sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d7ce0b37f0c6b6bd4ea5571e027f99b04c2f399a7ac169306979cccce77344c1 | MATLAB | 868 | 31 | function rid_colors = CBIG_setColorByAmyloid(ridList)
% rid_colors = CBIG_setColorByAmyloid(ridList)
% Red a+; green a-; blue unknown
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
rid_viscode_dummyCol_amyloid = CBIG_get_amyloid(ridList);
rid_amyloid = cell2mat(rid... |
817d98ce9870b824d8909c621b78550cadaa821b510e862fac1d37fd1749c700 | MATLAB | 869 | 22 | function y = pow_pos( x, p )
%POW_POS Power of positive part.
% POW_POS(X,P) = POS(X).^P = MAX(X,0).^P.
% Both P and X must be real, and P must be greater than or equal to 1.
%
% Disciplined convex programming information:
% POW_POS(X,P) is convex and nondecreasing in X; so when used in CVX
% expre... |
ff17755261fec64fc9966d047f78121cd1de1198f886027726e85079c4bbb867 | MATLAB | 869 | 28 | function cvx_setpath( arg ) %#ok
%CVX_SETPATH Sets the cvx path.
% CVX_SETPATH adds the internal cvx directories to Matlab's path so that the
% CVX system can find the functions that they contain. There is no reason to
% call this function during normal use of CVX; it is done automatically as
% needed. Howe... |
0ea7e3659d8d7342688b9f94c24bed014d18fc979385dba6fd8c349c5bad1514 | MATLAB | 870 | 36 | function [conn,connnum,count]=neighborelem(elem,nn);
%
% [conn,connnum,count]=neighborelem(elem,nn)
%
% create node neighbor list from a mesh
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2007/11/21
%
% input:
% elem: element table of a mesh
% nn : total node number of the mesh
%
% output:
% conn: ... |
bee446a12c937785714ef5e5b2a658af784bdcf7797a146a306d5ce3fce6551f | MATLAB | 870 | 24 | function E = epochs_from_arrays(all_hbo, all_hbr, Fs, baseline_sec, block_sec, all_aux)
%EPOCHS_FROM_ARRAYS Build epoch struct E from epoched arrays in memory.
% E = nirsproc.epochs_from_arrays(all_hbo, all_hbr, Fs, baseline_sec, block_sec, all_aux)
%
% Inputs
% all_hbo : nBlocks × T × nCh
% all_hbr : nBlocks × T... |
eb2afc51e551b4123f5d68634366bb21a18f9811bd77c134babc7640bcbdbf58 | MATLAB | 871 | 75 | function B=permutation(n, dif_subjs)
% This script is used for permutations.
B=[];
bootstrap_num=0;
k=n;
for i = 1:n,
A(i) = 1;
end
while A(1)<n,
for i = 1:n,
array(i) = 0;
end
for i = 1:n,
array(A(i))=1;
end
sum=0;
for i = 1:n,
sum=sum+array(i);
... |
72b48f1ef45d22454f2f97456d17725707edfbc352557f20195b3ab6eb716ece | MATLAB | 872 | 20 | function copyROIs(headpath,fileexpnum)%change back to regular if you want to use regular
%function to copy the handdrawn ROIs to all other directories.
%might need to add error checking. Can update hand drawn ones individually
%if there needs to be shifts
[ROIfile,ROIpath]=uigetfile('*.*'); %user picks ROI f... |
3f0fe09889be1d95d433fd775d52bfa26957d2234b03be3e8de8adf2ee5451fb | MATLAB | 873 | 43 | function varargout = permission(varargin)
% Format
% For getting the value
% dat = permission(obj)
%
% For setting the value
% obj = permission(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: permission.m 1340 2008-... |
9dd944fd61a202027089776559f19c18bf90f65384225f454908a737ebebe193 | MATLAB | 873 | 29 | function [xir,xjc] = sdpasplit(xcol,maxnnz)
% ------------------------------------------------------------
% Allocate enough space
% ------------------------------------------------------------
n = length(xcol);
if nargin < 2
maxnnz = n;
end
xir = zeros(maxnnz,1);
xjc = zeros(maxnnz+1,1);
% --------------------... |
04d1123e18011e603d644132b5a26c2b5a8dc9a8fbd6fb54fd5658f29f55f0b9 | MATLAB | 874 | 18 | function z = mldivide( x, y )
% Disciplined convex/geomtric programming information for MLDIVIDE:
% The MLDIVIDE operation X\Y can be employed with X as a scalar. In
% that case, it is equivalent to the LDIVIDE operation X.\Y, and
% must obey the same rules as outlined in the help for CVX/LDIVIDE.
% ... |
3858b0b898b8866fdbb72823659c17e39f41d926e1136302c82d6304abfefe4e | MATLAB | 875 | 23 | function [fluordatas,fluordata_reds,fluordata_diffs] = combineFluordata(flyname)
% Use this if you run multiple experiments of the same type on the same
% fly. This will combine the fluordata, fluordata_red, and fluordata_diff
% structs.
matfiles = dir(['*' flyname '*analysis2.mat']);
ex=load(matfiles(1).name);
... |
22d56a9a9304b7816b2662c12d2f34a7857fd5b0162eae4016d1e03b4d10c542 | MATLAB | 876 | 23 | function [adfreq, n, ts, fn] = plx_ad_gap_info(filename, ch)
import CMBHOME.PLX2Mat.*
% plx_ad_gap_info(filename, channel): Read a/d info from a .plx file
%
% [adfreq, n, ts, fn] = plx_ad_gap_info(filename, ch)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% channel - 0-based channel number
%
%... |
f2d1e91c5e50023c458298eb4f54d185a21b3adeac38892df583048ab6bca3a0 | MATLAB | 876 | 18 | function obj=coord_flip(obj)
% coord_flip Flips plot axes
%
% Using coord_flip flips the plot axes, i.e. x data will be on the vertical axis and y data on
% the horizontal axis. This is mainly useful to draw stat_ visualisations horizontally,
% such as boxplots, violin plots, etc. Coord flip sets the following axes pro... |
1c895cae613497823bde59c461c2aa594bcd02aad7cbece537a5452a3c01ec28 | MATLAB | 877 | 29 | function setPosition( o, p, u )
%setPosition Set position of graphics object
%
% setPosition(o,p,u) sets the position of a graphics object o to value p
% with units u.
%
% In contrast to setting the Position property directly, this function
% honors the ActivePositionProperty of axes.
% Copyright 2009-2016 The M... |
349290a6b452dc208c10e518fcd363df3249f4a2f2b99820bb4eb6e74faea34a | MATLAB | 877 | 28 | function p = PlotSlope(x,y,slope,len,varargin)
%PlotSlope - Plot line with given slope.
%
% USAGE
%
% p = PlotSlope(x,y,slope,len,<options>)
%
% slope line slope
% x,y coordinates of central point
% len segment length along the x axis
% <options> line and color speci... |
39f4adfcaba515889fd876d180af819a174ae3653298055cd1f4ec2976f76889 | MATLAB | 877 | 23 | % isnumeric() - returns 1
%
% 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 Foundation; either v... |
3e795e1976ac28102f0bf0944d77abead597bde294aea1d9ad96a5945ba89dc8 | MATLAB | 877 | 27 | %% plot every trial as unique comparisons (no averaging across flies)
alldRdiffs=[];
alldLdiffs = [];
% allhdjdiffs = [];
% allhdbdiffs = [];
for y = 1:15
% allhdjdiffs = [allhdjdiffs;hdjdiffs{y}];
% allhdbdiffs = [allhdbdiffs;hdbdiffs{y}];
alldLdiffs = [alldLdiffs;pfndLdiffs{y}];
alldRdiffs =... |
7b7faca1fc4a40fc43c95843eaae12e4936f339aa3b54540b071489e704afdc8 | MATLAB | 877 | 42 | % Demonstration of hierarchical model fits
%
% SF 2014
clear all
Ntrials = 200;
Nsub = 30;
c = -0.3;
c1 = [-1.5 -1 -0.5];
c2 = [0.5 1 1.5];
group_d = 2;
group_mratio = 0.8;
sigma = 0.5;
mcmc_params = fit_meta_d_params;
mcmc_params.estimate_dprime = 0;
for i = 1:Nsub
% Generate dprime
d(i) ... |
2bfacc2d3178220746f5a78d46ad66a2d78785f1e5ddae6def7b09c47dffeb49 | MATLAB | 878 | 22 | function blocks = day_to_blocks_v2(datadir)
all_folders = dir(datadir);
all_folders = all_folders([all_folders(:).isdir]);
all_folders = all_folders(~ismember({all_folders(:).name},{'.','..'}));
blocks = length(all_folders);
for b = 1:blocks
clear block_number all_block_files
block_number = str2num(all... |
8d7e67d69a4caf7788761004289c896a0d5d0fdb018cd2415ca66206d5d81b95 | MATLAB | 878 | 24 | function xlabelLowHighPkRespRatio(colors)
xlabel({'',''})
num = '$$ \textrm{Peak Low Contrast}\; \Delta \textrm{F/F} $$';
barLine = '$$\rule{5.2cm}{0.1mm}$$';
den = '$$ \textrm{Peak High Contrast}\; \Delta \textrm{F/F} $$';
tNum = text(1,1,num,'Interpreter','latex','Units','Normalized');
tBar = text(1,1,barLine... |
b49773aabd0b50ee8f60b0098e38b66c097bf88f9e9b7396102a54165675138f | MATLAB | 878 | 37 |
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... |
2c836c5d51ad825ae447a5b0249085b8c8c43460cb24d66d4c2b70fd2dd21557 | MATLAB | 879 | 19 | function outputPaths = ea_get_oss_outputPaths(options,S)
% Prepare various paths to conform with Lead-DBS BIDS structure.
% by Butenko and Li, konstantinmgtu@gmail.com
arguments
options % lead-dbs options for electrode reconstruction and stimulation
S % lead-dbs stimulation settings
end
outputPaths.sub... |
76ac97a82f89b68a76f5063f2d016a17bcef18c973ff702d874b6f08d4920737 | MATLAB | 879 | 33 | function [ convolution_result_fft ] = FConv( kernel, signal, varargin )
%FConv(kernel,signal) convolves a signal with a kernal via the fourier
%transform for speedy delivery.
%Note: as is, kernel is centered.
% Adapted from Cohen Chapter 13
%
%TO DO:
% -add varargin in for centered or left-aligned kernel
%
%Last U... |
c908aa75228ce280dce05d180845e5706c3a0c4fbf62fa777ff381ab57526d47 | MATLAB | 879 | 34 | function [y_model,fit_params,rsquare,goodness] = SaturatingRegression(x, y)
% Does a natural growth fit and returns the model expected values,
% parameters of best fit, rsquare value, and other goodness object.
%
% [fit,params,rsquare,goodness] = CMBHOME.Utils.LogRegression(x,y)
if length(x)~=length(y)
error('LogR... |
cab135007059f1e3d7a4234cb1f2c3bf0fad23d3e2a40afb8386085134526174 | MATLAB | 880 | 37 | %%*********************************************************
%% smat: compute the matrix smat(x).
%%
%% M = smat(blk,x,isspM);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%**********************************************************
function M = ... |
df7d73bd79414f7ac3fb29f32d6b2e5ad84365e93451143954fd3472b05131df | MATLAB | 880 | 35 | function savetetgennode(node,fname)
%
% savetetgennode(node,fname)
%
% save a mesh node list to tetgen .node format
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% node: node coordinates, dimension (nn,3)
% columns beyound the 3rd column are treated as
% markers and attributes as... |
ae24fa916d4bfd91052d4b86d1c387568d7461261134688eeeb85c0a4067cffb | MATLAB | 881 | 25 | function [Xpix,Ypix,FrameRate,Zframes,fbframes]=findkeyparams_newThor5D()
%use this function to get the FOV and the framerate of aquisition
%you have to parse the XML file from thor.
%this sucks and is definitely not elegent
disp('Show me where the XML file is for any experiment from this set');
[matexpfile... |
daef80fffa3dd21b5b14ca522595e31faabcd476905c114eb86c67801e82017f | MATLAB | 881 | 48 | function [pnt, tri] = read_vtk(fn)
% READ_VTK reads a triangulation from a VTK (Visualisation ToolKit) format file
% Supported are triangles.
%
% Use as
% [pnt, tri] = read_vtk(filename)
%
% See also WRITE_VTK
% Copyright (C) 2002, Robert Oostenveld
%
% $Id$
fid = fopen(fn, 'rt');
if fid~=-1
npnt = 0;
while... |
e798bf49447e578690a41eae7f6040cab6b9621eec9d3d94c16e8a7a37adb46d | MATLAB | 881 | 35 | function cwt = loadCwtMultiChannelCrop_(filePaths, trialIdx, fIdx, tIdx, useSingle)
% Return: nTrialSelected x nChannel x nFreqSelected x nTimeSelected
if islogical(trialIdx)
trialIdx = find(trialIdx);
end
nTrial = numel(trialIdx);
nCh = numel(filePaths);
nFreq = numel(fIdx);
nTime = n... |
23f5d022dadafc6825fba70f34fe24ecf871ad2f988e71e8593bea4dad76b432 | MATLAB | 882 | 39 | function frame = getnext(vr)
%FRAME=GETNEXT(VR)
% This method is a shortcut for
% if (next(vr))
% frame = getframe(vr);
% else
% frame = [];
% end
%
% Although this method can be more convenient than calling NEXT and GETFRAME
% separately, there is no way to distinguish between a zero-sized frame ... |
3355bd2a9293b68268e42ce18c5c8b893f87adf776abac0034f3e9883399cefe | MATLAB | 882 | 27 | function data=createdatamatc(data,E,Fs,win)
% Helper function to create an event triggered matrix from univariate
% continuous data
% Usage: data=createdatamatc(data,E,Fs,win)
% Inputs:
% data (input time series as a column vector) - required
% E (events to use as triggers) - required
% Fs (sampling frequen... |
58ffd6a478f3d04442f3be411d05e996d255783ce8842ce63cb8e5718f5b45c4 | MATLAB | 882 | 49 | function M1 = vox2ras_0to1(M0)
% M1 = vox2ras_0to1(M0)
%
% Converts a 0-based vox2ras matrix to 1-based, ie,
% Pxyz = M0*[c r s 1]' = M1*[(c+1) (r+1) (s+1) 1]'
%
%
% vox2ras_0to1.m
%
% Original Author: Doug Greve
% CVS Revision Info:
% $Author: nicks $
% $Date: 2011/03/02 00:04:13 $
% $Revision: 1.3 $
%
% Co... |
7551b31fadfbeb1f25a475d97f34cbc68fd7bbba726e3b3f70afce54602f6cd0 | MATLAB | 883 | 32 | function [x,y]=to_polar(obj,theta,rho)
%If the graph is set as polar, x and y are interpreted as rho and
%theta respectively, and data is converted in cartesian x and
%y. Passthrough if is_polar is false
if obj.polar.is_polar
if iscell(theta)
x=cell(size(theta));
y=cell(size(theta));
for k=... |
58b15ed815617d70f55b82956d39f632c78ff71b677ea32ed7ca69af1164f596 | MATLAB | 884 | 42 | function [f]=OIS_corr2(data,reference)
% Usage ... f=OIS_corr2(data,reference)
%
% reference - reference waveform for correlation
% Image-course approach
sumim=0;
sumref=0;
count=0;
sumnx=0; sumny=0; sumnxy=0; sumnx2=0; sumny2=0;
%t=clock;
%disp(['Time:']);
%disp(t);
disp(['Initiating Analysis...'])... |
9912ccdcaf92e68873b03209dc7920c81b67cf1cd095f698525b758f51377883 | MATLAB | 884 | 24 | mean_rr1a_micronsWsm=mean(all_rr1a_micronsWsm,2);
mean_rr1aSEM_micronsWsm=mean(all_rr1aSEM_micronsWsm,2);
mean_rr1a_percentWsm=mean(all_rr1a_percentWsm,2);
mean_rr1aSEM_percentWsm=mean(all_rr1aSEM_percentWsm,2);
mean_rr2a_micronsWsm=mean(all_rr2a_micronsWsm,2);
mean_rr2aSEM_micronsWsm=mean(all_rr2aSEM_micronsWsm,2);
... |
9c5a7f45946f337169e6dfeed53ce83670e199a58e1d835014d4dba7973ada8a | MATLAB | 884 | 29 | function [isLFP] = bz_isLFP(lfp)
% USAGE
% [] = bz_isLFP(lfp)
%
% INPUT
% lfp - struct with the following fields
% .lfp
% .timestamps
% .samplingRate
% .channels
%
%
% OUTPUT
% logical true if struct meets lfp crite... |
c18dccf7ddb916b68113b6615d722b31f2c4dc806a4aa0052a857d2bd7361df9 | MATLAB | 884 | 33 | % Exercise 4.3: Solve a simple QP with inequality constraints
% From Boyd & Vandenberghe, "Convex Optimization"
% Joëlle Skaf - 09/26/05
%
% Solves the following QP with inequality constraints:
% minimize 1/2x'*P*x + q'*x + r
% s.t. -1 <= x_i <= 1 for i = 1,2,3
% Also shows that the g... |
c53196f0fb37cf1ff80b53dc35a60f6875d8ce35eb15f193303f793bde94c7f8 | MATLAB | 884 | 19 | function Lambda=BarycentricCoordinatesTriangle(VN0,VN1,VN2,rx,ry)
% Normalization factors
f12 = ( VN1(2) - VN2(2) ) * VN0(1) + (VN2(1) - VN1(1) ) * VN0(2) + VN1(1) * VN2(2) - VN2(1) *VN1(2);
f20 = ( VN2(2) - VN0(2) ) * VN1(1) + (VN0(1) - VN2(1) ) * VN1(2) + VN2(1) * VN0(2) - VN0(1) *VN2(2);
f01 = ( VN0(2) - VN... |
31c4ee340b1cfc1bacfaaa4a3ea12919dbd4bb781b7b512edb8781e54436a042 | MATLAB | 885 | 28 | function minimise( varargin )
%MINIMISE Specifiies a convex (or affine) objective to be maximized.
global cvx___
prob = evalin( 'caller', 'cvx_problem', '[]' );
if ~isa( prob, 'cvxprob' ),
error( 'No CVX model exists in this scope.' );
elseif isempty( cvx___.problems ) || cvx___.problems( end ).self ~= prob,
... |
5e06d78a43283ba56085a985db98b1d60cfc6808a270b3faa63ac831fadfc6a6 | MATLAB | 885 | 36 | function m=jVecToSymmetricMat(v,msize,offset)
% converts a vector into a square symmetric matrix
%
% IN:
% v: nx1 vector of numbers
% msize: scalar, resulting matrix size (msize rows by msize columns)
% OUT:
% m: square symmetric matrix
%
% v1.0 Nov 2009 Jonas Richiardi
% - initial release
% v1.... |
80681409f53613396614ba72d7cb708646f1f6aa553c76653d665d652479365b | MATLAB | 885 | 28 | function minimize( varargin )
%MINIMIZE Specifiies a convex (or affine) objective to be maximized.
global cvx___
prob = evalin( 'caller', 'cvx_problem', '[]' );
if ~isa( prob, 'cvxprob' ),
error( 'No CVX model exists in this scope.' );
elseif isempty( cvx___.problems ) || cvx___.problems( end ).self ~= prob,
... |
01366a011cb9bc467b5f50b06ee8b8ba35ca757851558df931505f2be562cf30 | MATLAB | 886 | 24 | function isMotorStop = motorStop(stepperHandle, panelHandle)
unitStep = fix(360/0.13*16);% pulses per mm
timeDelay = 5;
valPtr = libpointer('int64Ptr', 0);
calllib('phidget21', 'CPhidgetStepper_getCurrentPosition', stepperHandle, 0, valPtr);
currPosition = get(valPtr, 'Value');
calllib('phidget21', 'CPhidge... |
3ba298da83a0e44e8069272a5f7e821e88d8840890f3625a76b8c9ac6d33ac94 | MATLAB | 886 | 28 | function maximize( varargin )
%MAXIMIZE Specifiies a concave (or affine) objective to be maximized.
global cvx___
prob = evalin( 'caller', 'cvx_problem', '[]' );
if ~isa( prob, 'cvxprob' ),
error( 'No CVX model exists in this scope.' );
elseif isempty( cvx___.problems ) || cvx___.problems( end ).self ~= prob,
... |
4e8bdb92c1dacdb9f6809241cbd8a5c13f3da98ea4e22810f983d404fd567a40 | MATLAB | 886 | 28 | function maximise( varargin )
%MAXIMISE Specifiies a concave (or affine) objective to be maximized.
global cvx___
prob = evalin( 'caller', 'cvx_problem', '[]' );
if ~isa( prob, 'cvxprob' ),
error( 'No CVX model exists in this scope.' );
elseif isempty( cvx___.problems ) || cvx___.problems( end ).self ~= prob,
... |
827375cc625c854b720ec068a09405dcdb4935136c3f315ea952b2a52b617721 | MATLAB | 886 | 33 | %%%%%%%%%%%%%%%%%%%
%% Zicheng Yang CCMU
%% origin averaged calcium signal of several mice; heatmap
%% Version: 0.1-2024/07/08-YZC-initial version
%%%%%%%%%%%%%%%%%%%
clear all;
close all;
% parameters
nko=5;
nwt=5;
Ts=1/100;
mcako =xlsread('x');
mcawt =xlsread('x');
avmcak =mean(mcako,1);
stmcak=s... |
d8f2423cd7d21018113749c03d126ee6f06fc536001c3903bb16274294ac8767 | MATLAB | 886 | 27 | function z = colon( x, y )
if ~isa( x, 'cvxdual' ),
z = x; x = y; y = z;
end
global cvx___
try
dvars = cvx___.problems( x.problem_ ).dvars;
q = builtin( 'subsref', dvars, x.name_ );
catch
error( 'CVX:Corrupt', 'Internal CVX data corruption. Please CLEAR ALL and rebuild your model.' );
end
if q.attached_... |
f0869e39140549149fa1dea845dfca2e672fd5ca02d4af18e7838b8f49592cf3 | MATLAB | 886 | 31 | function [varargout]=kolmogorov_max_flow(A,u,v,varargin)
% KOLMOGOROV_MAX_FLOW Kolmogorov's max flow algorithm
%
% Kolmogorov's algorithm implements a variation on the augmenting path idea
% to compute a maximum flow or minimum cut in a network.
%
% See the max_flow function for calling information and return paramet... |
3a2a6c9ee553131943fe5b18027560af4add4b2de3bd723fb82e9e8885668fe0 | MATLAB | 887 | 33 | %GetNextItem - Get next item from a Batch object (iterator mode).
%
% This is a helper class to easily read and parse batch files.
%
% USAGE
%
% [b,item,line] = GetNextItem(b);
%
% b batch object
% Copyright (C) 2007 by Michaël Zugaro
%
% This program is free software; you can redistribute it and/o... |
7966dc8b2f03c815be608104d29962ca7580e279ac6e75abcd3086caf5f9544f | MATLAB | 888 | 34 | function ea_acpcdetect(inputimage, outputimage)
% Wrapper for acpcdetect
%
% Detect AC and PC locations, set the origin of the input NIfTI image to
% the AC-PC midpoint. Output image will be tilt-corrected and in RAS
% orientation.
if nargin < 2
outputimage = inputimage;
end
ea_libs_helper;
basedir = fileparts(m... |
7bb71274bbb10605aabefb473f9933c26b52ea36ae922eefcc24afa84b79e487 | MATLAB | 888 | 37 | function y = log_normcdf( x )
%LOG_NORMCDF Internal CVX version.
narginchk(1,1);
if ~isreal( x ),
error( 'Argument must be real.' );
end
persistent a b nb ob
if isempty( a ),
a =sqrt( [ 0.018102332171520
0.011338501342044
0.072727608432177
0.184816581789135
... |
f8f3484e7026f172e188260e75461efb1962ed54284ce01704464aad24ed2888 | MATLAB | 888 | 36 | function spy( x, mode )
global cvx___
% SPY is not a computational function, so it can be applied to any
% CVX variables.
switch nargin,
case 0,
error( 'Not enough arguments.' );
case 1,
mode = '';
case 2,
if ~ischar( mode ) || size( mode, 1 ) > 1,
error( 'Second... |
1ac79cb769a796d3d5022677b22b216e954ccdf84aba20385e37ac11806d3b30 | MATLAB | 890 | 30 | function [V,F,nF,T,nT]=process(V,F,nF,T,nT,Frows,F_Local,F_Local_new, Vertex_id)
% Remove faces by replacing them
Frows=sort(Frows(:),1,'descend');
for i=1:size(F_Local,1),
F(Frows(i),:)=F(nF,:); nF=nF-1;
end
for i=1:size(F_Local_new,1)
F2=F(1:nF,:);
checkduplicate=(any(F2==F_Local_new(i,1),2)&a... |
291f4d48448728f6aa68bc9a80c24eb5ddef864f7d369f08b3afb79488b655dc | MATLAB | 890 | 36 | function [n,names] = plx_chan_names(filename)
% plx_chan_names(filename): read name for each spike channel from a .plx or .pl2 file
%
% [n,names] = plx_chan_names(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
%
% OUTPUT:
% names - array of channel name strings
% n - number... |
daca599351c060c296a85414719549817ff6b2482dc2aa13869ced01f877ec1d | MATLAB | 890 | 32 | function y = cvx_blkdiag( varargin )
% A reimplemenetation of MATLAB's blkdiag function, which is broken in
% certain versions of MATLAB.
if nargin == 1,
y = varargin{1};
else
isYsparse = false;
for k = 1 : nargin,
x = varargin{k};
[ p2(k+1), m2(k+1) ] = size(x); %#ok
if issparse(x... |
fac64acdab55dad883a1f83e75d6dc7a459ff1e2d32ec41140eec703cf2af797 | MATLAB | 890 | 19 | function z = mrdivide( x, y )
% Disciplined convex/geomtric programming information for MRDIVIDE:
% The MRDIVIDE operation X/Y is quite often employed with Y as a
% scalar. In that case, it is equivalent to the RDIVIDE operation
% X./Y, and must obey the same rules as outlined in the help for
% ... |
fadf78a550b12bad254c55eef01c9a739bb158bacebdac54db1f197604e41559 | MATLAB | 890 | 34 | % W = dwt3(V, wl)
%
% Implements the discrete 3D wavelet transform, using Matlab 2D functions.
%
% See also: idwt3
% Code written by Iman Aganj.
function W = dwt3(V, wl)
for i=1:3
s(i) = length(dwt(zeros(size(V,i),1), wl));
end
W.wl = wl;
W.dec = cell(2,2,2);
for i=1:2
for j=1:2
for ... |
1f9d1b8e6c241aed055ea76f95024b9e85d2a6e1f928f2fcc2d2c681d3288975 | MATLAB | 891 | 21 | function xmax=findpeaks_chronux(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 exc... |
5ec1a5ce946561fad4649bdc239c8ca2dbe45989aeccc85514af96e96f6316b8 | MATLAB | 891 | 41 | function [] = Batch_Alignment()
% reference image for allignment
ref = 750;
% Prompt for manual browse to image folder
folder_name = uigetdir(pwd, 'Select Folder containing Prairie Images');
if folder_name == 0
error('no folder selected')
end
display(folder_name);
files = dir([folder_name, '/TS... |
8b8065d4f95f37f677bd45be2c70d9e17b9561df2c6d6537994a4d4597652c73 | MATLAB | 891 | 37 |
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/npy.ipynb for
% more.
%
[shape, dataType, fortranOrder, littleEndian, totalHeader... |
ba29e80b8d05e597e12ec05d0054b6b756df93fc9f90398738b2110d13d97fd8 | MATLAB | 891 | 32 | function atlases = ea_loadatlas(atlases,resultfig,ht)
% Load atlases and do struct2roi conversion when needed
if ischar(atlases) % Input is not atlases struct itself
if isfile(atlases) % Input is atlas_index.mat file path
load(atlases);
else % Input is atlas name (suppose in MNI space)
load([ea... |
faad6649a0824edddccf3a8e3287fb69cee1a54222e4807076b473cee728fd26 | MATLAB | 891 | 27 | function foldID = makeGroupedFolds(nGroups, K)
% makeGroupedFolds Assign groups (not rows) to K cross-validation folds.
%
% foldID = makeGroupedFolds(nGroups, K)
%
% Randomly distributes nGroups group labels across K folds as evenly as
% possible. In the paired PLS-DA pipeline the groups are SUBJECTS, so both of... |
28b4ecbb1f67d9d6bd44d6b18969e0d834b7f7341d556b472e0358ef8378a18b | MATLAB | 892 | 36 | %% statejit - jitter states
% Jitters states with adjacent states in time order, trial order, or
% whatever order they are presented. The jittering is performed using a
% Gaussian distribution with a supplied standard deviation (in units of
% bins).
%
% Syntax: [randstates] = statejit(states,std)
%
% Input:
% states... |
321facf733c220dbd2979a54f3db5c09247589464394e70985e531e68bd2d06f | MATLAB | 892 | 24 | function [adfreq, n, ts, fn, ad] = plx_ad(filename, ch)
import CMBHOME.PLX2Mat.*
% plx_ad(filename, channel): Read a/d data from a .plx file
%
% [adfreq, n, ts, fn, ad] = plx_ad(filename, ch)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% channel - 0-based channel number
%
% a/d data... |
65eb4ca8a9fa786b096dcf826f306105f138d1b5554a7324257cf66c670a9be3 | MATLAB | 892 | 45 | function v = cvx_vexity( x )
global cvx___
s = x.size_;
if any( s == 0 ),
v = cvx_zeros( s );
return
end
p = cvx___.vexity;
b = x.basis_;
n = length( p );
nb = size( b, 1 );
if nb < n,
p = p( 1 : nb, 1 );
elseif n < nb,
p( nb, 1 ) = 0;
end
if ~any( p ),
v = cvx_zeros( x.size_ );
if x.slow_,
... |
36b70da4ba8b79d95c76843a0e46014a102596451f2f2d4e2454b186ec1cffc9 | MATLAB | 893 | 31 | function [ self, cel, args] = infieldness_p(varargin)
% Handles infieldness required fields to an input parser
if strcmp(class(varargin{1}),'inputParser')
p = varargin{1};
varargin = varargin(2:end);
else
p = inputParser;
end
p.StructExpand = true;
p.KeepUnmatched = true;
if isstruct(varargin{1})
if is... |
8611e4043f611127788a8335732612a443c2665b4a2c9eda23ad7f762c39c6c6 | MATLAB | 893 | 30 | function [varargout]=push_relabel_max_flow(A,u,v,varargin)
% PUSH_RELABEL_MAX_FLOW Goldberg's push-relabel max flow algorithm
%
% This function calls Boost's implementation of Goldberg's push relabel
% algorithm to compute a maximum flow in a graph.
%
% See the max_flow function for calling information and return param... |
eedd4708c15e80a956485ef3a03112cc08f20ea50fa506d37a060b63f992846a | MATLAB | 893 | 38 | function plotBordersCCF(dorsalMaps, randomBorders, lw, color, alpha)
% Plots a simplified allenMap with specified randomized borders on top
if nargin < 3
lw = 0.1420;
end
if nargin < 4
color = 0.35*[1,1,1];
end
if nargin < 5
alpha = 0.75;
end
% Figure
allenMapSMc(dorsalMaps, [-3.6, 0, -2, 3]) % Creates ... |
113a72bc01bc9a3ddae88c249b894d4038660ed69563409ca14b23a3674f35d1 | MATLAB | 894 | 34 | function [CFCdata,time] = getISPCCFCchannelTime(deltaphase,thetaphase,alphaphase,betaphase,featureLabel)
% Get the bands phase
switch featureLabel(1)
case 0.5
phase1 = deltaphase(featureLabel(3),:,:);
case 4
phase1 = thetaphase(featureLabel(3),:,:);
case 8
phase1 = alphaphase(feature... |
527a8b838b399ed0a57160be8592f96ba1ceb09fbc4684c7f1bce65609d3364c | MATLAB | 894 | 22 |
tmpvars={'do_crop','do_load','do_loadall','do_motc','do_realign',...
'do_maskreg','do_intc','do_bin','do_binfirst','do_average',...
'do_arfilt','do_ffilt','do_arfilt_apply','do_intc_apply',...
'do_motc_apply','do_motcmask','do_detrend',...
'do_timing','do_sequential','do_seqint... |
7913fbc06fb46c477ce547e197d9b28c6d66169c53508cc749c7ebaf1d4e9d02 | MATLAB | 894 | 30 | function data=createdatamatpb(data,E,Fs,win)
%
% Helper function to create an event triggered matrix from a single
% channel of data.
% Usage: data=createdatamatpb(data,E,Fs,win)
% Inputs:
% data (input time series as a single vector) - required
% E (events to use as triggers) - required
% Fs (sampling fre... |
85090643acead7e5bdd41a3768cd01c8ac724248517b66050a7443f2cedc114a | MATLAB | 894 | 45 |
%
% check dijkstra for only positive values
%
% write graph xml reader
%
% add graph struct type...
%
% ctrl-c mex files
%
%
%
% graph constructions
% - butterfly graph [A xy labels] = butterfly_graph(levels)
% - cycle graph [A xy] = cycle_graph(nodes)
% - complete graph [A xy] = complete_graph(nodes)
% - hypercub... |
f6438d81b44aa3d47cbe6e938a2e26cffc70aa95bc8023ea0f9e5d0ef2d8a36e | MATLAB | 894 | 22 | function cvx_optval = det_root2n( X )
%DET_ROOT2N 2nth-root of the determinant of an SPD matrix.
% For a square matrix X, DET_ROOT2N(X) returns
% POW(DET(X),1/(2*size(X,1))
% if X is symmetric (real) or Hermitian (complex) and positive
% semidefinite, and -Inf otherwise.
%
% This function has b... |
25a86df55eaa17f34511380dc7e9562ef5b9ac6fccaf6e5f150c6d4aee986b2e | MATLAB | 895 | 31 | function child = children(tree,uid)
% XMLTREE/CHILDREN Return children's UIDs of node uid
% FORMAT child = children(tree,uid)
%
% tree - a tree
% uid - uid of the element
% child - array of the UIDs of children of node uid
%__________________________________________________________________________
%
% Return UID'... |
6a4dbf30da86726886d428b40949dd26941fb7d7bd99f073110f3476b3ed492a | MATLAB | 895 | 28 | function z = lambda_max( Y )
% LAMBDA_MAX Maximum eigenvalue of a symmetric matrix.
% For square matrix X, LAMBDA_MAX(X) is MAX(EIG(X)) if X is Hermitian
% or symmetric and real; and +Inf otherwise.
%
% An error results if X is not a square matrix.
%
% Disciplined convex programming information:
% ... |
8899ff56734d5118af026789f6b500f4e8d85edfd0ba1941ddbd476a8def4955 | MATLAB | 895 | 24 | function C = CORE_histxt(X,d)
%CORE_HISTXT Core computational routine for HISTXT.
% C = CORE_HISTXT(X,D), where X is an M x N matrix, returns a D x N
% matrix C such that C(i,j) = #[X(:,j)=i].
%
% CONDITIONS
% ----------
% X must only contain integer values between 1 and D.
% X must be of type double... |
ec6ead38528e0837daea2a040826f78c2c0969663ff55f35dd636716ec1142d9 | MATLAB | 895 | 25 | function CBIG_ASDf_gamma2table(gamma_file, output_name)
% CBIG_ASDf_gamma2table(gamma_file, output_name)
%
% This function normalizes estimated gamma to get Pr(Factor|Participant)
% (i.e., factor compositions of participants),
% and write to a text file specified by output_name.
%
% Input:
% - gamma_file:
% ... |
5b4e97799ddb37f2895a99c47587e8355c4dc587053a4a271d362b3169217630 | MATLAB | 896 | 38 | function [thetahat kappa] = circ_vmpar(alpha,w,d)
% r = circ_vmpar(alpha, w, d)
% Estimate the parameters of a von Mises distribution.
%
% Input:
% alpha sample of angles in radians
% [w number of incidences in case of binned angle data]
% [d spacing of bin centers for binned data, if supplied
% ... |
8e8fe5198e5cf6a2e7bf40c49fd911d86653933e0296bfb02c92bd21fbde8a97 | MATLAB | 896 | 23 | function baselines = processColData(headpath,lowestper)
% To process columnar imaging data. 'lowestper' is the lowest percent of
% values you want to take the mean of to calculate the baseline intensity
% for an ROI across concatenated data.
load('cat_MC_Videocdf2.mat');
[rois timepoints] = size(Cin);
bgCorr = ... |
c8bb7b313f42734bdda29c28dee97877767034e0decde38ec8eb85652c284711 | MATLAB | 896 | 41 | function CBIG_hypoTest_3t(betas, stats)
% CBIG_hypoTest_3t(betas, stats)
% Overall
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
H = [0 1 0 0 0 0; 0 0 1 0 0 0];
c = [0; 0]; % H*b = c
p = linhyptest(betas, stats.covb, c, H, stats.dfe);
fprintf('Overall p = %e\n', p)... |
6a2a8768c8aa04f666819f74af7994d1497670a383dc8657ac0eeb42f309fe1f | MATLAB | 897 | 37 | % Euclidean projection on the nonnegative orthant
% Section 8.1.1, Boyd & Vandenberghe "Convex Optimization"
% Joelle Skaf - 10/07/05
%
% The projection of x0 on the proper cone K = R+^n is given by
% minimize || x - x0 ||^2
% s.t. x >= 0
% It is also given by: P_K(x0)_k = max{x0_k,0}
% Inpu... |
9e66b28dffe47d89703d776093b638294e45caf5ac849badee8c3077be26ed08 | MATLAB | 897 | 25 | %FindField - Find field in a map, e.g. firing field in a firing map.
%
% Find field in a map, i.e. the connex area around the peak, where the values
% are above a given threshold.
%
% Note: This function should not be called directly. Use <a href="matlab:help FiringMap">FiringMap</a>, <a href="matlab:help FiringCurve">... |
5bf6003ba311dc63843571525c803243f6f266fe3e72ac3bcfa3a0bc432fcb94 | MATLAB | 898 | 21 | function [surflist, vollist] = cifti_diminfo_dense_get_structures(diminfo)
%function [surflist, vollist] = cifti_diminfo_dense_get_structures(diminfo)
% Get the names of all the structures used in the dense mapping.
%
% The diminfo argument should usually be "cifti.diminfo{1}".
if ~isstruct(dimi... |
511e295778db9430258cad6f39eb81b9ed0608839215dfa432467c5ab7f9fffa | MATLAB | 899 | 25 | function [ts] = PL2Ts( filename, channel, unit )
% PL2Ts( filename, channel, unit ): read spike timestamps from a .pl2 file
%
% ts = PL2Ts( filename, channel, unit );
% ts = PL2Ts( filename, 'SPK01', 1 );
% ts = PL2Ts( filename, 2, 3 );
%
% INPUT:
% filename - if empty string, will use File Open dialog
% c... |
3c0312fabf91f6920b1630eec6398cf1ab13849cb252ef45f613b8a09f27b7ae | MATLAB | 900 | 23 | function baselines = getconcatbaselines(headpath,lowestper)
% To process columnar imaging data. 'lowestper' is the lowest percent of
% values you want to take the mean of to calculate the baseline intensity
% for an ROI across concatenated data.
load('cat_MC_Videocdf2.mat');
[rois timepoints] = size(Cin);
bgCor... |
3cf358b7770056c4854d1f9f970cdf8f0a9d78a0ea045705515da26378dedd42 | MATLAB | 900 | 47 | function pval = circ_medtest(alpha,md)
%
% [pval, z] = circ_medtest(alpha,w)
% Tests for significance of the median.
% H0: the population has median angle md
% HA: the population has not median angle md
%
% Input:
% alpha sample of angles in radians
% md median to test for
%
% Output:
% pval p... |
a98753658b0d20c457d6f81fb9ebed96fd640f48cc22855d18350e42c9f32312 | MATLAB | 900 | 28 | % Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
addpath(spm_dir)
% Read rid.txt file
fid=fopen(id_list);
rid=textscan(fid,'%s');
fclose(fid);
rid=rid{1,1};
% Calculate the GM and ICV of all subjects
for i = 1:length(rid)
gm_file = [output_dir '/mri... |
af92f2e83ed4daabc35f2426962591e7aa71354ad48c185dfc80389fd53ec0d2 | MATLAB | 900 | 23 |
% https://www.xquartz.org/
% https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads
% https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_mac
% [projected, projected_seg] = CBIG_RF_projectfsaverage2Vol_single(lh_input_array, rh_input_array, interpolation, path_to_mapping, path_to_mask)
cifti_struct = cifti_read('tra... |
20530fb9fd2260993374fb4a7de4edfbcbd29aa632f705b2fef60a04c96dc63f | MATLAB | 901 | 34 | function plotModulationMapCCF(dorsalMaps, allROIs, propField, color)
% Creates a binned and smooth map of cell count 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;
smoothSD = ... |
eedeeda22cffe5ad5ce0ee9126daa2c324c4c1ba54e9919aa4e3a0a47c95822d | MATLAB | 901 | 23 | % end() - last index to memmapdata 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 Founda... |
f3b81371a24218f1a8e0c5f910222272c816c49a61f0e6c6d3654c70c754578e | MATLAB | 901 | 46 | function [node,elem]=readasc(fname)
%
% [node,elem]=readasc(fname)
%
% read FreeSurfer ASC mesh format
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
% date: 2009/04/02
%
% input:
% fname: name of the asc file
%
% output:
% node: node positions of the mesh
% elem: element list of the mesh
%
% ... |
3df517500ee481e3345331ba3e30dcf68fc75294841aa2eeab47c17d499a304c | MATLAB | 902 | 31 | function [N,C]=check_consistency(data1,data2,sp)
% Helper routine to check consistency of data dimensions
% Usage: [N,C]=check_consistency(data1,data2,sp)
% Inputs:
% data1 - first dataset
% data2 - second dataset
% sp - optional argument to be input as 1 when one of the two data sets is
% spikes times stored as a 1d a... |
833641a0f08e03e37eb7e8f1975177999a7b3b5fcc9a8f0ebaa67d76861632cb | MATLAB | 903 | 30 | function [R, mean_theta, S] = MeanResultant(self, cel)
% MRL of head tuning
%
% Returns length, angle and circular variance pertaining to the mean
% resultant of directionality of neuron spiking.
%
% RETURNS:
% R, mean_theta and S. M x N array where N is the number of cells, and
% M is the number of epochs
%
% see equa... |
9a145cfde8ec5addb562d9fcf4e739906b31a3df4c708e8642d7bfafdea5e9cc | MATLAB | 903 | 30 | function obj = Empty( varargin )
%uiextras.Empty Create an empty space
%
% obj = uiextras.Empty() creates an empty space that can be used to add
% gaps between elements in layouts.
%
% obj = uiextras.Empty(param,value,...) also sets one or more property
% values.
%
% See the <a href="matlab:doc uiextras.Empt... |
ca1d121e7169a24a21476055650c70a63c6d0e873e52921aba67572257620459 | MATLAB | 903 | 31 | function [] = restorehold(ax, prevhold)
%RESTOREHOLD restore hold status.
% RESTOREHOLD(ax, prevhold) restores the hold status of axes object with
% handle ax, to the state defined by prevhold. To save prevhold for use
% with this function, call takehold or ishold.
%
% usage
% RESTOREHOLD(ax, prevhold)... |
d4993e81f31835d808b276b4d9c4313cb3d4af7a8f362fda9abe3b20c7f8f1c7 | MATLAB | 903 | 32 | function root = MergeEpochs(root)
% Returns root with epochs that do not overlap. Touching epochs are merged.
%
%
% Assumes that all epochs are on the timescale of root.b_ts (all epochs
% have samples within them. any epochs without samples within them are
% deleted)
% root = CMBHOME.Utils.MergeEpochs(root);
if ~strcm... |
f82610b796bfa8dee1c3ef8579fa91df3904b522ed6ebdbdf0b59ff406c62ec7 | MATLAB | 903 | 40 | function outface=outersurf(node,face)
%
% outface=outersurf(node,face)
%
% extract the out-most shell of a complex surface mesh
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% node: node coordinates
% face: surface triangle list
%
% output:
% outface: the out-most shell of the surface mesh
%
% --... |
01bbb3c9eb382d82c36ad489f9f758211f98fe0b56ba4ce12e35cf15cc77ac54 | MATLAB | 904 | 31 | 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 input AND in output
%
% See also XMLTREE
uid = uid(:);
for i=1:length(uid... |
be23798d0ff03aecfc5dc8da16fa761cf00daf945ed180422fabd8c61d2f8d23 | MATLAB | 904 | 39 | function y = avg_abs_dev_med( x, dim )
%AVG_ABS_DEV_MED Internal cvx version.
if ~cvx_isaffine( x ),
error( 'Disciplined convex programming error:\n ABS_AVG_DEV_MED is convex and nonmonotonic in X, so X must be affine.', 1 ); %#ok
end
try
if nargin < 2, dim = []; end
[ x, sx, sy, zx, zy, nx, nv, perm ] =... |
bf11031618c7bfafd81761a4b7361a91e9b4bc3b160901da32bfe45a90cfc4bf | MATLAB | 904 | 41 | function [r mu] = circ_axialmean(alphas, m, dim)
%
% mu = circ_axialmean(alpha, w)
% Computes the mean direction for circular data with axial
% correction.
%
% Input:
% alpha sample of angles in radians
% [m axial correction (2,3,4,...)]
% [dim statistic computed along this dimension, 1]
%
% ... |
f175b2bbaeda5d13154be407ffd3b0e6d05373c3e2a3829019032d574297c38e | MATLAB | 904 | 27 | % Example of why B_other in eqcont segregation is not the same in across
% system types when there are only two system types
% create random 6x6 matrix
B = toeplitz(randi([0 9],6,1));
% assumeing 3 systems, 1:2, 3, 4:6
% assuming 2 systype, 1:3, 4:6
% between system wither others for system type 1
sys_type1_b_othe... |
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