours of a coronal slice, i.e. at one AP (x) location
% xSlices = round(sliceSpacing/2):sliceSpacing:size(volData,1);
xSlices = origin(1)+(-1000:1000)*sliceSpacing;
xSlices = xSlices(xSlices>0 & xSlices<=size(volData,1));
c... |
github | xyza11808/MATLAB-master | loadStructureTree.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/loadStructureTree.m | 1,717 | utf_8 | 08c2311a5387d00cfbbbff013a0c77c3 |
function structureTreeTable = loadStructureTree(fn)
% function structureTreeTable = loadStructureTree(fn)
% note: use an edited version that doesn't have commas in any fields...
% fn = 'structure_tree_safe.csv';
if nargin<1
p = mfilename('fullpath');
fn = fullfile(fileparts(fileparts(p)), 'structure_tree_sa... |
github | xyza11808/MATLAB-master | sliceOutlineWithRegion.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/sliceOutlineWithRegion.m | 880 | utf_8 | cf5362cd61f0b36ae1d5601953764207 |
function [im, h] = sliceOutlineWithRegion(avSlice, regInd, regColor, ax)
if nargin<2
regInd = [];
regColor = [];
end
if nargin<4
ax = [];
end
diffilt = -1/8*ones(3,3);
diffilt(2,2) = 1;
thisd = conv2(avSlice, diffilt, 'same');
thisbw = abs(sign(thisd));
se = strel('square', 2);
im = imerode(thisbw, se)... |
github | xyza11808/MATLAB-master | plotNeuronOnSliceFromCoord.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/plotNeuronOnSliceFromCoord.m | 627 | utf_8 | 656d71b098e8a0e5653437bcc2d2ca54 |
function plotNeuronOnSliceFromCoord(ccfCoord, acr, ax, av, allenst, regColor)
% function plotNeuronOnSliceFromCoord(ccfCoord, acr, ax, av, allenst)
%
%
if nargin<6
regColor = 0.75*[1 1 1];
end
% indices to highlight
thisid = ['/' num2str(allenst.id(strcmp(allenst.acronym, acr))) '/'];
indAndCh = find(cellfun(@(... |
github | xyza11808/MATLAB-master | allen_ccf_npx.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/allen_ccf_npx.m | 31,878 | utf_8 | 3e39a7d7b10d49de274c541f79fc7fb5 | function allen_ccf_npx(tv,av,st)
% allen_ccf_npx(tv,av,st)
% Andy Peters (peters.andrew.j@gmail.com)
%
% GUI for planning Neuropixels trajectories with the Allen CCF
% Part of repository: https://github.com/cortex-lab/allenCCF
% - directions for installing atlas in repository readme
% - some dependent functions from th... |
github | xyza11808/MATLAB-master | isAreaOrContains.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/isAreaOrContains.m | 1,126 | utf_8 | 2dcfb2371807ffae498b42f0850442a0 |
function isA = isAreaOrContains(testAcr, targetAcr, st)
% function isA = isAreaOrContains(testAcr, targetAcr, st)
%
% Determines whether an area with acronym given in testAcr is the same as
% targetAcr or is below targetAcr in the hierarchy. E.g.:
% isAreaOrContains('MG', 'TH') = true (medial geniculate is in the
% t... |
github | xyza11808/MATLAB-master | get_offset_map.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/get_offset_map.m | 1,466 | utf_8 | d1079f2835b252bb0dd12a8678f9efec | % ------------------------------------------------------------
% Generate offset map (for third dimension of a tilted slice)
% ------------------------------------------------------------
function offset_map = get_offset_map(slice_angle, ref_size)
offset_map = zeros(ref_size);
% get range of offsets along 1st an... |
github | xyza11808/MATLAB-master | addAllenCtxOutlines.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/addAllenCtxOutlines.m | 1,471 | utf_8 | 5b8bd5d8cc9e0b17794f3ecc81ab30e4 |
function addAllenCtxOutlines(bregma, lambda, lineColor, pixSize)
% to get bregma/lambda, do:
% >> figure; imagesc(myImg); axis image;
% then use the cursor to click on bregma, then swap the coords (if cursor
% says X=xx and Y=yy, then bregma is [yy, xx]).
% or leave blank to get prompted with ginput.
% lambda just ... |
github | xyza11808/MATLAB-master | loadCCFtoFP.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/loadCCFtoFP.m | 380 | utf_8 | 28efe764837ecde5f7bb56508996cde2 |
function CCFtoFPtable = loadCCFtoFP(fn)
% load the lookup table from CCF to FP slices
[~, fnBase] = fileparts(fn);
fid = fopen(fn, 'r');
titles = textscan(fid, '%s%s%s%s%s%s', 1, 'delimiter', ',');
titles = cellfun(@(x)x{1}, titles, 'uni', false);
data = textscan(fid, '%d%s%s%d%f%f', 'delimiter', ',');
CCFtoFPta... |
github | xyza11808/MATLAB-master | plotTopDownOutlines.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/plotTopDownOutlines.m | 3,278 | utf_8 | 84d9f13663acad5fb6bea3befd035290 |
function plotHands = plotTopDownOutlines(st, av, apCoords, mlCoords)
addLabels = false;
addColors = false;
cortexOnly = false;
downsamp = 2; % for speed, doesn't affect graphics much
av = av(1:downsamp:end,1:downsamp:end,1:downsamp:end);
% find first point on the way down
[~,ii] = max(av>1, [], 2);
ii = squeeze(ii... |
github | xyza11808/MATLAB-master | hierarchicalSelect.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/hierarchicalSelect.m | 2,906 | utf_8 | 1330ce8eddedb1dbb6607c55eb960fe2 |
function selIdx = hierarchicalSelect(st)
selID = 567; % Cerebrum, default to start
[boxList, idList] = makeBoxList(st, selID);
ud.idList = idList; ud.st = st;
% make figure
f = figure; set(f, 'KeyPressFcn', @doOK);
% selector box
ud.hBox = uicontrol(f, 'Style', 'listbox', 'String', boxList, ...
'Callback', ... |
github | xyza11808/MATLAB-master | plotBrainOutlinesByAxis.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/plotBrainOutlinesByAxis.m | 514 | utf_8 | 2cc9f635e9d53f2f2a6b020b655eacbd |
function plotBrainOutlinesByAxis(axH,av)
for v = 1:3
axes(axH(v)); box off; hold on
sliceIm = squeeze(max(av,[],v)>1);
c = contourc(double(sliceIm), [0.5 0.5]);
coordsReg = makeSmoothCoords(c);
for cidx = 1:numel(coordsReg)
h = plot(axH(v), coordsReg(cidx).x,coordsReg(cidx).... |
github | xyza11808/MATLAB-master | makeSTtree.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/makeSTtree.m | 1,519 | utf_8 | 78634f1734a1b7f4e5e550568e5d9aea |
function [treePairsInd, treePairs] = makeSTtree(st)
% make structure tree into a list of parent/child relationships. This makes
% it very quick to find all indices that are a child of another, etc.
%
% Use "loadStructureTree" to get the input argument
%
% output has three columns: parent, child, number of levels betw... |
github | xyza11808/MATLAB-master | distinguishable_colors.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/distinguishable_colors.m | 5,753 | utf_8 | 57960cf5d13cead2f1e291d1288bccb2 | function colors = distinguishable_colors(n_colors,bg,func)
% DISTINGUISHABLE_COLORS: pick colors that are maximally perceptually distinct
%
% When plotting a set of lines, you may want to distinguish them by color.
% By default, Matlab chooses a small set of colors and cycles among them,
% and so if you have more than ... |
github | xyza11808/MATLAB-master | transformed_sliceBrowser.m | .m | MATLAB-master/allenCCF-master/Browsing Functions/transformed_sliceBrowser.m | 7,827 | utf_8 | 76189bc8a8b8282b27ef45c2e439af3a | function transformed_slice_figure = transformed_sliceBrowser(transformed_slice_figure, save_location, f, highlight_point, relevant_slice, min_dist, ...
clickX, clickY, point_ind, add)
% go through histology at the same time
transformed_images_folder = fullfile(save_loca... |
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