sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f525b4c1478656e79be301bab79869d66d1dccbfb5cb707ce1ad841e85bc324f | MATLAB | 486 | 21 | function t = CBIG_ttest_paired_stat_only(x)
% Calculate one sample t test value.
%
% t = CBIG_ttest_paired_stat_only(x)
% Input:
% x: N x M matrix, N is number of samples, M is number of trails.
% Output:
% t: 1 x M vector, M is number of trails
%
% Written by CBIG under MIT license: https:... |
3f4c14bc8b5ef8f84d6d2ee79fc301a66ed0e91ed25425a3399b0b36ccea892c | MATLAB | 487 | 21 | %%
% Draws numSamples random directions on a spherical shell.
%
function [theta, phi] = randOnSphere(numSamples)
if ndims(numSamples) == 1
theta = rand(1, numSamples);
phi = rand(1, numSamples);
elseif size(numSamples,1) == 2
theta = numSamples(1, :);
phi = numSample... |
53cd3b7bd19d1cfd6ece10f7c41ae7118044bd9094c1a0b14b7672870d2bc71a | MATLAB | 491 | 17 | %% function to get # of events and ROS relationship
function [MedianROS, counts,edges] = GetROS_NEvent(Nevent,RateOverlapScore, step)
edges = 0:step:ceil(max(Nevent)+4);
Nbins = length(edges);
BinnedN = discretize(Nevent, edges);
MedianROS = zeros(Nbins,1);
counts = zeros(Nbins,1... |
fef0a8d36d539a85dc3e8abe29ab3eaf2e7dde7ff675129c4edba5ab042c0cc1 | MATLAB | 492 | 13 | function [h_colormap,dab_colormap] = create_hdab_colormaps()
%% Create H DAB colormaps for easier visualisation
% @author: pdzialecka
%%
dab_col = (1-[0.26814753,0.57031375,0.77642715]);
h_col = (1-[0.6500286,0.704031,0.2860126]);
dab_colormap = [(linspace(dab_col(1),1,256)'),(linspace... |
0080c9a893a2e126e35ada140c7ed25f7ae28160a86e7caab179a1c63644a0dd | MATLAB | 495 | 13 | %clear all;close all;clc;
addpath(genpath('/home/ajoshi/projects/bfp/src'))
fmribase = '/home/ajoshi/tmp_study_dir/sub08001/func/sub08001_rest_bold';
anatbase = '/home/ajoshi/tmp_study_dir/sub08001/anat/sub08001_T1w';
config.FSLPATH = '/home/ajoshi/webware/fsl'
config.FSLOUTPUTTYPE='NIFTI_GZ';
config.AFNIPATH = '/home/... |
a47fbcc40729f4a462a637cc8af5e1d851134440e7fd0d41632633bbc35a620c | MATLAB | 495 | 20 | function [gmm_idx] = gmm_eval(x, idx, sigma)
% Evaluate gaussian mixture model on points X.
% idx contains the previous clustering results
% sigma is a fixed covariance for the gaussian mixture.
dim = size(x,2);
% calculate mean of each cluster
mu = zeros(max(idx), size(x,2));
for i=1:max(idx)
clc mu(i,... |
71ee32231836ba44fea26edd4333a9dc1596e3c07e056d50d7a400c575bfbd39 | MATLAB | 497 | 20 | function [target] = setstruct(target, value, fieldPattern)
% SETSTRUCT Sets specified fields in the target struct to the given
% value.
if nargin < 3
fieldPattern = '.*';
end
for field = rowvec(fieldnames(target))
for iPattern = 1:numobj(fieldPattern)
matches = reg... |
909e14a677c59a51fb60561abb57a465dd93ac55499502baa9030ef91ac79f94 | MATLAB | 497 | 8 | function [dapi_colormap,BrdU_colormap,DCX_colormap,NeuN_colormap] = create_IF_colormaps()
%% Create IF colormaps for easier visualisation
%
BrdU_colormap = [(linspace(0, 255, 256))'/256, linspace(0, 255, 256)'/256, zeros(256, 1)];
dapi_colormap = [zeros(256, 1), zeros(256, 1), (linspace(0, 255, 256... |
e39edf1dab4a7073a6d4996b795e47ee36705fe0b91f0e11919f24fe164448a8 | MATLAB | 497 | 28 | function plotSpectrogram(spec,freqAxis,timeAxis,smoothSpan,interpFactor,cLabel)
%
% Smooth
C = smoothSignal(spec,smoothSpan);
% Interpolate
C = interp2(C,interpFactor);
% Plot
imagesc(timeAxis,freqAxis,C);
axis('xy');
%% Formatting
cbar = colorbar;
colormap(jet(512));
%caxis(specLimits);
xlim(timeAxis([1,end]));
yl... |
2841de8d11d6dc0f9970072c9e4c17edcede9ae8833c41305a474e6c9b7c671e | MATLAB | 498 | 22 | %
%extracts events from a neuralynx events file.
%
%urut/may04
function events = getRawTTLs(filename)
FieldSelection(1) = 1;%timestamps
FieldSelection(2) = 0;
FieldSelection(3) = 1;%ttls
FieldSelection(4) = 0;
FieldSelection(5) = 0;
ExtractHeader = 1;
ExtractMode = 1;
%ModeArray(1)=fromInd;
%ModeArray(2)=toInd;
[time... |
37f04c1a9192ec32c48a784d5eea3bb69a2f64733427fec42bb5f5d111435079 | MATLAB | 501 | 14 | function out = ifft3(x)
% Function that computes the inverse 3D Fourier transform of the input array x,
% along the first three dimensions.
%
% Input parameters:
% --x: 4D array of size [N1, N2, N3, Nc], where N1, N2, N3 are spatial
% dimensions and Nc is the number of channels.
%
% Output parameters:
% ... |
3d682aaf19bcc543cf107be34617455f8c321f4ca6220c5ad07d045c2ab6626f | MATLAB | 501 | 23 | function [y]=nt_mat2trial(x,w)
%[y]=nt_trial2mat(x) - convert 3D matrix to trial cell array
%
% y: trial array (each trial is channels * samples)
%
% x: matrix (samples * channels * trials)
% w: weights (samples * 1 * trials)
%
% Weights, if provided, control the size of each trial.
if nargin<2; w=[]; end
[nsampl... |
e17c2b2ec94326ab98113b0012433c0b54ee3517a512bc65ddfbca71ca7b7516 | MATLAB | 504 | 17 | % Like diag(), except that slices (3rd and higher dimensions) are supported in that the diagonal
% elements are extracted independently per slice.
function D = diag3(A, k)
if nargin < 2 || isempty(k)
k = 0;
end
%% Get indices of diagonal elements
szA = size(A);
iDiag = diagIndex(A, k... |
27cd772b51502521bccbd40ae5874e7259459c7d8fcf8d44fc6b6e102949e5d7 | MATLAB | 505 | 22 | format longG
q = [ 9000000.0000 9100000.0000
15200000.0000 16200000.0000
17900000.0000 18400000.0000
22400000.0000 23800000.0000
59000000.0000 59500000.0000
22400000.0000 23800000.0000
62900000.0000 64600000.0000
71500000.0000 71700000.0000
67000000.0... |
aeb76ba8850e7089ba734c1181ec2bd1a7c56b4aa8c46dc594cb9b2c9b65cc50 | MATLAB | 505 | 13 | %% function to calculate vector remapping (Pearson's between tuning curves in A and B)
function VectorRemap = GetVectorRemap(HDir_Rate)
[Ncell,~,~] = size(HDir_Rate);
VectorRemap = zeros(Ncell,1);
for c = 1:Ncell
Curve1 = HDir_Rate(c,:,1);
Curve1(Curve1 == 0) = randn(length(find(Curve1 == 0)),1)./1e9; %... |
d830708f4818f04cade769616318cb6801dcbd325123c6a8ee91b2e166cd0a47 | MATLAB | 505 | 17 | %% AUM %%
%Shree Ganeshaya Namaha
%function gen_brainordinates(subname,studydir)
clear all;close all;clc;
restoredefaultpath;
addpath(genpath('/ImagePTE1/ajoshi/code_farm/bfp/dev/gifti-1.6'));
addpath(genpath('/ImagePTE1/ajoshi/code_farm/svreg/src'));
addpath(genpath('/ImagePTE1/ajoshi/code_farm/svreg/3rdParty'));
BS... |
2337d6934a50630dce47880c24f2cf0fbbe8a855eb0b942d54efd6e3af20d9a4 | MATLAB | 507 | 26 | function txt = coloredText(txt, color)
%%
if ischar(txt)
txt = coloredText({txt}, color);
txt = txt{1};
return
end
%%
if isinteger(color)
color = double(color) / 255;
end
if size(color,1) == 1
rgb = color;
end
%%
for iTxt = 1:numel... |
ae96e27df7553cb4235a22186bd6c3d60400259d4654181dd762ff0bda702608 | MATLAB | 510 | 21 | % Compute the geometric average of X along dimension dim (default 1)
function gm = geometricMean(X, dim, omitNaN)
%% Default arguments
if nargin < 2 || isempty(dim)
dim = 1;
end
if nargin < 3 || isempty(omitNaN)
omitNaN = false;
end
%% Use log transform to avoid numerical under/ov... |
0a15cb5d5750ae797d384b1b843bd49588405d4f834ee70b7a7c55cfd9d888b0 | MATLAB | 512 | 13 | %% function to get angular difference between two contexts for a subset of cells
function [AngDiff,IsOrthogonal] = GetAngularDifference(HD_list, HD_table)
AngDiff = zeros(length(HD_list),1);
IsOrthogonal = zeros(length(HD_list),1);
for i = 1:length(HD_list)
idx = find(HD_table.cellID == HD_li... |
ef83860177e930c5eb1a87aa20face305ab4894123d82af8bcd0e9e18fc4d2e6 | MATLAB | 512 | 15 | % Pregenerate filter weights
function kernel = gaussianKernel2D(kernelWidth, nSigmas)
if nargin < 2
nSigmas = 4;
end
filterSize = 2 * ceil(nSigmas * kernelWidth) + 1;
x = linspace(-nSigmas * kernelWidth, nSigmas * kernelWidth, filterSize);
[x1,x2] = meshgrid... |
0cb68b8af84a85de3c761f91f76b03814c19934c71c5cf65ed7737fd96b6ac92 | MATLAB | 513 | 18 | %%
% Bin centers for a uniform division of the range xMin to xMax into nBins
function centers = uniformBinsAround(xMin, xMax, xMiddle, dx)
if nargin < 4
dx = xMiddle;
xMiddle = xMax;
nBins = xMin;
half = floor( nBins/2 );
centers = linspace(xMiddle - half*dx, xMiddl... |
c70cf0bfbb0fd03993ef35ea3fe8cb9cf33d2ddcec26f9913b37729a080cc85c | MATLAB | 515 | 21 | function [deltas] = delta_mod(data)
%% Calculates the difference (delta) between two points
%
% **Usage:** [deltas] = delta_mod(data)
%
% Input(s):
% - data : Input data vector (BS data)
% Output(s):
% - deltas : Differences between samples from input data
%
% Author: R.M.D. Kock, Leiden University
%%
... |
00e3b49a2b2372010430d2338dff43788c348cb3cb4f3ad460f5fed8a87bf7b2 | MATLAB | 516 | 25 | %#function gcp
function tNLMPDFGOrdfMRI(GOrdInFile,GOrdOutFile,fpr,memory,MultiThreading, scbPath)
load(GOrdInFile);
option = tNLMGPDF();
option.FPR = str2double(fpr);
if ~strcmpi(memory,'auto')
memory=str2double(memory);
end
if ischar(MultiThreading)
MultiThreading = str2double(MultiThreading);
end
if Mul... |
66298e713149a05de483ab80f7434547702f1aefd4ce892b393c479567f3c8f6 | MATLAB | 517 | 15 | function coef_vals = SolveMP_wrapper(dictionary_n, x_im, opts)
% coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
%
% Wrapper for Matching Pursuit
%
% Last Modified 6/10/2010 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Run l1ls on the desired parameters
coef_vals... |
e444323595c93c1d7ffc4ea5465d5bb6471576f86ed6215cb37deec538349e35 | MATLAB | 518 | 18 | % Returns the 2D rotation matrix to rotate points counterclockwise by an angle theta (in radians)
function M = rotationMatrix2D(theta)
if isrow(theta)
theta = theta(:);
end
cosTheta = cos(theta);
sinTheta = sin(theta);
M = nan([2,2,size(theta)]);
for iSl... |
f7e10985142388b9e71bcc689f337f23d9fd14818170b9b416b4fc903f970352 | MATLAB | 519 | 18 | function MAP = getColormap()
% returns our standard Tuebingen Colormap
%function getColormap()
%midBlue = [0 105 170]./255;
midBlue = [165 30 55]./255;
%lightBlue = [80 170 200]./255;
%lightBlue = [125 165 75]./255;
lightBlue = [210 150 0]./255;
steps = linspace(0,1,100)';
%MAP = bsxfun(@times,s... |
71850b39dbd0fceafd78cb5e4fe83fb4fdc2d35ee0f8023cf6b0c24ba255e956 | MATLAB | 520 | 20 | %% wrap mismatch
function [FiringPref, RZ_ID, MeanRate] = WrapMisMatch(workdir)
FiringPref = [];
RZ_ID = [];
MeanRate = [];
for f = 1:length(workdir)
load(strcat(workdir(f),"\processedData\MisMatchTbl.mat"));
rfield_idx = find(Mismatch_tbl.IsActive == 1 & Mismatch_tbl.RewZone > 0);
RZ_ID = [R... |
bc2d43ec58378089a31bcacc59a37d25d02e01261025f896399c0df8ae5adec0 | MATLAB | 520 | 18 | %% function to bin distance from reward and calculate mean and std of ros in each bin
function [ROS_dist, counts, edges] = GetROS_Dist(RewDist, RateOverlapScore)
edges = 0:2.50000001:ceil(max(RewDist))+2.50000001;
Nbins = length(edges);
BinnedDist = discretize(RewDist, edges);
ROS_dist = zeros(Nbins,3);
count... |
de094e6ccd6efe5f960a4f4cd517ad3177a87fd939e4a05e74293f72fd09d5f5 | MATLAB | 520 | 22 | %
%extracts events from a neuralynx events file.
%
%urut/may04
function events = getRawTTLs(filename)
FieldSelection(1) = 1;%timestamps
FieldSelection(2) = 0;
FieldSelection(3) = 1;%ttls
FieldSelection(4) = 0;
FieldSelection(5) = 0;
ExtractHeader = 1;
ExtractMode = 1;
%ModeArray(1)=fromInd;
%ModeArray(2)... |
f496b638f7ca629014e414bb5c753d459e2e898bc417833d0c14918db9fada48 | MATLAB | 522 | 23 | function [y] = at(x, i, noCellStr)
% AT Smart(er) array addressing.
%
% Strings are treated as singletones unless the provided index i is a
% non-singleton vector, or not 1.
%
% Otherwise returns x{i} for cell arrays and x(i) for other types of arrays.
if nargin < 3
noCellStr = false;
end
... |
69dfb96cb143e016fd0bc9ccbd3f5001d10581da6a1db9c42a18b741c94745f1 | MATLAB | 523 | 26 | function frequencyValue = Frequency(OriginalSignal,EventMatrix)
% USAGE
%
% frequencyValue = Frequency(denoisedMatrix,event)
%
% Calculate the frequency of the events in a signal.
%
%
% OriginalSignal Original signal (matrix)
% EventMatrix Contains all the detected events (matrix)
%
... |
b70b7360e4064d6c2e94f0a97fded706455e513d03160b8a71d56027e5206753 | MATLAB | 524 | 23 | function nt_plot_mmx(a,b,c)
%nt_plot_mmx - plot data using min-max pairs
%
% nt_plot_mmx(x): plot x
% nt_plot_mmx(abscissa,x): plot x using abscissa
% nt_plot_mmx(abscissa,x,N): plot x using abscissa, with specified target number of min-max pairs [default: 1000]
error('not yet implemented');
if nargin < 3 || i... |
109b722160ca60ac73f92596037b2d471e3fa8bd70ee52511f3d694f9c4b467a | MATLAB | 525 | 26 | function C = nancorr( X,Y )
% NANCORR calculates the sample correlation coefficient
% for the series with NaNs expected.
% X is the one series, Y is another.
X=X(:);
Y=Y(:);
L1=length(X);
L2=length(Y);
if L1 ~= L2
error('The samples must be of the same length')
end
for i=1:L1,
if isnan(X(i... |
35bef08d72d6aeed79505bf74c77628382a9d26c6c9e0839fc4900bb7fd954c7 | MATLAB | 526 | 20 | classdef HoldoutParameters
properties
TrainRatio double % 0.0 ~ 1.0
NumSplits {mustBeInteger}
RngSeed = [];
end
methods
function obj = HoldoutParameters(trainRatio,numSplits,options)
arguments
trainRatio double
numSplits {mustBeInt... |
46e4d30aca60ff652948be77773ba55064a49f6d3ed328bd7deff16cbf466a94 | MATLAB | 526 | 20 | function outpict = rgb2hwb(inpict)
% RGB2HWB(INPICT)
% Convert an RGB image to HWB (Hue, Whiteness, Blackness)
% This is a variant of HSV proposed by Alvy Ray Smith (1996)
% http://alvyray.com/Papers/CG/HWB_JGTv208.pdf
%
% INPICT is an RGB image of any standard image class
%
% Return type is double... |
6a863978710d888f84e50baf3fafaa2226c7e326720e94a862c3774acce847b8 | MATLAB | 526 | 19 | function b = get_box_num
% Checks connected USB devices and returns the device number corresponding
% to the scanner button box (box_id should be set the the productID of
% the button box used locally).
% Written by KGS Lab
% Edited by AS 8/2014
% change to productID number of local button box
box_id = 8; b = 0; d = P... |
40e96a7fc190de0b5e406209d8462ecf73c17e71c331ade8f0edb464fd84f10d | MATLAB | 527 | 17 | %%
% Extrapolates the given array by the requested left/right number of
% items.
%
function [extended] = extend(array, left, right)
delta = array(2) - array(1);
moreLeft = uniformBinEdges(left -1, array(1)-left *delta, array(1) - delta);
moreRight = uniformBinEdges(right-1, array(end) +... |
e36eeb2fe59bb8575765c8c1979cdad2405e01ae526bc3ce144e3adef61ee7b5 | MATLAB | 527 | 21 | %%
% Bin centers for a uniform division of the range xMin to xMax into nBins
function [centers] = uniformBinCenters(nBins, xMin, xMax, logarithmic)
if nargin > 3 && logarithmic
xMin = log(xMin);
xMax = log(xMax);
dx = (xMax - xMin) / nBins;
centers = exp( (xMin + dx/2):dx:(xMax -... |
409ef033a22b8a6cb2265413a8119c6e26e063f6fff9651fe9d0360243ce4d21 | MATLAB | 528 | 18 | %% Concatenate results of arrayfun() along the specified dimension.
function varargout = accumfun(dim, func, varargin)
if ~isnumeric(dim)
error('accmufun:input', 'dim must be a number.');
end
if iscell(varargin{1})
fcn = @cellfun;
else
fcn = @arrayfun;
end
... |
5f59f0e9a33db813c60dcf4659f4ac37e99c449ddf984a1d888f7a8c64ef64bc | MATLAB | 528 | 19 | %% function to get mismatch matrices
function rate_ordered = GetMisMatchMatrix(rate,id,pref)
% split fields into ctx A and B RZ fields
idx = cell(2,1);
pref_split = cell(2,1);
rate_split = cell(2,1);
rate_ordered = cell(2,1);
for i = 1:2
idx{i} =find(id == i);
pref_split{i} = pref(idx{i});
rate_... |
b5d6fd4c8c76342b89d2d02065c3b0d235b33f194e8eb136809f01e42c07996e | MATLAB | 528 | 18 | function permut = CBIG_permutation_given_inversion(inv_vec)
% Given the inversion of a permutation (4 3 2 1 5), get the permutation.
%
% permut = CBIG_permutation_given_inversion(inv_vec)
% Input:
% inv_vec : inversion vector e.g. 4 3 2 1 5
% Output:
% permut : permutation e.g. 5 4 3 2 1
%
% Written... |
e0a4c294f5079cfbfe24b0c35cfded22d8adffa375785e3c0141165aa5d65e47 | MATLAB | 528 | 19 | %% Returns a vector of length n with all zero entries except at position k, which has value 1
% one = 1 by default, and can be used to override the value of the hot bit.
% dim = 1 by default, and specifies the dimension along which the vector has length n.
function v = onehot(k, n, one, dim)
v = zeros(n... |
e6f2fc5041bf854aaa40a946f72eff32bfe0e4f1aeaad88d1da270146c4309a7 | MATLAB | 528 | 20 | function next = set_image_index(input)
indices = containers.Map('KeyType', 'uint32', 'ValueType', 'uint32');
function index = produce_index(series)
if indices.isKey(series)
index = indices(series) + 1;
else
index = 1;
end
indices(ser... |
fb7a85c5da867a1ec8e0868dd232ee36f3512132e2bb83a141939b534367e654 | MATLAB | 528 | 16 | function [spikePhase] = getPhaseLocking(signalFilt, spikeIndx)
%% By Joachim
% Calculates spike-LFP phaselocking
% dependencies
% HilbertTransf (Located in Preproccessing)
% Inputs:
% signalFilt: Filtered signal
% spike_indx: spikeTimes as index for when they occurred during
% signal
% Output:
% ... |
990568b37e0731cf945492ceaafdc69f70a2c19abea4ec98440ebf4dfc7c9e75 | MATLAB | 529 | 15 | function coef_vals = perform_omp_wrapper(dictionary_n, x_im, opts)
% coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
%
% Wrapper for Orthogonal Matching Pursuit
%
% Last Modified 6/10/2010 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Run l1ls on the desired parame... |
fd81ac3aa34b9ae517141a6f9f4ce0320eac412fe483d95b59d01529ef979034 | MATLAB | 530 | 17 | %%
% Creates an array of bin centers, uniformly spread and covering [xMin,
% xMax) with the given pitch dx. Note that xMax is the upper bound and
% therefore not included in the range.
function [centers] = bestBinEdges(xMin, xMax, dx)
% First determine the segmentation
xRange = xMax - xMin;
numB... |
b8bc8c1c4902d3a278469ab18d0203a90f225945299b2ec3e8bc8a322133a391 | MATLAB | 535 | 14 | function next = create_ismrmrd_image(input, header)
function image = create_image(image)
image = gadgetron.types.Image.from_data(image.data, image.reference);
image.header.image_type = gadgetron.types.Image.MAGNITUDE;
image.header.field_of_view = [ ...
header.encoding.re... |
cc3fc16039a6fdcf256ba37c6a9f5befa8a6aef393f6a2f952acc6b9c63ed558 | MATLAB | 536 | 22 | function cov_xy = CBIG_cov_matrix(x,y)
% function cov_xy = CBIG_cov_matrix(x,y)
%
% Calculates the covariance matrix given two matrices x and y.
%
% Inputs:
% - x
% N*K1 matrix, N is # observation, K1 is # variables
%
% - y
% N*K2 matrix, N is # observation, K2 is # variables
%
% Outputs:
% - cov_xy:
% K1*K2 ... |
e7093f88439220975cd444d58d84dcbbd27665d0e7f5054542ad1aaaac2a6aaf | MATLAB | 537 | 36 | function y = filter_iir(x,a,b,N)
size_x = size(x,1);
y = x;
w_a = 0;
w_b = 0;
N = N;
for i = 1:N
for j = 1: i
w_a = b(j) * x(i-(j-1)) + w_a;
end
if(i == 1)
w_b = 0;
else
for j = 2: i
w_b = a(j) * y(i-(j-1)) + w_b;
end
end
y(i) = w_a - w_b;
w_b = 0;
w_a = 0;
en... |
26ffa92cefefd452721f52716a02cbc236bc1e1c7fbc7484df0d4066737694cf | MATLAB | 538 | 23 | function x=nt_fixsign(x)
%y=nt_fixsign(x) - flip signs to maximize inter-component correlation
if ndims(x)<3;
y=nt_pca(x);
y=y(:,1)'*x; % correlation with PC
x=x*sign(diag(y));
else
[m,n,o]=size(x);
if 0
% can't remember the logic of this...
for k=1:n
x(:,k,:)=reshape(nt... |
5e9b267b1c2bdcec42843f55c940c1f41b2bc3dce7869509a9727caa0ed7ce1d | MATLAB | 538 | 15 | function coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
% coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
%
% Wrapper for the l1ls minimization function
%
% Last Modified 6/10/2010 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Run l1ls on the desired parameters... |
632117998b39241fa9f1f4d94e1cf5926cf0d52ef90b38dbdc1fbb7650707b71 | MATLAB | 538 | 22 | function result = correlateImages(images)
% input: images should be a cell array, each cell contains an N-dimensional
% image
numImages = length(images);
for i=1:numImages
% if there are more than 2 dimensions for this image, average along the
% other dimensions until you get a 2d image
while (length(size(... |
7a62b360626ecf37035c4b93194a6522d71be785a07f5b0a26815f99c281a538 | MATLAB | 538 | 22 | function z = jointEntropy(x, y)
% Compute joint entropy z=H(x,y) of two discrete variables x and y.
% Input:
% x, y: two integer vector of the same length
% Output:
% z: joint entroy z=H(x,y)
% Written by Mo Chen (sth4nth@gmail.com).
assert(numel(x) == numel(y));
n = numel(x);
x = reshape(x,1,n);
y = reshape(y... |
4f18a2b4102879efba4cb392fda0a5ce181f5892cdac9bf06dd48d3e212d512c | MATLAB | 539 | 21 | %% function subsample population and recalculate 1) difference between median and 25th pctile of two pops 2) ranksum
function [DistDifference, p_val] = SubSamplePopulation(popToSubSamp, popToMatch, repeat)
DistDifference = zeros(repeat,2);
p_val = zeros(repeat,1);
NsubSize = length(popToMatch);
for r = 1:rep... |
773940375f10bf3692e83ca8f4cb6b1b573529f626b98ed8015ccb3eca5c389f | MATLAB | 539 | 12 | %Run the Spike batch and save the result.
%clear
%Select the analysis main function
mfile='W:\Analysis\MEA\MEA_Toolbox\Batch_SpikeDetection.m';
%Select the batch file
bfile='W:\Analysis\MEA\2022-11-22\IIA_spikes_detection\Slice2\IIABatch16h59.bat';
%Run the analysis for all the lines in the batch file
batch = StartBat... |
b3f1187ba20010c4488b94c7c457c710a36a3c7d8979d3aaed88c0d95f3c553d | MATLAB | 539 | 21 | function cell_nums = nums_from_ids(datarun, cell_ids)
% convert cell ids to row vector of cell numbers
%
% 2010-01 phli
%
cell_nums = zeros(1,length(cell_ids));
for cc = 1:length(cell_ids)
% look for the specified cell id in the list of cell ids
temp = find(datarun.cell_ids == cell_ids(cc));
if ~isempty... |
8532d74b1acb5cd9306e5cc0cd0ed03356726937f37622bf4cc754530e9a0b4f | MATLAB | 540 | 17 | %%
% Creates an array of bin centers, uniformly spread and covering [xMin,
% xMax) with the given pitch dx. Note that xMax is the upper bound and
% therefore not included in the range.
function [centers] = bestBins(xMin, xMax, dx)
% First determine the segmentation
xRange = xMax - xMin;
numBins ... |
ad54e89b3caa2e0afe87d717cc14d4b56c8f6f68e835135132e9ed7244cfa419 | MATLAB | 540 | 16 | function [peaks, isPeak] = localPeaks(data, minHeight)
dRight = [data(2:end,:) - data(1:end-1,:); zeros(1,size(data,2))];
dLeft = [zeros(1,size(data,2)); -dRight(1:end-1,:)];
isPeak = ( data >= minHeight ) & ( min(dRight,dLeft) < 0 ) & ( max(dRight,dLeft) <= 0 );
% ... |
ae8d59b0eb38948cc1d1dab8b575f409d19e626cfef6fb295d26e2fe609f37b6 | MATLAB | 543 | 21 | function setaddaxisdata(axishandle,data,flag);
% setaddaxisdata(axishandle,data,flag)
%
% internal function for addaxis to update the added axes handles and plot
% handles, or to save the original figure position.
if nargin<3, flag = 'axisdata'; end;
aad = getappdata(axishandle,'addaxis_data');
... |
ddd2c1ccfb68ff8d3b371668b14d5ebabde34b84810c9767db6bd3016b5e57cc | MATLAB | 543 | 25 | classdef Waveform
properties
header
data
end
methods
function self = Waveform(header, data)
self.header = header;
self.data = data;
end
function tf = isequal(self, other)
tf = ...
isequal(self.head... |
23cfff6b4edf3c13335fb7e4a6124b435b543223f2c5b12a19de12f135e36b38 | MATLAB | 547 | 23 | %%
% Bin edges for a uniform division of the range xMin to xMax into nBins
function [edges] = uniformBinEdges(nBins, xMin, xMax, integral, logarithmic)
if nBins < 1
edges = [];
elseif nargin > 4 && logarithmic
xMin = log(xMin);
xMax = log(xMax);
dx = (xMax - xMin) / nB... |
65bf6b44afcd4d17af673f4af89e9010089f572378bfa9074b5e9454ed443835 | MATLAB | 547 | 24 | function CBIG_cell2text(cell_var, filename)
% CBIG_cell2text(cell_var, filename)
%
% This function writes a cell array (cell_var) into a text file "filename".
%
% Inputs:
% - cell_var
% The cell array that the user wants to write out.
%
% - filename
% Full path of the output text file.
%
% Written by C... |
9e250da71b22d2d40d19c3b7fd8e1e429bd68615e853f5eb6a905a1c377be456 | MATLAB | 547 | 13 | function sens = ESPIRiT_calc_sens(dat, dimRef)
% FORMAT sens = ESPIRiT_calc_sens(dat, dimref)
% dat - k-space [ro p1 p2 cl]
% dimRef - either a vector with reference vol dimentions (epi) or a structure of PPIparams (MPM) - parameters describing the acceleration
global N_order
if isstruct(dimRef)
% PPIparams ... |
6b172e966429fea28a48302efd272005d13a016778ff382e2dce43cd2d855656 | MATLAB | 548 | 23 | classdef ReconstructionParameters
properties
DimPI (1,1) {mustBeInteger}
ThreshWidth (1,1) double
end
methods
function obj = ReconstructionParameters(dimPI,threshWidth)
obj.DimPI = dimPI;
if mod(1/threshWidth,1) == 0
obj.ThreshWidth = threshWi... |
4d6f9d318f05b3cdce4f9eee84cff745290a6db90e0913dbe7bfe1c8b5e77931 | MATLAB | 549 | 16 | %% save() functionality for parallel computing. N.B. All arguments must be Matlab variables, e.g. an array element x(i) will break this code!
function parsave(filename, varargin)
options = {};
what = struct();
for iArg = 1:numel(varargin)
if ischar(varargin{iArg}) && ~isempty... |
e16700594f0bed33fc02d9eeb6eb04475138915ce38d30e2e2e153a1fb8dabea | MATLAB | 551 | 24 | function h=nt_banner(text)
%h=nt_banner(text) - annotate with text at head of figure
%
% h: handle to annotation
%
% text: string to print
%
% default horizontal position is 'center'
%
% NoiseTools
c=get(gcf,'children');
% find the top of uppermost subplot
y=0;
for k=1:numel(c)
pos=get(c(k),'position');
... |
e77d25ab639fe81f9e0c729f11705a9b2572521d24425546a711cfe0632d6f80 | MATLAB | 551 | 15 | clear all;close all;clc;
restoredefaultpath;
addpath(genpath('/home/ajoshi/Projects/bfp/src'));
bfpdir='/home/ajoshi/Projects/bfp';
%fmridatfile='/home/ajoshi/coding_ground/fMRIReg/src/task_diff_dyn.mat';
fmridatfile='/home/ajoshi/Downloads/for_parsa/bfpoutput/sub1/func/sub1_task-restingstate_bold.32k.GOrd.mat';
%'/d... |
ffab9a54807fd2322984dd05db2ca0907c960f8ca8e4a43c906169f40880fd2e | MATLAB | 551 | 16 | %
addpath /Users/stephen.whitmarsh/WhitmarshEpilepsy/
addpath /Users/stephen.whitmarsh/fieldtrip/
ft_defaults
patient_directory = '/Users/stephen.whitmarsh';
patient_directory = '/Volumes/epimicro/Donnees-analyses/Stephen/pat_02230_0674/eeg';
directory_searchstring = '02230_2015-02-25_*';
directory_sear... |
b1293f5490e87bb9694c85d47f2723c13e0686e9857c6c69719ccf65ddfd4ff7 | MATLAB | 553 | 20 | function lab = lch2lab(lch)
% LAB = LCH2LAB(LCH)
% Perform a simple polar-rectangular conversion on color data.
%
% LCH is a 3-channel image formatted with its lightness component first
% and with its hue channel in degrees.
%
% Output LAB is of the same scale as LCH. The output does not have to
% be CIELAB... |
062136ad5dbb2eb011877c45f15af4d8fd78631c14132a14dc22143fe00808d6 | MATLAB | 554 | 21 | %% Output the arithmetic mean of all arguments: (x_1 + x_2 + ... + x_n ) / n
% Test:
% data = {randn(5,3), randn(5,3), randn(5,3)};
% accummean(data{:}) - mean(cat(3,data{:}),3)
function mu = accummean(varargin)
%% Special case for no inputs
if isempty(varargin)
mu = 0;
return
end
... |
803d566fb02d35b52183b9ef0383f4c06f2e0f4906e44d3a337bf5b9a05486b7 | MATLAB | 554 | 15 | function coef_vals = SolveOOMP_wrapper(dictionary_n, x_im, opts)
% coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
%
% Wrapper for Optimized Orthogonal Matching Pursuit
%
% Last Modified 6/10/2010 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Run l1ls on the desire... |
ca54d35ec0f267bb0ee59c5b8f4b0fc183acfe53e6fa98845183284e4df96780 | MATLAB | 558 | 21 | function x = CBIG_StableAtanh(x)
% Stable version of atanh. It constrains the input within [-1 1] and output within [atanh(-1+eps) atanh(1-eps)].
%
% x = CBIG_StableAtanh(x)
% Input:
% x: a matrix
% Output:
% x: a matrix
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab... |
237bbb006ac4e79cdfe064535cfbdce25ce3b0f085366a07f72e8976f97e471d | MATLAB | 559 | 20 | % PAIRWISECORR Fast calculation of Pearson's correlation coefficient for each pair of columns in X and Y
function [corrCoeff, stdX, stdY] = pairwiseCorr(X, Y, omitNaN)
if nargin < 3 || isempty(omitNaN)
omitNaN = false;
end
%% Convert to unit vectors in data space
[X, stdX] = unitSpreadDirec... |
31fc05412387cdb2cc53497c6166a48f0be2775f6130c4d87147dca836c587d7 | MATLAB | 559 | 17 | function corr_mat = CBIG_self_corr(s_series)
% Calculate self correlation within a matrix.
%
% corr_mat = CBIG_self_corr(s_series)
% Inputs:
% s_series: T x N matrix, T is number of frames, N is number of voxels
% Outputs:
% corr_mat: N x N matrix, N is number of voxels
%
% Written by CBIG... |
5f76dcec2c5e68fa74daa0e85bb28715b3e349e523fc093cc272d834859330d5 | MATLAB | 559 | 15 | function ticks = niceTicks(range, numDivisions)
%%
stdRes = [0.01 0.1 0.5 1 2 5 10 50 100 500 1e4 1e5 1e6 1e8 1e10];
range = extrema(range(:));
resolution = abs(range(2) - range(1));
resolution = stdRes( binarySearch(stdRes, resolution/numDivisions, 0, 2) );
%%
range = [flo... |
3ac462c82b43f295fcf0b50163e9ab7974fd1bc8db9a69095cea6805cd3df2be | MATLAB | 560 | 15 | function coef_vals = cg_l2l1_wrapper(dictionary_n, x_im, opts)
% coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
%
% Wrapper for the l2l1 conjugate gradient minimization function
%
% Last Modified 6/10/2010 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Run l1ls on ... |
e1935a1e10226d6a3a4bf75b28551f5e1ffee383d32d1d83ae94abe755b29b8f | MATLAB | 561 | 15 | function coef_vals = groupLCA_wrapper(dictionary_n, x_im, opts)
% coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
%
% Wrapper for the block l1 minimization function
%
% Last Modified 1/28/2015 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Run l1ls on the desired pa... |
c380be0287f536d8ff514b87a93f0ce4f8fe328d470200dcefa2749261c034cb | MATLAB | 562 | 20 | function result = erws2(ampa_current, gaba_current, params, v_0, rec_step)
if nargin < 4
v_0 = 0;
end
if nargin < 5
rec_step = 2.0;
end
tau_AMPA = params(1) * power(v_0, -params(2)) + params(3);
tau_GABA = params(4) * power(v_0, -params(5)) + params(6);
alpha = params(7) * p... |
c4ffae8a0f5a1fe8300052fb70bc78b9e1d1d98a4085b4da84941f4437197cd4 | MATLAB | 562 | 12 | function buffer_recon(connection) % 'Buffer' is a colloquial name for Recon Data.
next = gadgetron.examples.steps.create_slice_from_recon_data(@connection.next);
next = gadgetron.examples.steps.basic_reconstruction(next);
next = gadgetron.examples.steps.combine_channels(next);
next = gadgetron... |
8d112d758929edf1eabd89a252314a675f8c24049851d54015a8565843927534 | MATLAB | 563 | 15 | function coef_vals = l1ls_nneg_wrapper(dictionary_n, x_im, opts)
% coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
%
% Wrapper for the l1ls non negative minimization function
%
% Last Modified 6/10/2010 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Run l1ls on the ... |
6d5c9c89af4bbd08266f5cbbad318e951bceb4152080772efd298612fbe94747 | MATLAB | 567 | 17 | %%
% Draws nPoints random points in a spherical shell with radius
% [rMin,rMax]. The return value is a 3 x nPoints matrix where the rows
% are x,y,z coordinates of the points respectively.
%
% Reference:
% http://www.mathworks.com/matlabcentral/answers/353-uniform-distribution-of-n-points-within-a-sph... |
08b18fb4c9aa5c73e86049ec166a644777e454d1891637bc1fcf627908ad2ce9 | MATLAB | 568 | 21 | function varargout = findOrZero(varargin)
varargout = cell(nargout, 1);
if nargout <= 1
varargout{1} = find(varargin{:});
elseif nargout == 2
[varargout{1}, varargout{2}] = find(varargin{:});
elseif nargout == 3
[varargout{1}, varargout{2}, varargout{3}] = find(varargin{:})... |
6075a6575bc755f1d9ebc120588330ed17f92eb235d0ff37c8a35e111f08cb25 | MATLAB | 568 | 30 | function v_ref = fMRI_findRefv(v,k,verbose)
% v = nifti file
% k = searches only multiple of k timepoints
% verbose: 1 or 0
% author: soyoung choi USC
if isstruct(v)
vls = v;
else isa(v,'char');
if exist(v,'file')
vls = load_untouch_nii_gz(v);
end
end
n= floor(size(vls.img,4)/k);
smeasure = zeros... |
c502f6a23b63997d7761db8819826d27d4d2cc488e266174db17cefad2e603bd | MATLAB | 568 | 15 | function out = ft3(x)
% Function that computes the 3D Fourier transform of the input array x,
% applying fftshift and ifftshift for proper centering.
%
% Input parameters:
% --x: 4D array of size [N1, N2, N3, Nc], where N1, N2, N3 are spatial
% dimensions and Nc is the number of channels.
%
% Output parame... |
c78bdcb60e2d1450b823d4c92c9d3c08a505ee2c9b696ec0393361ce4633ecd4 | MATLAB | 568 | 26 | %%
%
function [edges] = toBinEdges(centers)
if numel(centers) < 1
error('At least one bin center must be provided.');
end
% Guesstimate in case of triviality
if numel(centers) < 2
edges = centers + [-0.5 0.5];
return;
end
dx1 = centers(2) - centers(1);
dx2... |
d070b4dc7da209bc6f7180fe44ffeaee219c39d3b46efc0eac132be998ee7b0c | MATLAB | 571 | 15 | function coef_vals = greed_omp_qr_wrapper(dictionary_n, x_im, opts)
% coef_vals = l1ls_wrapper(dictionary_n, x_im, opts)
%
% Wrapper for the QR implementation of Orthogonal Matching Pursuit
%
% Last Modified 6/10/2010 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Run ... |
1d6aa8effca591521dff9f547adc84bc9477c74befe2918334b29d17270e66aa | MATLAB | 573 | 17 | %% Information entropy–based fitness function
function [ff] = infoEntropyCost(c, data)
X = data;
alpha = fix(c(1)); % Penalty factor (moderate bandwidth constraint)
K = fix(c(2)); % Number of modes (IMFs) for decomposition
%--------------- Perform VMD decomposition on the input signal --------------
[u, u... |
3e23b1d0f63659a93d8c823852ed4dbe092a347f9b8154fa271500ec7777d712 | MATLAB | 573 | 21 | function [S,C] = conncomp(G)
% CONNCOMP Drop in replacement for graphconncomp.m from the bioinformatics
% toobox. G is an n by n adjacency matrix, then this identifies the S
% connected components C. This is also an order of magnitude faster.
%
% [S,C] = conncomp(G)
%
% Inputs:
% G n by n adjacency m... |
88eaa3fde412f398c1f9e088e993dcc2f281bb218a79267b59aa8f5d474f1c94 | MATLAB | 574 | 13 | function yeahitis = isimageclass(inpict)
% ISIMAGECLASS(INPICT)
% Check if an array is of a standard image class.
% Returns true for the following datatypes:
% 'double','single','uint8','uint16','int16','logical'
%
% See also: ismono, issolidcolor, isopaque
% yes, ~isempty(find(strcmp())) is faster tha... |
7dddded1802b209c28a57043c0b6dbb120fcad1029c15b431c2144594cf88c97 | MATLAB | 575 | 15 | function [MuseStruct_updated] = updateBadMuseMarkers(cfg, MuseStruct_updated)
% don't write original muse markers to file
cfg.muse.write = false;
MuseStruct_new = readMuseMarkers(cfg, true);
for ipart = 1 : size(MuseStruct_new, 2)
for idir = 1 : size(MuseStruct_new{ipart}, 2)
try
Muse... |
56688452aa4cef0506e467298dd0f08cbbf00417445dc1d774d4c0e9ec3363ee | MATLAB | 576 | 18 | function PPC = computePPC(phases)
% by Mattia: computes PPC given a vector of phases. It is in vectorized
% form and therefore not easy to read. For an explanation of
% the computation steps, see Vinck et al (2010)
% INPUT
% phases : - vector of phases (in radians)
% OUTPUT
% PPC : -... |
00fffdd0d44c10d8993998aa9674746d4fc2ed9d330ebde56706af4910deec06 | MATLAB | 578 | 13 | %Run the IIA batch and save the result.
%clear
%Select the analysis main function
mfile='W:\Analysis\MEA\MEA_Toolbox\Batch_InterictalDetection.m';
%Select the batch file
bfile='W:\Analysis\MEA\2022-11-22\IIA_spikes_detection\Slice2\IIABatch16h59.bat';
%Run the analysis for all the lines in the batch file
batch = Star... |
63b1edd503f4c773b32cb3bf560869ca8b44f092d0f57ce33b70ed2bc66362f0 | MATLAB | 578 | 13 | %-----------------------------------------------------------------------
% Job saved on 16-Sep-2024 09:48:40 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
load('tmp_jobs/workspace_spatial_smoothing.... |
293f098d074cb5eecb36d157a2d8f7b6051cbb73f3ecfc83f697f7de8d3fc37f | MATLAB | 579 | 29 | function [B,A] = nt_filter_peak(Wo,Q)
%[B,A] = nt_filter_peak(Wo,Q) - second order resonator filter
%
% Wo: peak frequency (1 == nyquist)
% Q: quality factor
%
% NoiseTools
if nargin<2; error('!'); end
if Wo>1; error('normalized centre frequency should be < 1'); end
BW=Wo/Q;
% frequencies are normalized by pi.
BW = ... |
f7dfe30a940bda76d879ec21f817400b091948526514567b7007171355de1ba2 | MATLAB | 579 | 27 | function amplitude = MeanAmplitude(DetectedEventsMatrix)
% USAGE
%
% amplitude = MeanAmplitude(DetectedEventsMatrix)
%
% Calculate the mean amplitude of all the events which are in the input
% matrix
%
%
% DetectedEventsMatrix Matrix which contains all the detected
% ... |
781370114b8fd5b1b6ea1c5f679a35bf017612692e611bb834d366dae63c4e4f | MATLAB | 580 | 20 | function lch = lab2lch(lab)
% LCH = LAB2LCH(LAB)
% Perform a simple rectangular-polar conversion on color data.
%
% LAB is a 3-channel image formatted with its lightness component first
% and with its chrominance information centered around zero.
% This does not have to be CIELAB. It can be LUV or YPbPr, etc.... |
8df48501234c28f44310cbd4cf04b9f72f71ac327dbae484ef1e94e6afbad7e5 | MATLAB | 580 | 19 | classdef Nil
methods (Access=public)
function list = cons(nil, element)
list = gadgetron.lib.LinkedList(nil, element);
end
function nil = head(nil), end
function nil = nth(nil, ~), end
function nil = tail(nil), end
function nil = take(nil, ~), end... |
dd6d1ded5484e7b37550992bb9df34bd36534022c44f089410a2fdba44463c47 | MATLAB | 580 | 18 | function hAx = getOrCreateAxes(parentArg)
% getOrCreateAxes: Return axes handle based on provided Parent argument.
%
% Usage:
% hAx = getOrCreateAxes(opts.Parent);
%
% If parentArg is provided (non-empty), it is returned as hAx.
% If parentArg is empty, a new axes is created in the current figure.
% (Figure is NOT cr... |
6107f03a20c47ced9fe203f33afeaba17627b7ae39b02ab50b4089abcd93b702 | MATLAB | 582 | 23 | function div = CBIG_KLdiv_sym_pairwise(prob_mat)
% Calculate pairwise symmetric KL divergence for each row of input matrix.
%
% div = CBIG_KLdiv_sym_pairwise(prob_mat)
% Input:
% prob_mat: N x T matrix, N is # of variables, T is # of outcomes
% Output:
% div : N x N matrix, N is # of va... |
b10e465280c74ba4da10eea03ae76f1731f437ad44aca9b6de4fbe49d232949a | MATLAB | 582 | 20 | function k = get_keyboard_num
% Checks to make sure that the laptop keyboard is used in case another
% device connected at the scanner also has the usageName Keyboard
% (keyboardID should be set to the productID of the native keyboard).
% Written by KGS Lab
% Edited by AS 8/2014
% change to productID number of native ... |
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