sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
45d2f9259d4fc48f0c452514a88f3a52e170950859f4b554de124089411d3c72 | MATLAB | 1,179 | 33 | function worked = seek(vr,fnum)
%WORKED=SEEK(VR,FNUM)
% Attempts to go to frame number FNUM in video VR. Returns 0 if the user
% attempts to seek past the end of the video. For most video plugins, the
% first frame is 0 (not 1), thus in the following example, both IM1 and
% IM2 should be the same for most pl... |
b58b48a2972976111f6217720c5a1aec9adc8805657b1e7a8906209d980697e2 | MATLAB | 1,179 | 44 | function [curv] = write_curv(fname, curv, fnum)
% [curv] = write_curv(fname, curv, fnum)
%
% writes a curvature vector into a binary file
% fname - name of file to write to
% curv - vector of curvatures
% fnum - # of faces in surface.
%
%
% write_curv.m
%
% Original Author: Bruce Fischl
% CVS Revision Info... |
09a22097e4e884c33fbab04abda2241de6105207dda2f023e4b9d44a401bb2fc | MATLAB | 1,180 | 36 | % display() - display an EEG data class underlying structure
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2008
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the ... |
300ef4ad1fc2110594cd266a028ceb39a2854bb5d61ec9bfee9add48462c28a1 | MATLAB | 1,180 | 29 | function xmax=findpeaks(data,threshold)
% Helper function to find peaks in a given continuous valued time series x
% Usage: xmax=findpeaks(data,threshold)
% Input:
% data (data in time x channels/trials form or a single vector)
% threshold (if specified returns locations of peaks at which data exceed... |
a24d5543240db19456cb36a59d49e7692796d4263d45da3e80293dd7772fdc6d | MATLAB | 1,180 | 41 | function [mintime, maxtime]=minmaxsptimes(data)
% Find the minimum and maximum of the spike times in each channel
% Usage: [mintime, maxtime]=minmaxsptimes(data)
% Input:
% data (spike times as a structural array of multiple dimensions e.g. channels; channels x trials;
% can also accept a 1d matrix of spi... |
b7ed6fda588a1229d53813860b4aaffb2119ad4684e7bfb5763089f782c9c511 | MATLAB | 1,180 | 48 | function handles = featuredetect_init(handles)
%%%%%%%% initialize handles, set default value %%%%%%%%%%%%%%%%%%%
close(figure(4)) % manual dendritic tracing
close(figure(15)) % manual spine feature
close(figure(7)) % cross-session registration
% clc
para_default = defaultparameter;
handles.savingflag = 0;
% handles... |
f0f1bba739c65ab5df645634905a3860de7048b7fd0376cfe8cbb29b4573f1f5 | MATLAB | 1,180 | 39 | % l1 trend filtering
% Written for CVX by Kwangmoo Koh - 12/10/07
%
% The problem of estimating underlying trends in time series data arises in
% a variety of disciplines. The l1 trend filtering method produces trend
% estimates x that are piecewise linear from the time series y.
%
% The l1 trend estimation problem ca... |
f395064737d50f888c42d500d1a5a48468a58c188ef92ba7d7513384c6eff349 | MATLAB | 1,180 | 37 | function max_card_match=test_matching(A,m,varargin)
% TEST_MATCHING Tests if a matching is maximum cardinality
%
% max_card_match=test_matching(A,m) returns 1 if m is a maximum cardinality
% matching on A.
%
% This method works on undirected graphs (symmetric matrices) and ignores
% edge weights.
% The runtime is O... |
1cf51c376c69db7e15ba5123830a7bccd4fec09e41f493acbc543838b4bedf77 | MATLAB | 1,181 | 40 | % Undo the flipping and rotations performed by xform_nii; spit back only
% the raw img data block. Initial cut will only deal with 3D volumes
% strongly assume we have called xform_nii to write down the steps used
% in xform_nii.
%
% Usage: a = load_nii('original_name');
% manipulate a.img to make array... |
8304ff4ecbc6fbddefada9fa33a7c98962c7077f222f22f3c3700cd921ae2eac | MATLAB | 1,181 | 35 | function y = log_sum_exp( x, dim )
%LOG_SUM_EXP log(sum(exp(x))).
% LOG_SUM_EXP(X) = LOG(SUM(EXP(X)).
%
% When used in a CVX model, LOG_SUM_EXP(X) causes CVX's successive
% approximation method to be invoked, producing results exact to within
% the tolerance of the solver. This is in contrast to LOGSUMEXP_S... |
aad10cd30dfcd0c6692a1f828ea3f3e03464f55bc0779f14140d9b90b59e78e7 | MATLAB | 1,181 | 58 | function kappa = circ_kappa(alpha,w)
%
% kappa = circ_kappa(alpha,[w])
% Computes an approximation to the ML estimate of the concentration
% parameter kappa of the von Mises distribution.
%
% Input:
% alpha angles in radians OR alpha is length resultant
% [w number of incidences in case of binned ... |
1ff6fe4652895f6a4d1b6e87d5892d9d4cd69a34b948dbce5654c5833ed41d83 | MATLAB | 1,182 | 33 | function fn = step(vr, delta)
%WORKED=STEP(VR,DELTA)
% Moves the frame counter by DELTA frames for video VR. This is a
% generalization of NEXT. Returns 0 on an unsuccessful STEP. Note that
% not all plugins support stepping, especially with negative numbers. In
% the following example, both IM1 and IM2 shou... |
313c7c9a8071db13c93361bdae4501ca40d7b97a7915b9d68cf31629eca97268 | MATLAB | 1,182 | 43 | %%*********************************************************
%% lmifun2: generate SDP data for the LMI constraint
%% of the form:
%%
%% [A*P*B'+B*P*A' C*P*D']
%% [D*P*C' 0 ]
%%
%% P is the variable, P is symmetric.
%%
%%*********************************************************
function Avec... |
7f2b882e87e79e5bc8dfe76a000cd1b171f08d2247aef3777fcb6b7632359023 | MATLAB | 1,182 | 34 | function CBIG_reorderNuisance(brainListFile, nuisanceVarsFile, concatOrderFile)
% CBIG_reorderNuisance(brainListFile, nuisanceVarsFile, concatOrderFile)
%
% Helper function that reorders the lines in nuisanceVars so that now they
% match the line order of concatOrder. Before this function, they match the
% line order ... |
90e78dbd453d66552c260293b548d07bf7001cc0cfccd70514bd6cee22d1c808 | MATLAB | 1,182 | 30 | %% CANlab_help_examples second-level batch scripts example
%
% This code downloads sample data from figshare.com and contains basic
% steps for running a standard batch set of analyses on 2nd-level fMRI data
% (contrast images).
%
%% The dataset
% The dataset contains fMRI contrast images from 59 participants, for bo... |
c66704e8832bdf57b45eb34b93efcb52000c94d641bb7176dd04f5812618b034 | MATLAB | 1,182 | 27 | function colPlot3D(lines,col,csc)
N = 256;
cmap = autumn(N);
cmap = hot(N);
lw = 1;
delete(findobj(gca,'tag','fibplot3D_colplot3D'));
for k = 1:length(lines),
fib = lines{k}';
fib = fib';
if size(fib,1) > 1,
sp = 1;
if nargin == 1,
dif = (fib(... |
7ac9014fa60152c43151ec8a90e09dfb6d466cf59592a64b39ef4a3e86ccb420 | MATLAB | 1,183 | 30 | function [ad] = PL2AdSpan(filename, channel, startCount, endCount)
% PL2AdSpan(filename, channel, startCount, endCount): read a span of a/d data from a .pl2 file
% returns a/d values in millivolts
%
% examples:
%
% ad = PL2AdSpan(filename, channel, startCount, endCount)
% ad = PL2AdSpan(filename, ... |
1218bc47323280e30aa8b369396edbab179c4a36423fdfa689d180bbec1c6815 | MATLAB | 1,184 | 57 | function CBIG_fitGLM_hypoTest(rid_prob, rid_icv_vol, subCol, corCol)
% CBIG_fitGLM_hypoTest(rid_prob, rid_icv_vol, subCol, corCol)
%--------------------------------------------- Fit GLM
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
% Construct X and y
noSubs = siz... |
673835d4c43065a19a06916f677dea282ecd943b37b48e788304db39d8f381e0 | MATLAB | 1,184 | 56 | function imat=ea_gencontrastimage(imat,howto)
switch howto
case 2
%% use raw tra version
imat=squeeze(imat(:,:,:,1));
case 3
%% use smoothed tra only
imat=squeeze(imat(:,:,:,1));
imat = smooth3(imat,'gaussian',3);
case 4
%% use smoothed mean of tra and c... |
db8ecbd036abbc4f206d609546f00a767b44f789668e4554c6ea2db3850c62c4 | MATLAB | 1,184 | 26 | function rval=rtest_7_karsi
% Test the flow-graph that Karci identified as causing a problem with the
% min-cut computation. The min-cut value should always be equal to the
% max-flow value.
G = [0 46 0 46 0 0 0 0 0 0 461;
0 0 46 0 46 0 0 0 0 ... |
de816cee37dd8bec385b876423784d193a73aae8493154012fd968ad4c774e38 | MATLAB | 1,184 | 27 | function scalingFactor = readOEMetaFile(metaFile)
% JF
% read open ephys meta file and extract scaling factor (bit_volts) value
% ------
% Inputs
% ------
% metaFile: string, full path to meta file (should be a structure.oebin file)
% ------
% Outputs
% ------
% scaling factor: double, scaling factor value to convert r... |
f01ebf3ee08cc844290ffaab089c280d95759439fcfe26b2a4d9068ee0ac7425 | MATLAB | 1,184 | 55 | function plotMetricPDFAreas(allROIs, metricField, areas, cmap, minmax, kdeBW)
% Creates KDE plots for metric value distributions separated by area
if nargin < 5
minmax = [];
end
if nargin < 6
kdeBW = [];
end
% Check size matches
assert(length(areas) == size(cmap,1))
% Create figure
fig;
hA = gca;
hold on;
... |
a0f7010f0978717d29b2e003ab9da4c57e472b66695e6a916af0934db2e44c01 | MATLAB | 1,185 | 37 | %% Calculate the arc length of an interval on a parameterized polynomial in R3
% Params:
% polyCoeff - coefficient matrix
% lowerLimit
% upperLimit
%
% lowerLimit / upperLimit parameters can take scalar as well as vector inputs,
% in the vector case arc lengths are returend for all pairs of intervals
% betw... |
524a3b6beed8a22869e4cbc8227e5689af3c591e749ddd84040cfd415ef8f4b1 | MATLAB | 1,186 | 28 | function data_out = Trinh_makecontinData(data_in, conditions,refrainonsets,triallength,prestim)
%% Function for segmenting the data and appending them into continous data stream
% segments the condtitions and appends them to make continous data streams
% insert the trial info for the needed conditions
% Trinh nov22... |
8d0ffc9887efb549ada921c4c4e17c3065ff7403e7413c585b947303f9208638 | MATLAB | 1,186 | 17 | % Helper functions for FMAToolbox.
%
% Parameter testing.
%
% isstring_FMAT_FMAT - Test if parameter is an (admissible) character string.
% isdscalar - Test if parameter is a scalar (double) satisfying an optional list of tests.
% isdvector - Test if parameter is a vector of d... |
fcab2e732a92dff2d565a7c6e5b90c5c9693e967fd0fcdb0cb12aa68a5b5aeb3 | MATLAB | 1,186 | 32 | function y = sum_log( x, dim )
%SUM_LOG Sum of logarithms.
% For vectors, SUM_LOG(X) is the sum of the logarithms of the elements of
% the vector; i.e., SUM(LOG(X)). If any of the elements of the vector are
% nonnegative, then the result is -Inf.
%
% For matrices, SUM_LOG(X) is a row vector containing the ap... |
001994e4ea961d7590e995b19b81e133ff8587f18234465db26ce42e75ac5630 | MATLAB | 1,187 | 56 | function mstruc = createCM_GT(ftr,ROI,Nsz,centroids)
display('building connect mat');
lens = single(cellfun(@len,ftr.curveSegCell));
fibs = ftr.curveSegCell;
rois = ROI.dataAy;
T = inv(ROI.edges)*ftr.hMatrix;
terms = cellfun(@(x) [x(1,:); x(end,:)],fibs,'UniformOutput',false);
terms = cat(1,terms{:})';
terms = (T*... |
9846596c705011ffd587230f8ccaab5644a6ada2a06ea4f027005e4e99dd804a | MATLAB | 1,187 | 43 | function coeffs = calc_eigendecomposition(data, eigenvectors, method)
% calc_eigendecomposition.m
%
% Decompose data using eigenvectors and calculate the coefficient of
% contribution of each vector
%
% Inputs: data : data [MxP]
% M = number of points, P = number of independent data
% ... |
a3a13c696479b2f33f9afd2e885694125f9c1bac40855b89db439241feb646b5 | MATLAB | 1,187 | 36 | function [IDout,group]=...
inf_determineCVgroups(IDin,k)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically relevant behaviors of the ecosystems.
% Copyright (C) 201... |
be79f8ebe096883909ce3ff4170db84aae1a24d6e11e8e804f131a7c05dd24e7 | MATLAB | 1,187 | 40 | function plotPrevalenceMapCCF(dorsalMaps, allROIs, subpop, smoothSD, color)
% Creates a binned and smooth map of subpop proportions based on the
% field propField
% Figure
allenMapSMc(dorsalMaps, [-3.6, 0, -2, 3]) % Creates figure by itself
% Plot params
xLimits = [-4 0];
yLimits = [-2.35 3.3];
gridRes = 50;
% Creat... |
ea03ea23278757a73c359a67f7a762e5c4b0e348f969749b436aa19a673a4c7a | MATLAB | 1,187 | 36 | function uid = root(tree)
% XMLTREE/ROOT Root Method
% FORMAT uid = root(tree)
%
% tree - XMLTree object
% uid - UID of the root element of tree
%__________________________________________________________________________
%
% Return the uid of the root element of the tree.
%________________________________________... |
0626e1c902e388a394f13ef47280dc9296e35f9896c9c30db463974489776a23 | MATLAB | 1,188 | 33 | %% A Hierarchy of Layouts Example
% This example shows how to use layouts within other layouts to achieve
% more complex user interface designs with the right mix of variable and
% fixed sized components.
%
% Copyright 2009-2014 The MathWorks Ltd.
%% Open the window
% Open a new figure window and remove the toolbar an... |
1c46dfb4d19542c62927111fbd3a736770ddc430fc782a7a549598c772d5ac9f | MATLAB | 1,188 | 36 | function handles = selectsinglefiles(handles)
if handles.datatype == 1
[filelist, filepath, cCheck] = uigetfile({'*.tif'; '*.tiff'}, 'Select Movies To Be Processed');
if (cCheck~=0)
handles.filepath = filepath;
if ~isempty(filelist)
if ~isempty(filelist)
handles.filen... |
eb92ff290d124c60336aa80bf4c7cbbecc13b0d389bf5d116ff04cd166f7ac3b | MATLAB | 1,188 | 28 | function apref = ea_antspreset_ants_wiki(cmd)
% from https://github.com/ANTsX/ANTs/wiki/Anatomy-of-an-antsRegistration-call
if ischar(cmd) % 'query' mode, return the name of the preset
apref = 'ANTs Anatomy of an antsRegistration call';
return
end
apref.rigid.gradientstep = '0.1';
apref.rigid.metric = 'MI';
a... |
710190ad0672ff834475955c26383cdf19162acb1aea571c9985b20c437102e8 | MATLAB | 1,189 | 36 | function tree = delete(tree,uid)
% XMLTREE/DELETE Delete (delete a subtree given its UID)
%
% tree - XMLTree object
% uid - array of UID's of subtrees to be deleted
%__________________________________________________________________________
%
% Delete a subtree given its UID
% The tree parameter must be in ... |
1b3c2df43b02b8702f90070b204f646ad2251f2b410b5bdcbf129bbf05b745bb | MATLAB | 1,190 | 52 | %isradians - Test if parameter is in range [0,2pi] or [-pi,pi].
%
% USAGE
%
% test = isradians(x)
%
% x array to test (NaNs are ignored)
%
% OUTPUT
%
% range 0 if uncertain (issues a warning)
% 1 for [-pi,pi]
% 2 for [0,2pi]
% SEE ALSO
%
% See als... |
340a393295a70edceca72061c3817f8419dc4722bc8d047d607470eb2e3bbd78 | MATLAB | 1,190 | 36 | function countSpots(imPath, wellPath, sgeID)
d = dir(fullfile(imPath, '*.mat'));
fname = d(sgeID).name;
load(fullfile(imPath, fname));
x = strsplit(fname, '_');
jsonname = fullfile(wellPath, x{1}, 'scalefactors_json.json');
w = jsondecode(fileread(jsonname));
R = ceil(w.spot_diameter_fullres/2);
tbl = ... |
b5386446e861be507079719e71892700292267b5be0a15ee74e18a146966341c | MATLAB | 1,190 | 30 | addpath('.'); addpath('helperFunctions');
clear all; close all; clc;
globalsMain;
cd('../03_data/01_raw_data/');
for s=1:numel(subjects)
cd(num2str(subjects(s)));
for e=1:2
cd(exp{e});
% control
folder = dir(sprintf('e*v%db*c1',subjects(s)));
for f=1:numel(folder)
... |
67a4d1a429a50ad77497b55393167ecb89cf2ea938a55ced35ceaa40ea7abf24 | MATLAB | 1,192 | 21 | function outinfo = cifti_diminfo_dense_get_surface_info(diminfo, structure)
%function outinfo = cifti_diminfo_dense_get_surface_info(diminfo, structure)
% Get information on how to map cifti indices to gifti surface vertices.
%
% >> leftinfo = cifti_diminfo_dense_get_surface_info(cifti.diminfo{1}, '... |
230325f58512bf5c9e2e492bf1425b2ace561d501fa51645fd23e25d9c819278 | MATLAB | 1,193 | 42 | % Section 4.3.1: Compute and display the Chebyshev center of a 2D polyhedron
% Boyd & Vandenberghe, "Convex Optimization"
% Joëlle Skaf - 08/16/05
% (a figure is generated)
%
% The goal is to find the largest Euclidean ball (i.e. its center and
% radius) that lies in a polyhedron described by linear inequalites in this... |
9c36c6a37de2f61a3c62552a0472002392e1cc0849c0c60989fb322adb48cc3a | MATLAB | 1,193 | 49 | function yy=ring2(inmat,rrad,rwid,xy0,ang)
% Usage ... y=ring2(inmat,rad,wid,xy0,ang)
%
% xy0=[0 0] will place ring in the center of the image floor(sz/2)
if ~exist('ang','var'), ang=0; end;
if ~exist('xy0','var'), xy0=[]; end;
if isempty(xy0), xy0=[0 0]; end;
if length(inmat)==2,
yy=zeros(inmat);
else,
yy=... |
8f7903bf59cd27270a4aded96fe47842a6ba079280cc3a821e38e837c96c9ca2 | MATLAB | 1,194 | 37 | function handles = input_refresh(handles, dataID)
f_wait = waitbar(0.5,'Data loading');
% load data
handles = loadtrace(handles, dataID);
if ~isempty(handles.im_norm)
%%%% show spine rois
handles = get_spineROImask(handles);
roi_mask = handles.roi_mask;
% roi_mask = zero... |
9443e33049901138d62fef9d7ee3baff6eb824b2c4dcc00fe18701400138e226 | MATLAB | 1,194 | 44 | function create(obj,wrt)
% Create a NIFTI-1 file
% FORMAT create(obj)
% Write out the header information for the nifti object
%
% FORMAT create(obj,wrt)
% Also write out an empty image volume if wrt==1
%__________________________________________________________________________
% Copyright (C) 2005-2013 Wellcome Trust C... |
a2c1c2c78e4dd042c89c5163e6105c6174af9d96f0d36b87fe6634679691241b | MATLAB | 1,194 | 26 | function [n,dspchans] = plx_chanmap(filename)
import CMBHOME.PLX2Mat.*
% plx_chanmap(filename) -- return map of raw DSP channel numbers for each channel
%
% [n,dspchans] = plx_chanmap(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% OUTPUT:
% n - number of spike channels
% dspchans ... |
ef118fcf3eedc5636155797a9c4106110bb09f1cdb1936ed7abd514927705568 | MATLAB | 1,194 | 32 | function cvx_save_prefs( varargin )
%CVX_SAVE_PREFS Saves current CVX settings for future MATLAB sessions.
% CVX_SAVE_PREFS saves the the current global CVX settings to a special
% prefences file (stored in the "prefdir" directory). This enables CVX to
% remember your preferred settings (solver, precision, etc... |
8c4463904c9ca678734fb6da9877923eb674b749f1edc5017009416bae40c43c | MATLAB | 1,195 | 36 | function [interp_cmap]=interpolate_cbrewer(cbrew_init, interp_method, ncolors)
%
% INTERPOLATE_CBREWER - interpolate a colorbrewer map to ncolors levels
%
% INPUT:
% - cbrew_init: the initial colormap with format N*3
% - interp_method: interpolation method, which can be the following:
% 'nearest' - n... |
fcd79ef9bf38d06e0fcb4b950d92edfacb016892f28def00b6304bb44ff71d0c | MATLAB | 1,195 | 46 | function kappa = Concentration(angles)
%Concentration - Estimate the concentration parameter for circular data.
%
% Estimate the concentration parameter for circular data assuming a Von Mises distribution.
% Uses the approximation described in "Statistical Analysis of Circular Data" (Fisher, p. 88).
%
% USAGE
%
% ... |
a1e4f26238af0815a9525f82a5afe2554f86aed8b172ce58fb2d486ef63c5c35 | MATLAB | 1,196 | 34 | figure;
subplot(1,2,1)
hold on;
xvals= 0:.01:175;
[yvals,pval] = linear_fit_eval(cday(1:16), mbeh(1:16,1),xvals);
plot(xvals,yvals,'c-','linewidth',2)
xvals= 200:.01:365;
[yvals,pval] = linear_fit_eval(cday(21:28), mbeh(21:28,1),xvals);
plot(xvals,yvals,'c--','linewidth',2)
plot(cday([1:16 21:28])',mbeh([1:16 21:28],1)... |
3f3e8dfcea01bb293c5cd620f3db2212a436210e3ee4ef6f0c7dd25a04267724 | MATLAB | 1,198 | 27 | function [apoe2, apoe4] = CBIG_MMLDA_get_apoe(APOERES_file, rid)
% [apoe2, apoe4] = CBIG_MMLDA_get_apoe(APOERES_file, rid)
%
% Get apoe2 and apoe4 gene number for each subject.
%
% Input:
% - APOERES_file : path of APOERES.csv spreadsheet
% - rid : cell array of rid for subjects
%
% Output:
% - apoe2 ... |
5b4d5302c47bd75c29308bea59ea150e291d1e82ae6b550fbb4e91fe2a315e5f | MATLAB | 1,198 | 22 | function output = SOFAappendText(Obj,attribute,new)
%SOFAappendText
%
% output = SOFAappendText(input,new) appends the new text to the
% attribute using the correct SOFA separators. If the attribute is empty
% or non-existing, the output will be the new text only.
%
% SOFA API - function SOFAappendText
... |
927d511ab0437ed4eacd4bcd384558346e89ff51ddb610c595fdf1de3519938b | MATLAB | 1,198 | 28 | function GCO_SetNeighbors(Handle,Weights)
% GCO_SetNeighbors Set (weighted) pairwise connectivity of all sites.
% GCO_SetNeighbors(Handle,Weights) determines which sites are neighbors
% and thereby have a SmoothCost associated with them. Weights is a
% sparse NumSites-by-NumSites matrix, where Weights... |
d3113b3c8afa341d5aa72eec8e6decea847bb721ac8b2b34bf09f61b6834249b | MATLAB | 1,198 | 45 | function y = rms(x, dim)
%RMS Root mean squared value.
% For vectors, RMS(X) is the root mean squared value in X. For matrices,
% RMS(X) is a row vector containing the RMS value from each column. For
% N-D arrays, RMS(X) operates along the first non-singleton dimension.
%
% Y = RMS(X,DIM) operates along the ... |
50c542965325f341149943bfea9421cf077ce3c0f62be64ef1c73062a6e1f218 | MATLAB | 1,199 | 37 | function amyloid = CBIG_get_amyloid(rid_of_interest)
% amyloid = CBIG_get_amyloid(rid_of_interest)
% Fetch amyloid from .csv files
%
% Input:
% - rid_of_interest: the RID's of subjects of interest
%
% Output:
% - amyloid: 1st col is RID, 2nd col is (dummy) VISCODE, 3rd is (dummy)
% EXAMDATE, 4th is value
%
%... |
a3f885be1740d57a56c7cfdc6a052c3c7b137b928e748c51657f0dc8fff78264 | MATLAB | 1,199 | 45 | function cvx_optval = norms_largest( x, k, dim )
%NORMS_LARGEST Computation of multiple norm_largest() norms.
% NORMS_LARGEST( X, K, DIM ) provides a means to compute the largest-k
% norms of multiple vectors packed into a matrix or N-D vector. This is
% useful for performing max-of-norms or sum-of-norms calcula... |
e7bff0843f2da3ca3b031446c7e233280feed5dc63b5d57c6e67bacf552913b0 | MATLAB | 1,199 | 36 | function [xsmooth, Vsmooth, VVsmooth_future] = smooth_update(xsmooth_future, Vsmooth_future, ...
xfilt, Vfilt, Vfilt_future, VVfilt_future, A, Q, B, u)
% One step of the backwards RTS smoothing equations.
% function [xsmooth, Vsmooth, VVsmooth_future] = smooth_update(xsmooth_future, Vsmooth_future, ...
% xfilt,... |
3b304e3431d291dabf42bc4d39713b165b30cca20c095044cd809d871d0397b6 | MATLAB | 1,200 | 35 | function CBIG_MMLDA_matrix2doc(output_filename, input_mtx)
% CBIG_MMLDA_matrix2doc(output_filename, input_mtx)
%
% This function convert input matrix to output document which is an input of
% CBIG_MMLDA_est.sh or CBIG_MMLDA_inf.sh. For the docmument format, please refer to
% $CBIG_CODE_DIR/external_packages/mmlda-c-di... |
6a344681471164c2d68d2f358d92e851a8aab20f242a55796cd4fc72eec96bbe | MATLAB | 1,200 | 49 | function varargout= make_connected(A,varargin)
% MAKE_CONNECTED Add edges to construct a connected graph
%
% C = make_connected(A) generates a new graph C with additional edges
% to make C connected.
%
% [ei,ej] = make_connected(A) returns the additional edges instead.
%
% ... = make_connected(A) takes a set of
% key... |
863b5901155d41673616405724300ea87f52e842533ff94ae48b03161acdb996 | MATLAB | 1,200 | 26 | function ea_add_sweetspot(~,~,leadgroup,resultfig)
% small function to open ea_discfiberexplorer. lead group can be a path to
% either lead group analysis file or saved fiber explorer.
if ismember('M', who('-file',leadgroup)) % Add new discfiber analysis
exp = ea_sweetspotexplorer(leadgroup,resultfig);
sweetId... |
32c8df1b7c2879515201e97d9122d2ac73b18a77d66dc3c7021b6811356d1c6f | MATLAB | 1,201 | 18 | % Chapter 6: Approximation and fitting
%
% deadzone.m - Section 6.1.2: Residual minimization with deadzone penalty
% fig6_15.m - Figure 6.15: A comparison of stochastic and worst-case robust approximation
% fig6_19.m - Figure 6.19: Polynomial fitting
% convex_interpolation.m - ... |
584cdc29d8824fd681a282c7cd2692aea87651369d692f6365975451d9847031 | MATLAB | 1,201 | 40 | function [newnode,newelem]=mergesurf(node,elem,varargin)
%
% [newnode,newelem]=mergesurf(node1,elem1,node2,elem2,...)
%
% merge two or more triangular meshes and split intersecting elements
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
%
% input:
% node: node coordinates, dimension (nn,3)
% elem: ... |
58b2be69cf23493a3a637754f3d6b86ff1b3ca21c07f72156880b742df1a4ad4 | MATLAB | 1,201 | 24 | function cvx_expert_check( fname, varargin )
global cvx___
if cvx___.expert, return; end
if ~isempty( varargin ) && ~any(cellfun('isclass',varargin,'cvx')), return; end
url = [ 'file:///', cvx___.where, cvx___.fs, 'doc', cvx___.fs, 'advanced.html#the-successive-approximation-method' ];
fprintf( 1, [ 'CVX Warning:\n',... |
6a1b7a7c5a7fff4b0e4763cc3f49db3b8bc35cfbab253ae984e3d2d106e83c1e | MATLAB | 1,201 | 42 | function dPrime = cellFRA2dPrime(FRA,varargin)
p = inputParser;
addRequired(p,'FRA',@ismatrix)
addOptional(p,'nAmpl',3,@(x) isnumeric(x) && isscalar(x));
addOptional(p,'nFreq',28,@(x) isnumeric(x) && isscalar(x));
addOptional(p,'nBoots',1000,@isnumeric);
parse(p,FRA,varargin{:});
FRA = p.Results.FRA;
boots = ... |
bb306c7fa8d696ed9d8733d8b5b5db713a10481f4dc572a61466dc7839935f7a | MATLAB | 1,201 | 42 | function [L, Lratio, df] = L_Ratio(Fet, ClusterSpikes, m)
% [L, Lratio] = L_Ratio(Fet, ClusterSpikes)
%
% L-ratio
% Measure of cluster quality
%
% Inputs: Fet: N by D array of feature vectors (N spikes, D dimensional feature space)
% ClusterSpikes: Index into Fet which lists spikes from the cell ... |
007ddbd6581dbc6600de9cce5a8672d6568b6d3125eb573f368ca6ddb9f4cf7e | MATLAB | 1,202 | 42 | function [trace_noBAP, coef] = BAPremove_auto(spinedff, dend_dff, inputcoef)
x0 = dend_dff;
y0 = spinedff;
coef = [];
Maxiter = 5;
Maxtolt = 0.05;
if nargin<3
inputcoef = [];
end
if isempty(inputcoef)
f = fittype('a.*x', 'dependent',{'y'}, 'independent', {'x'}, 'coefficients',{'a'});
xx = linspace(min(min(... |
979862c09e97f04b02e1592def502306b87dba8ec31cc4b2b2153aa6d540bc6a | MATLAB | 1,202 | 39 | function IMR = calcImr(m,im)
%CALCIMR Calculates the Ideal Mask Ratio (IMR)
%
% IMR = IOSR.BSS.CALCIMR(M,IM) calculates the ideal mask ratio (IMR) from
% the calculated mask M and ideal mask IM. Masks can be logical or
% double, but must only contain values in the interval [0,1].
% Copyright 2016 University o... |
2be3c92095c54fa4cae109cae04475b6aeecd9eef1d55ac2cc7159f6d8789f56 | MATLAB | 1,203 | 33 | function figure_size = LeG_getnicedialoglocation(figure_size, figure_units)
% adjust the specified figure position to fig nicely over GCBF
% or into the upper 3rd of the screen
% Copyright 1999-2010 The MathWorks, Inc.
parentHandle = gcbf;
convertData.destinationUnits = figure_units;
if ~isempty(parentHandle)
% ... |
d3f4f40e67b30dba0cd5042defc0a3f91305c476c30b687140a2a592d12038a8 | MATLAB | 1,203 | 59 | function [mu ul ll] = circ_mean(alpha, w)
% Computes the mean direction for circular data.
%
% mu = circ_mean(alpha, w)
%
% Input:
% alpha sample of angles in radians
% [w weightings in case of binned angle data]
%
% Output:
% mu mean direction
% ul upper 95% confidence limit
% ll lower... |
fe7db8d08720dbaa20b49924ad100074a7c67279c476621ff99928c1f71ee26a | MATLAB | 1,203 | 46 | function models = fitAreaGMMs(allROIs, metricField, options, areas)
% Fits Gaussian mixture model distributions to the feature vectors of
% neurons specific to given anatomical area
% Get metrics z-scored for all neurons
switch metricField
case 'PCs'
metrics = cat(1, allROIs.PCs);
metrics = metrics... |
185a1a50f19cd621b531ab5e40f5f1cc26d0b6ff458e04da8537aaa2b2cd0c97 | MATLAB | 1,204 | 29 | function [yinds,dists] = mindist(X,Y)
%MINDIST Finds indices of closest vectors.
% YINDS = MINDIST(XLIST,YLIST), where XLIST is an M x D matrix and Y is
% N x D, returns an M x 1 vector YINDS such that YINDS(i) is the row
% number in YLIST that has the minimum (Euclidean) distance to the i^th
% row in... |
61a9b6b41ed023fa3cb3945b6fc5db8a6936e54dedff417ea7673ef5f6f17292 | MATLAB | 1,204 | 39 | function [tx_equil, ty_equil] = force_moment_equilibrium(tx,ty,r,theta)
%
% [tx_equil, ty_equil] = force_moment_equilibrium(tx,ty,r,theta)
%
% Adjust x and y tractions to approach force and moment equilibrium.
% Run this function iteratively for best results.
%
% INPUTS
% tx, ty: x and y components of tractions
% ... |
a4aad8c1e599dc6a055761612690a1df1b0d00b92a64c9a7cde3499ef5ab7b4d | MATLAB | 1,204 | 40 | function ea_run_cluster(~, ~, clusterfunctionname, handles, cmd)
ea_busyaction('on', handles.leadfigure, 'lead');
options = ea_handles2options(handles);
options.macaquemodus = getappdata(handles.leadfigure,'macaquemodus');
% handle 'prefs', 'lc' and 'd2' options
options.prefs = ea_prefs('');
options = ea_amendtoolbo... |
d8db3f783eb898a69eeba7bc65ebd85f5221ad58c849fbbd80f75cd311a0a572 | MATLAB | 1,204 | 37 | function fibValThreshold = ea_explorer_applythresholding(threshstrategy, vals, threshold)
switch threshstrategy
case 'Percentage Relative to Peak'
range = vals(1) - vals(end);
fibValThreshold = vals(1) - threshold/100 * range;
if range == 0
if vals(1) > 0
fibValTh... |
99bfaf8d5a0e889228e4ecd2e4684455b916fa6264a2f522e58089a8cf5bcd15 | MATLAB | 1,205 | 26 | function z = minus( x, y, cheat )
% Disciplined convex programming information for MINUS:
% Terms in a difference must have opposite curvature. Real affine
% expressions are both convex and concave, so they can be involved
% in a difference with any nonlinear expression. Complex affine (or
% cons... |
ce0415d96a1c51f1eb15db8b0f004bfc762b2d8d4e1b03983bae736e5946018c | MATLAB | 1,205 | 32 | %% categorization
% AC as source
GC_tuning_AC2PFC_topoAC = zeros(nDay, nChAC, length(fIdx), length(tIdx));
for fIndex = 1:length(fIdx)
for tIndex = 1:length(tIdx)
GC_tuning_AC2PFC_topoAC(:, :, fIndex, tIndex) = mean(grangerspctrm_AC2PFC_topoAC(:, :, fIdx{fIndex}, tIdx{tIndex}), [3, 4]);
end
end
% PFC a... |
058cb712b02130f1cd2d3e501388bc147a03e25a9fa9ca282d91dfc2c5ef5173 | MATLAB | 1,206 | 31 | % Input/output functions (including batch handling) for FMAToolbox.
%
% NOTE
%
% Although individual data files can be handled by these 'low-level' functions,
% it is generally easier to use <a href="matlab:help SetCurrentSession">SetCurrentSession</a> and related <a href="matlab:help Data">Get...</a> functions
% ... |
4e5583e411f7a9611a60453ee180a1be5f0a250d33f051ff124e73d21e5cc31f | MATLAB | 1,206 | 32 | function ea_credits
% The following code-snippets / software packages are being used and/or
% have been incorporated by the LEAD-Toolbox:
% SPM (http://www.fil.ion.ucl.ac.uk/spm/), mainly for normalization and
% volume handling
% Inhull.m - (c) John D'Errico
% Tools for NIfTI and ANALYZE image - (c) Jimmy Shen
% Dr... |
8497c0f87791d05530b87e1bdb60545f4507a1a6c5140275d4c7fab374b377c8 | MATLAB | 1,207 | 34 | %% Applying Tone Mapping to CT Data Enabling Simultaneus Display of Bony and Soft-Tissue Structures
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2016 - 2017
% mail@andreashusch.de, husch.andreas@chl.lu
function CTCo... |
a190bbdd5bb654920f62fdea1d3519c62a333d00384148c193848cfb603df11e | MATLAB | 1,209 | 34 | function [data_var] = findHighVarianceOTUs(densities,experimentBlocks)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically relevant behaviors of the ecosystems.
% Cop... |
e33cb93b22047a4d8602a4a5fd459073043aebe0346044a3c6d3af2e80800bcc | MATLAB | 1,209 | 39 | % eeglabciplot(lower,upper)
% eeglabciplot(lower,upper,x)
% eeglabciplot(lower,upper,x,colour)
%
% Plots a shaded region on a graph between specified lower and upper confidence intervals (L and U).
% l and u must be vectors of the same length.
% Uses the 'fill' function, not 'area'. Therefore multiple shad... |
28e3f3c2bc7eec08d3ab75964f3564c87e2e3c3697c35dcb59b98cc1e720e98e | MATLAB | 1,210 | 41 | function propStackedBar(counts, groupLabels, cmapCategory)
% propStackedBar Plot proportional stacked bar chart from counts.
%
% propStackedBar(counts, categoryLabels, groupLabels)
% creates a stacked bar plot where each bar represents a group,
% and the segments are proportional to the total counts.
%
% Input... |
8ad8ba38e0925d4b183171e6c260b23a2d8b7ad071cb2b0d54efcfe6a825df45 | MATLAB | 1,210 | 46 | function multiplot_segment(xx, yy, er, segX, seglist, ttlabel, figiniID)
featureseg = unique(seglist);
cc = colormap(hsv(length(featureseg)));
N = size(yy,2);
if N<=20
h1 = figure(figiniID+1);
subc = round(sqrt(N));
subr = ceil(N/subc);
for i = 1:N
subplot(subr, subc, i),
genera... |
9ef0f39abafb5d272598ea5440053b245591ed2d5b0aa329cd7d4fd6a26611f0 | MATLAB | 1,210 | 57 | function kappa = circ_kappa(alpha,w)
%
% kappa = circ_kappa(alpha,[w])
% Computes an approximation to the ML estimate of the concentration
% parameter kappa of the von Mises distribution.
%
% Input:
% alpha angles in radians OR alpha is length resultant
% [w number of incidences in case of... |
60f9ad5f7a64339f58843b7bf8588f0b05b1ad8c58f227e71ded6bd061e7eb02 | MATLAB | 1,211 | 48 | % reads multi-channel recording file to a matrix
% function .lfp] = function readmulti(fname,numchannel,chselect)
% last argument is optional (if omitted, it will read all the
% channels
function .lfp] = readmulti_ss(fname,numchannel,chselect)
if nargin == 2
datafile = fopen(fname,'r');
.lfp = fread(datafile,[num... |
c845aed83bedd357c44430370130cce63c8aa2412519261e64e1db092500406f | MATLAB | 1,211 | 67 | function [x,y] = embed(z,v,w)
% [x,y] or x= embed(z,lags) or embed(z,dim,lag)
% embed z using given lags or dim and lag
% embed(z,dim,lag) == embed(z,[0:lag:lag*(dim-1)])
% negative entries of lags are into future
%
% If return is [x,y], then x is the positive lags and y the negative lags
% Order of rows in x and y th... |
024f0c27560fe91cf12b83616cdd82863e413e1cbe3cac8de96dd7ccd4ab35b5 | MATLAB | 1,212 | 36 | % sum() - sum of memory mapped underlying array
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2008
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software... |
65564684a070536e5237143bb88f6b918c211c48a98d3a5b62814594d9413ccf | MATLAB | 1,212 | 32 | function CC = moserac(X, X2, threshold)
% Returns 2-d autocorrelation of matrix M with normalization standards as used by Mosers
%
% AC = CMBHOME.Utils.moserac(M1, M2, thresh)
%
%
% ARGUMENTS
% M1 N x M matrix, like a ratemap
% M2 (optional) O x P matrix, like a ratemap
% threshold (optiona... |
a3da765bc44cb199afebdf8643a26e08f579a895673083385f9b3b38b5cb1c6e | MATLAB | 1,212 | 32 | function [allflies,means,stds] = combineFlies(varargin)
% Use this to combine outputs of calc_dFF() (which is for single flies), if
% the flies are all part of the same experiment.
% These should be saved to the 'extracted' folder, so navigate there before
% you begin.
allflies={};
one=dir([varargin{1} '.mat'... |
cf07b1c781764c238cbef0caaa20df86dd015e72314fd25bd32753da452a613b | MATLAB | 1,212 | 36 | function [ w, cvx_optval ] = fdla( A )
% Computes the fastest distributed linear averaging (FDLA) edge weights
%
% [W,S] = FDLA(A) gives a vector of the fastest distributed linear averaging
% edge weights for a graph described by the incidence matrix A (n x m).
% Here n is the number of nodes and m is the number of ed... |
6628bff75425e8858de8c72ca034e4de343ac9bcfb047c025edb5859c606f242 | MATLAB | 1,213 | 35 | close all;
[x y] = pol2cart(squeeze(shortData(:,:,:,:,1)).*pi./180,squeeze(shortData(:,:,:,:,2)));
dist = [];
for e=1:2
for t=1:2
for s=1:numel(subjects)
for t1 = 1:size(x,4)
for t2 = (t1+1):size(x,4)
temp = hypot(x(e,s,t,t1)-x(e,s,t,t2),y(e,s,t,t1)-y(e,s,t,t2... |
882750c96b1f7d5e027abc2fbf9ce0ea2f3639f668ad6464ea98c42c7d1b621d | MATLAB | 1,214 | 41 | function cmap = chMap(M)
%CHMAP Create a monochrome-compatible colour map
%
% CMAP = IOSR.FIGURES.CHMAP returns a colour map CMAP (varying black -
% blue - green - yellow - white) that is monochrome-compatible, i.e. it
% produces a linear greyscale colour map. CMAP is size Mx3, where M is
% the length of the c... |
c59314d3b828008c9c329c46c5f67d11bd841ca4244a6dc198170c672a5d41b4 | MATLAB | 1,215 | 33 | function fn = step(vr, delta)
%WORKED=STEP(VR,DELTA)
% Moves the frame counter by DELTA frames for video VR. This is a
% generalization of NEXT. Returns 0 on an unsuccessful STEP. Note that
% not all plugins support stepping, especially with negative numbers. In
% the following example, both IM1 and IM2... |
e1c56c0321147239d11008a8666f0e620bfe30fe21e12739f7629222c21320bb | MATLAB | 1,215 | 35 | function [green_dFF,red_dFF] = calc_dFF(fluorArray,redArray,diffArray,exptitle,triallength)
% Make sure you're inside 'extracted' before running this function bc it
% saves workspace variables.
% This function calculates dF/F in each channel after you've done bg subtraction if
% necessary.
% triallength is in se... |
85c8265224cefbad2a2eb757f65f3536027851fb8e92d449bf130d9638171181 | MATLAB | 1,216 | 44 | function alldat=selectrespcolumns(headpath)
%start by using a manual picker
%eventually just change to something automatic
cd('extracted2');
filelist=dir;
alldat={};
for k=1:numel(filelist)
dataname=filelist(k).name;
%cd(headpath);
if contains(dataname,'_analysis2')
fileexpnum=dataname(1:end-14)... |
cb803cd173981da6499f7252cb4bd0eedea97563533cbd3c5b44dda96ef22a94 | MATLAB | 1,217 | 36 | function [f_cell, vel_dim] = VelocityRate(self, cel, vel_dim)
% Calculates the rate of firing for cell cel, for bins of running speed.
%
% If vel_dim is specified, bin edges of running speed are vel_dim
% If vel_dim is not specified, bin edges of running speed are [0 max_vel]
% in increments of 1 cm sec^-1.
%
% Remembe... |
9438b210c8cb8da052cc823e4c3811cb79dd9d0a4efeb7f02e3fdc1600260249 | MATLAB | 1,218 | 65 | %% figure 4
load('figure4_data')
%% Wave motif map
for icomp = 1 : 7
f = vector_plot(squeeze(iTWC_motif_vector_maps(:,:,icomp)),ch_inx_map,ch_image,180,icomp);
end
% close all
%% Time course
an_col = [30 58 205]/255;
aw_col = [229 32 21]/255;
f = figure('Position', [100, 100, 10... |
ae771ad63006d83db531bbcfabc34a82594f9ef1b635a0bfa7e4e5472a40ba04 | MATLAB | 1,218 | 37 | function varargout=ea_corr(X,Y,corrtype)
% wrapper for different correlation types
if ~exist('corrtype','var')
corrtype='pearson';
end
% Set inf to nan
X(isinf(X)) = nan;
Y(isinf(Y)) = nan;
switch lower(corrtype)
case 'pearson'
[varargout{1},varargout{2}]=corr(X,Y,'rows','pairwise','type','Pearson');
... |
d32eb35c33089dc48856cefae539f37cdafd3644aed299ba249431b6a230e2e5 | MATLAB | 1,218 | 41 |
parcellation_name = 'Shen';
%atlas_name = which('shen_2mm_268_parcellation.nii');
%% LOAD PARCELLATION FILE
savefilenamedata = fullfile(resultsdir, ['Parcellation_data_' parcellation_name '.mat']);
load(savefilenamedata, parcellation_name);
printhdr(sprintf('Loaded parcels: %s', parcellation_name));
% Store in p... |
ffcd0ffad7eaf22a6c4e2bc8ecf62f0f99a3efcc2b633a735c40f1e7d460384e | MATLAB | 1,218 | 30 | function reassignments = sortAssignments(assignments)
% SORTASSIGNMENTS Renumbers assignments
% reassignments = sortAssignments(assignments)
%
% Takes a list of assignment numbers and reassigns label numbers such
% that the largest size group is assigned label '1', the next largest
% is assigned label '2', and... |
5b8f4863e15860526210df236f1a08ce066b86e2566579d08185147e176ff8bc | MATLAB | 1,219 | 37 | % find potential conflict between Matlab functions
%
% A. Delorme, May 25th, 2012
matlabRoot = fileparts(fileparts(fileparts(fileparts(which('ispc')))));
folders = path;
delim = find(folders == ':');
delim = [ 0 delim length(folders)+1 ];
for iFolder = 1:length(delim)-1
currentFolder = folders(delim(iFolder)+1:de... |
809592f59c09dbc1fdd82b8d88954a1f7d83bbb3596e3e25f4bdadea34263698 | MATLAB | 1,219 | 25 | function dbURL=SOFAdbURL(dbURL)
% dbURL=SOFAdbURL
%
% dbURL=SOFAdbURL returns the internet URL to the directory containing
% HRTFs. The default URL is http://www.sofacoustics.org/data.
%
% dbURL=SOFAdbURL(newURL) sets the internet URL to the newURL for further calls
% of SOFAdbURL.
% SOFA API - func... |
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