sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
370ff055490fcd8644c2b618af2d3d6ee5cf03aa03b4e464eb3717410e4c94e8 | MATLAB | 369 | 16 | function combo_mat = all_combos(varargin)
num_vars = length(varargin);
tmp_str = '[';
for i = 1 : num_vars - 1
tmp_str = [tmp_str 'd_' num2str(i) ','];
end
tmp_str = [tmp_str 'd_' num2str(num_vars) ']'];
eval([tmp_str ' = ndgrid(varargin{:});']);
combo_mat = [];
for i = 1 : num_vars
eval(['combo_mat = [c... |
90800e506e3f3edc87cf38815414ede3f0697f8b0b7ba5454b0d5c42ac65c3aa | MATLAB | 370 | 17 | clear; close all; clc;
T = 200;
data1 = randn(600, T);
data2 = repmat(randn(1, T), 200, 1);
data = [data2; data1; data2];
data = data + 3 * randn(1000, T);
option = tNLMGPDF();
option.isPlot = false;
option.isVerbose = true;
option.memoryLimit = 'auto';
option.numCPU = 'auto';
option.SCBFile = fullfile(pwd, 'SCB.mat'... |
56c17e062f0737925720b5c20243d2efb97fe467210ac0ba70022df4d3803a27 | MATLAB | 371 | 11 | % Clean strings of non-printable characters or characters > 127
% characters > 127 get converted to utf-16 during fwrite, causing data positions
% to be shifted. This will prevent that.
% authored by David Shattuck
%
% simple test:
% x=char(rand(1,80)*255)
% fprintf(1,'%s\n%s\n',x,sanitize_ascii(x))
function str = s... |
7d003e7b37a907c2a408f480ace122e8372ffac12ec15fcfce1e3a79696e77c0 | MATLAB | 374 | 17 | %%
% Calls max() on multiple inputs, all of which are arrays.
%
function [x] = mmax(x, varargin)
% Locate arguments i.e. everything not the same size as x
function [yes] = testSize(y)
yes = ( size(y) == size(x) );
end
[arrays, arguments] = separate(@testSize, varargin{:});
for y = arrays
... |
c371e8cf7719a75799f3ad71d3f0be9247b65c1c6ec0b1bb2f443b5a02e9870d | MATLAB | 374 | 17 | %%
% Calls min() on multiple inputs, all of which are arrays.
%
function [x] = mmin(x, varargin)
% Locate arguments i.e. everything not the same size as x
function [yes] = testSize(y)
yes = ( size(y) == size(x) );
end
[arrays, arguments] = separate(@testSize, varargin{:});
for y = arrays
... |
ef9c17f2e9577411c6a6960e35e55008b4115ac4c58be0a99b455c53b906aec1 | MATLAB | 375 | 12 | function out = linear2rgb(inpict)
% OUTPICT=LINEAR2RGB(INPICT)
% Convert linear RGB to gamma-corrected sRGB
%
% INPICT is an RGB image of a floating point class.
% Output class is inherited from INPICT
%
% See also: lin2rgb, rgb2linear
mk = (inpict <= 0.0031306684425005883);
out = 12.92*inpict.*mk + (real(1... |
0d044c58f266647c87c964af6b9bc58ec83d3a6d2ee370b1aaad6e58bc657f20 | MATLAB | 377 | 19 | % Sets both the x- and y-axis labels for the given axes.
function xylabel(axs, xText, yText)
if nargin < 3 && ischar(axs)
yText = xText;
xText = axs;
axs = curraxes();
end
if isequal(axs, inf)
axs = allaxes();
end
for iAxs = 1:numel(axs)
xlabel(axs(iAxs),... |
61784909354d442c45ee2d5f4d77ab09e0e5b65fa3d198fa4469bca1f9d7005e | MATLAB | 378 | 17 | function w=nt_growmask(w,margin)
%ww=nt_growmask(w,margin) - widen mask
%
% ww: widened mask (samples * 1 or samples * 1 * trials)
%
% w: mask
% margin: samples, number of samples by which to widen the mask
%
% NoiseTools
[m,n,o]=size(w);
w=(w~=0);
w=nt_unfold(w);
w=filter(ones(margin+1,1),1,w)>0;
w=flipud(filter(o... |
3bb7bcb130425b960f79fa4371fd9c0071e7d86d6a3b65c4773e42406b243fbb | MATLAB | 379 | 22 | %% Close all figures and clear all variables/objects/MEX programs.
set(findall(0, 'Type', 'figure'), 'CloseRequestFcn', 'closereq');
nowait;
close all;
clear all;
drawnow
timers = timerfindall();
if ~isempty(timers)
timers = timers(isvalid(timers));
try
stop(timers);
delete(timers);
catc... |
0423fc16f5a157ec788dc248f6c2f40be1bdcdec57cc423531f3420726558c8f | MATLAB | 381 | 16 | function [biom_name] = find_biom_name(biom)
if strcmp(biom,'hoechst')
biom_name = 'Hoechst';
elseif strcmp(biom,'sox2')
biom_name = 'Sox2';
elseif strcmp(biom,'btub')
biom_name = '\beta-tubulin III';
elseif strcmp(biom,'gfap')
biom_name = 'GFAP';
elseif strcmp(biom,'map2')
biom_name = 'Map2';
elseif... |
20e2285b0cf090fd5d2af1bb3e5aed3c3a7fe4c3a9ca6243d9afd74f552cc868 | MATLAB | 382 | 19 | function get_key(key, laptop_key)
% Waits until user presses the key specified in first argument.
% Written by KGS Lab
% Edited by AS 8/2014
while 1
while 1
[key_is_down, ~, key_code] = KbCheck(laptop_key);
if key_is_down
break
end
end
pressed_key = KbName(key_code);
... |
917145063fd8bde123fe5bfd5e915404a104711ac92d42e4dcb8a7a3ff65e2bf | MATLAB | 383 | 13 | function next = create_slice_from_recon_data(input)
function slice = create_slice(recon_data)
slice.reference = structfun(@(arr) arr(:, 1)', recon_data.bits.buffer.headers, 'UniformOutput', false);
slice.data = permute( ...
recon_data.bits.buffer.data, ...
[4, 1, 2, 3] ...
... |
3bbe8b29766c1ad9baa522ff9c384e4e9ef9d61ba556dbf60b03b0ed98691e05 | MATLAB | 385 | 12 | function nf = framecount(inpict)
% NUMFRAMES = FRAMECOUNT(INPICT)
% Simple tool to get the number of frames from a 4D multiframe image.
% Assumes image dimensioning is [height width channels frames]
% The only reason this exists is to make the code descriptive.
%
% INPICT is an image array of any class
%
% ... |
7c36d7c0f851af7434a9c07ad7e4245cc67592082fb92ee4ecfbdc4833a22f87 | MATLAB | 386 | 20 | function [SpikeTrialsPSG] = rectifywindownr(cfg,SpikeTrialsPSG)
fprintf('sdf\n');
for ipart = 1 : size(SpikeTrialsPSG,2)
for itemp = 1 : size(SpikeTrialsPSG{1}.trial,2)
temptrials = unique(SpikeTrialsPSG{ipart}.trial{itemp});
for stage = 0 : 5
trialn... |
84dd4ab0669806d37a5cd12fc9573a679c15874e4cc76bc576057fda007df590 | MATLAB | 386 | 13 | function [] = dispAverageImages(images)
% input: images should be a cell array, each cell contains a 4-dimensional
% image
% displays a montage of channel 1, averaged across all images in the cell
% array
nDims= length(size(images{1}));
ImgAverage=mean(cat(nDims+1,images{:}),nDims+1);
figure
imagesc(stackToMontage(per... |
012bea12a8dab555df068e234adb213b6528e93e02cfcdaa609c4428e4d47168 | MATLAB | 387 | 17 | function verbPrint(verbLvl, verbCut, messOut)
% verbPrint(verbLvl, verbCut, messOut)
%
% Function to output messages at a given level of verbosity
%
% 2019 - Adam Charles
if verbLvl >= verbCut
fprintf('%s\n',messOut)
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%... |
e2aadd2b91ab3261726c2421c02d52ab5707f4de6e982a005650f24686015d9e | MATLAB | 387 | 13 | function [quantity, center, scale] = centerAndNormalizeRange(quantity, dim)
%% Default arguments
if nargin < 2 || isempty(dim)
dim = 1;
end
center = mean(quantity, dim, 'omitnan');
scale = 0.5 * (max(quantity,[],dim) - min(quantity,[],dim));
scale( scale == 0 ) = 1;
quantity = ... |
40466e97f3b0172dcc72eea06d2a78446f2c74fe50df799864ba72c683e3d6c5 | MATLAB | 388 | 13 | function [PPC]=getPPC(Spikephases)
% by Mattia
% input
% SpikePhases - vector of phases, with respect
% to the frequency band of interest
SpikephasesMatrix=repmat(Spikephases,length(Spikephases),1);
DotProd=cos(SpikephasesMatrix-SpikephasesMatrix');
DotProd(logical(eye(size(DotProd))))=0;
SumDotProd=sum(sum(DotProd))... |
dfaee162905d1d6a5e6e4881491226dabf4385737960700e766c10e7fbcec5cd | MATLAB | 390 | 14 | %% PARSEPATH Consistent file path/name+extension parsing across operating systems.
function [nameext, path] = stripPath(path)
tokens = regexp(path, '^(.*?)[/\\]*([^/\\]*)?$', 'tokens', 'once');
if iscell(path)
tokens = cat(1, tokens{:});
path = tokens(:,1);
nameext = tokens(:,2);
el... |
9b87d82012c74165a56520e41e9ef7136f246cc639dd64e0b5a4dad3004262cf | MATLAB | 392 | 11 | function Cor = getCor(result)
% calculates the correlation matrix accross parameters
%function Cor = getCor(result)
% it uses getCov to get the covariance matrix
% result should be a result struct which contains the full posterior
% Cor then is the correlation matrix
Cor = getCov(result);
std = sqrt(diag(Cor));
Cor =... |
c2eecd79143878efd5d3bbef6ed1c7ea089243b18a050563d95cce68c11ad49d | MATLAB | 392 | 10 | %% function to get GD occupancy in each context
function HDirOccupancy = HDir_Occupancy(framesToUse, binned_HDir, Nbins, framerate)
N_ctxt = length(framesToUse);
HDirOccupancy = zeros(Nbins,N_ctxt); % dimensions: angular bins, ctxts, rewards
for c = 1:N_ctxt
HDirOccupancy(:,c) = histcounts(binned_HDir(fram... |
22508506bc320abd1d772f772c8b3b6503b8914b249753dbe63f044a13cef0f5 | MATLAB | 394 | 24 | %
% numCores = findNumberOfCores()
%
% Description:
% find number of available cpu cores
%
% Input:
%
% Output:
% numCores - number of cpu cores
%
% Copyright:
% 2014-2018 (c) USC Biomedical Imaging Group (BigLab)
% Author:
% Jian (Andrew) Li
% Revision:
% 1.0.3
% Date:
% 2018/01/22
%
funct... |
c3ec9abc4508654dab2dc4a6d1dac87725994ab804c5f7782178d3cc62962624 | MATLAB | 399 | 18 | %%
function [varargout] = multiplex(subset, varargin)
if max(1,nargout) ~= nargin - 1
error('Number of outputs must be number of inputs minus one');
end
varargout = cell(size(varargin));
for iA = 1:numel(varargin)
x = varargin{iA};
if numobj(x) > 1
varargout{... |
f1f10150204db42a0acd81cb89bbf62d5cdbe3f32b88fa0cb570547dcc626001 | MATLAB | 399 | 13 |
%%
function neighborhood = generateNeighborhood(numParticles, numNeighbors)
neighborhood = zeros(numParticles, numNeighbors);
for i = 1:numParticles
startIdx = mod(i - ceil(numNeighbors/2) - 1, numParticles) + 1;
for j = 1:numNeighbors
neighborIdx = mod(startIdx + j - 1, numParticle... |
4852ac0bab12656fe3929141e4be3f6bff702f20ef065a18f552cb16420e3ba2 | MATLAB | 402 | 12 | function [retval] = fs_fread3(fid)
% freesurfer_fread3 - read a 3 byte integer out of a file
%
% !!! Modified by D. S. Schwarzkopf (15/09/2012) !!!
%
% [retval] = freesurfer_fread3(fid)
% see also freesurfer_write3, freesurfer_read_surf, freesurfer_write_surf
b1 = fread(fid, 1, 'uchar') ;
b2 = fread(fid, 1, 'uchar')... |
7a9db3453a48e8f1f4294f9273e7a0deac06d3373fa2461db5a6c8ad5bc58343 | MATLAB | 402 | 23 | classdef CCAResults
properties
A
B
r
U
V
stats
end
methods
function obj = CCAResults(XMatrix,YMatrix)
[A,B,r,U,V,stats] = canoncorr(XMatrix,YMatrix);
obj.A = A;
obj.B = B;
obj.r = r;
obj.U = ... |
8ef2f724582dd676250d0f9b20f02928f1ce0fdf3067a7d77f8de29e51d80cad | MATLAB | 402 | 15 | %% function to calculate PVC
function [mean_PVC, PVcorr]= GetPV(popfiringI, popfiringII)
[r,c,~] = size(popfiringI);
PVcorr = nan(r,c);
for i = 1:r
for j = 1:c
pI = squeeze(popfiringI(i,j,:));
pII = squeeze(popfiringII(i,j,:));
PVcorr(i,j) = nancorr(pI, ... |
59d3d37be74956a93b5b6b4bbfaba6d2adbaf59f2716492da97b595000c57f18 | MATLAB | 403 | 12 | function psi = typeIIRaisedCosineWavelet(t, scale, shift, beta)
%% Obtain wavelet from mother
t = (2.^scale) .* t - shift - 0.5;
T = 2*pi*t;
%% Evaluate mother wavelet
psi = ( sin( (1 - beta)*T) + sin( (1 + beta)*T) ) ./ (T .* (1 + 4*beta*t)) ...
- ( sin(0.5*(1 - beta... |
2e91cce44f3b057d8efbd1a707577b6e884a0f46136aa0ada2213c53dbe46b8c | MATLAB | 404 | 9 | %%
% Row and column indices for a given linear index and matrix dimensions.
% The linear index is assumed to go from 1 at (row,column) = (1,1), and
% increment in the column-wise direction.
function [indices] = toLinearIndex(linearIndex, numCols)
rowIndex = floor((linearIndex - 1) / numCols);
colIndex ... |
682b05f8ed00b23ac2c64dae93037fa34d34e0cce169996103ee60a966ae1fc0 | MATLAB | 404 | 20 | %%
%
function [leafs] = getPanelLeafs(pan)
if isempty(pan.children)
leafs = {{}};
return;
end
leafs = {};
for iChild = 1:numel(pan.children)
subLeafs = getPanelLeafs(pan(iChild));
for iSub = 1:numel(subLeafs)
subLeafs{iSub} = [iChild, sub... |
e5f7a9f7bb64c44ec35fd1207cf71348be3d5f1064e467a265ce2b467b8425a4 | MATLAB | 405 | 11 | %% Close most figures (except those with 'persist' in their Tag values) and clear all MEX programs.
MCC_TEMP_FIGURES = findall(0, 'Type', 'figure');
MCC_TEMP_FIGURES( arrayfun(@(x) ~isempty(regexp(lower(get(x,'Tag')), '\<persist\>', 'once')), MCC_TEMP_FIGURES) ) = [];
set(MCC_TEMP_FIGURES, 'CloseRequestFcn', 'cl... |
eaf8837990467653c465061b9b683479e172fe9813ef969304ae59b39dff4011 | MATLAB | 406 | 14 | % Remove dimensions only if of length 1 at the specified dimension(s), like a targeted squeeze
function B = squish(A, dim)
Bsize = size(A);
% dim = sort(dim);
for iDim = numel(dim):-1:1
if numel(Bsize) >= dim(iDim) && Bsize(dim(iDim)) == 1
Bsize = [ Bsize(1:dim(iDim)-1), Bsize(dim(iD... |
048ff2490a4186b37350b8a0aa1ab74b492605619f12ecc3814fa9e695c52242 | MATLAB | 407 | 28 | function [y,tweight]=nt_wpwr(x,w)
%[y,tweight]=nt_wpwr(x,w) - weighted power
%
% y: weighted ssq of x
% tweight: total weight
%
% x: data
% w: weight
%
if nargin<2; w=[]; end
x=nt_unfold(x);
w=nt_unfold(w);
if isempty(w)
y=sum(x(:).^2);
tweight=numel(x);
else
x=nt_vecmult(x,w);
y=sum(x(:).^2);
... |
4c79a67bcaf4f30793c6ec385a7b8e0919e236f72d084cb125c023989665b1b6 | MATLAB | 408 | 15 | %% function to bin position data of mouse
function [BinnedXY, edges] = BinPosition(XY, ArenaSizeCm, binSizeCm)
Nbins = ArenaSizeCm/binSizeCm;
edges = zeros(Nbins+1,2);
BinnedXY =zeros(size(XY));
for i =1:2
edges(:,i) = min(XY(:,i)):(max(XY(:,i))- min(XY(:,i)))/Nbins:max(XY(:,i));... |
44eca0d2bfea3f97efae8e7db812ba39465555fc03af714481c20cda0edbb045 | MATLAB | 410 | 20 | function out = catcellstruct(dim, cellstruct)
%%
eg = [];
for iIn = 1:numel(cellstruct)
if ~isempty(cellstruct{iIn})
eg = mstruct(fieldnames(cellstruct{iIn}));
end
end
%%
if isempty(eg)
out = struct([]);
else
[cellstruct{cellfun(@isempty, cellstruct... |
017287c51e4baddf26b2034d30c3cff0af880a1436db85fa2018eb7c7e833a79 | MATLAB | 412 | 22 | function [g,a]=ar1nv(x)
% AR1NV - Estimate the parameters for an AR(1) model
% Syntax: [g,a]=ar1nv(x);
%
% Input: x - a time series.
%
% Output: g - estimate of the lag-one autocorrelation.
% a - estimate of the noise variance.
% (c) Eric Breitenberger
x=x(:);
N=length(x);
m=mean(x);
x=x-m;
% Lag zero and on... |
0599aa1738176952c803933e5dee1880d48d15f83d28de098fcb2448f0fc464a | MATLAB | 412 | 22 | function [status, start_time] = start_scan
% This code will trigger the 3T GE scanner at CNI using the E-prime trigger
% cable. --Michael 09/30/2013
try
s = serial('/dev/tty.usbmodem12341', 'BaudRate', 57600);
fopen(s);
fprintf(s, '[t]');
fclose(s);
catch
err
end
if exist('err','var') == 0
sta... |
2199d2c99c509ea2927e99cc30c330ad81d9a748c6076b7dfb2a85366be7c363 | MATLAB | 413 | 13 | % Convert integer representation YYYYMMDD of a date into a string YYYY-MM-DD
function str = dateint2str(dateint)
%% Extract elements of date from an integer format
year = floor(dateint / 1e4);
dateint = dateint - year * 1e4;
month = floor(dateint / 1e2);
day = dateint - month * 1e2;... |
b876ad05332cb580098e08d3dd7784313041430c393dd1f4dc886c2e006b5887 | MATLAB | 415 | 18 | itrial = cfg.representtrials(1)
temp = rmfield(TFR_macro_single,'time');
temp.time{1} = TFR_macro_single.time;
cfg = [];
cfg.time = temp.time;
cfg.trials = itrial;
cfg.method = 'pchip';
dat_micro_resampled = ft_resampledata(cfg,dat_micro);
A = squeeze(TFR_macro_single.powspctrm(1,:,:))';
B = squeeze(dat_micro_resam... |
f7b053181de624776b468766fb07adf157699847cfd4cece91cbc53eeaabfc5f | MATLAB | 415 | 20 | %%
function [varargout] = show(handles)
%----- Get figure handles
if nargin < 1
handles = findobj('Type', 'Figure');
elseif ischar(handles)
handles = findobj('Type', 'Figure', 'Name', handles);
end
%----- Loop through figures
for handle = rowvec(handles)
set(handle,... |
328064b45d605e4e25978a1bb60b77b22a535b5aae4af7297cc6908b23057f0a | MATLAB | 416 | 18 | function psd_area = compute_psd_area(signal,fs,f_range)
% signal: Input signal
% fs: Sampling frequency
params.tapers=[3,5];
[S,f] = mtspectrumc(signal,params);
psd=S';
fx=f*fs;
idx=fx>f_range(1) & fx<f_range(2);
fx=fx(idx);
psd=psd(idx);
% Take the logarithm of frequency and P... |
39d96c7e3f3969ff75e23060bc89464b9d4635642f3819858ce51fc647d58632 | MATLAB | 416 | 14 | function history = get_history(order)
% Computes the number of times a given condition is preceded by all others
% assuming a single column input where each row is a condition.
% Written by KGS Lab
% Edited by AS 8/2014
num_blocks = size(order, 1);
num_conds = length(unique(order));
history = zeros(num_conds);
for n =... |
45c33de4b8cce199c526c6844831dda3c4b2a1d2b55205afb7ae0ac91b17fe46 | MATLAB | 416 | 20 | function [L,R,k] = curvature(X)
N = size(X,1);
dims = size(X,2);
if dims == 2
X = [X,zeros(N,1)];
end
L = zeros(N,1);
R = NaN(N,1);
k = NaN(N,3);
D = NaN(N,3);
for i = 2:N-1
[R(i),~,k(i,:),D(i,:)] = circ(X(i,:)',X(i-1,:)',X(i+1,:)');
L(i) = L(i-1)+norm(X(i,:)-X(i-1,:));
end
... |
df0c202b002ab75bd99dc9330da718009feb88f0d79271ab71e6be08cf83acb7 | MATLAB | 416 | 20 | %%
function [varargout] = hide(handles)
%----- Get figure handles
if nargin < 1
handles = findobj('Type', 'Figure');
elseif ischar(handles)
handles = findobj('Type', 'Figure', 'Name', handles);
end
%----- Loop through figures
for handle = rowvec(handles)
set(handle,... |
ff81e44721b35cb3ad4c19dc3d2bf345ec9417f4a3a978343c0eb84f892d5543 | MATLAB | 417 | 25 |
function nii2int16(in_nii, out_nii, normz)
if ~exist('normz','var')
normz = 1;
elseif ischar(normz)
normz = str2double(normz);
end
v=load_nii_BIG_Lab(in_nii);
v.hdr.dime.datatype=4; v.hdr.dime.bitpix = 16;
%amin=min(v.img(:)); v.img = v.img - amin;
v.img=double(v.img);
if normz
amax = max(v.img(:)); ... |
c3989b5f09278f28c206ed15e9185924f90ddd3c8e02d91893a3f67c3cd77821 | MATLAB | 418 | 17 | %%
% Note that the left edges of bins are inclusive and the right edges are
% exclusive.
function [bin] = findBucket(x, xEdges)
% If there is only one bin then can decide immediately
if length(xEdges) < 2
bin = 1;
return;
end
dx = xEdges(2) - xEdges(1);
bin = 1 + floor(... |
6234ec9569efd9e1a47f47a9286986e766a0da4c23b1bc5fa19338a61519429e | MATLAB | 420 | 12 | function patch_std(x, ymean, ystd, color)
if nargin < 4
color = 'k';
end
y = [ymean - ystd; ystd; ystd]';
filled_SD = area(x,y);
filled_SD(1).FaceAlpha = 0; filled_SD(2).FaceAlpha = 0.4; filled_SD(3).FaceAlpha = 0.4;
filled_SD(1).EdgeColor = 'none'; filled_SD(2).EdgeColor = 'none'; filled_SD(3).EdgeColor = 'none'... |
0f1509adfe6c69267d08e19ef5853c64c9f990f0c8f281d441b93c6e60eedb54 | MATLAB | 422 | 13 | function p = createFigureParser(extraParams)
% Create an inputParser with a standard 'Parent' parameter.
p = inputParser;
addParameter(p, 'Parent', []); % Always include Parent
if nargin > 0 && ~isempty(extraParams)
for i = 1:2:length(extraParams)
name = extraParams{i};
... |
2840aef9037c79fa71b5cbafdab0e31e40d1eb58772b7a7e9fb65174c8e36326 | MATLAB | 423 | 18 | %% function to get to which reward the HDC is tuned to
function [NReward, WhichReward] = GetWhichReward(TunedBin,RewBin)
WhichReward = nan(length(TunedBin(:,1)),1);
for i = 1:length(TunedBin(:,1))
for r = 1:length(RewBin)
if ~isempty(intersect(TunedBin(i,:), RewBin(r)))
WhichReward... |
b55e7d4039d1020f5b41f54d76d6ae693478ae0c2ea0c44510f2bfd5a4a15233 | MATLAB | 423 | 12 | % Returns a range [min,max] that covers the input range but with limits rounded to the given resolution
function range = roundRange(range, resolution, symmetric)
range = [min(range(:)), max(range(:))];
if nargin > 2 && symmetric
range = [-1 1]*max(abs(range));
end
range(1) = resol... |
e8a35e5f85eb39019e3a5bf7cdd3d686bc6763466a185ca84b70191847a85b3e | MATLAB | 423 | 17 | %%
function [value] = rget(handles, property, fixName, fixValue)
fixPrev = rset(handles, fixName, fixValue);
if iscell(property) && numel(property) == numel(handles)
value = cell(size(handles));
for iH = 1:length(handles)
value{iH} = get(handles(iH), property{iH});
end
... |
13bd33526a98a766b7cb09e1cacc4bdc1d3969586ea615d8f5b8c905324dfc8e | MATLAB | 424 | 19 | function [num] = numobj(x, noCellStr, noStruct)
% NUMOBJ Like numel(), but treats strings as a singleton.
if nargin < 2
noCellStr = false;
end
if nargin < 3
noStruct = false;
end
if ischar(x) ...
|| (noCellStr && iscellstr(x)) ...
|| (noS... |
e41b79d71a562cf8c545c7a29f371f7afd147c07353fa067b181699786004676 | MATLAB | 424 | 16 | function x=my_norminv(p,mu,sigma)
% implements the most common version of MATLABs norminv function
%function x=my_norminv(p,mu,sigma)
% ths function computes quantiles of the normal distribution
%input:
% p = percentage requested
% mu = mean of the distribution
% sigma = standard deviation
%
%output:
% ... |
0f07bf4dcf2e2bd007d110bab0e7b5d4a977e0dda3f2f18d441c57fa95770c07 | MATLAB | 425 | 20 | function [pathstr, baseName] = fileBaseName( fileName )
% Returns path string & the base name of the fileName (removing multiple
% extensions - see remove_extension.m)
%
% Usage:
% [pathstr, baseName ] = file_base_name(fileName)
% baseName = file_base_name(fileName)
%
[pathstr, baseName, ext] = fileparts(file... |
a17a768c4a67f1dfad1ca9a88c801f31153bae03200026cd4fcc0b918c9d96e3 | MATLAB | 425 | 16 | %% function to measure whether vector length is significant
function IsSignificant = TestSignificantRV(RVL_distribution_events, RV, pctile_thresh)
PercentileThreshold =prctile(RVL_distribution_events, pctile_thresh, 3);
[n_cells, ~] = size(PercentileThreshold);
IsSignificant=nan(n_cells,3);
IsSignificant(:,2:... |
c59859f1e2bf31b9581c47649f74e4508d59749008253b280f1adaf9e183ac93 | MATLAB | 425 | 20 | function [biom_ch] = find_channel_img(biom)
%% Find image based on biomarker
% @author: speressotti
%%
channel_order = {'hoechst','sox2','btub','gfap'}
if strcmp(biom,'hoechst')
biom_ch = 1;
elseif strcmp(biom, 'gfap')
biom_ch = 2;
elseif strcmp(biom,'s... |
a8c7724548f0f78d047dd92ade95656a5f4493ecc7756505edc82a7212d83021 | MATLAB | 427 | 16 | function importfile(fileToRead1)
%IMPORTFILE(FILETOREAD1)
% Imports data from the specified file
% FILETOREAD1: file to read
% Auto-generated by MATLAB on 01-Mar-2026 12:54:25
% Import the file
newData1 = load('-mat', fileToRead1);
% Create new variables in the base workspace from those fields.
vars =... |
2881693c129a50230e85152c251a79cf2153ce705edc61f7c3eac565775d808e | MATLAB | 428 | 17 | ntrial = length(data_all.trial);
nchans = length(data_all.label);
spikechan = zeros(nchans,1);
for i=1:ntrial
for j=8:8 % nchans
spikechan(j) = spikechan(j) + all(data_all.trial{i}(j,:)==0 | data_all.trial{i}(j,:)==1 | data_all.trial{i}(j,:)==2);
if ~all(data_all.trial{i}(j,:)==0 | data_all.trial{i}(j,:)==1 ... |
434df9dff97821f05dfe3a15b6f4bfaacc353b058ce3b54fbcec1acc7d65555e | MATLAB | 430 | 21 | %%
% Safe version of division, whereby 0/0 is taken to be 0. However note
% that x/0 where x is nonzero is still infinity.
%
function z = safediv(x, y, nil)
if numel(x) == 1
z = zeros(size(y));
sel = repmat(x ~= 0, size(y));
else
z = zeros(size(x));
sel = (x ~= 0);
end... |
b21a4aaf6184aa72a01186cfb4c060e1e7a15c6f11c26ae8d981b72b7cbc951b | MATLAB | 431 | 14 | clc;clear all;close all;restoredefaultpath;
%addpath(genpath('/big_disk/ajoshi/coding_ground/bfp/supp_data'))
addpath(genpath('/ImagePTE1/ajoshi/code_farm/bfp/src'));
%studydir='/ImagePTE1/ajoshi/ADHD_Peking_bfp';
studydir = '/ImagePTE1/ajoshi/maryland_rao_v1_bfp';
sessionid='rest';
a=dir(studydir);
for j=1:length(a... |
e18d2babfb3c4a90a709a724f759437ad04653371027bb1311ae94de2b0a3382 | MATLAB | 431 | 19 | %%
function [minimum, maximum] = erange(array, exceptTest)
% Exclusive minimum and maximum, over all elements except those passing
% the exceptTest.
if nargin < 2
exceptTest = @iszero;
end
minimum = nan;
maximum = nan;
for iX = 1:numel(array)
if ~exceptTest(array(iX))
... |
896267ea14bbb976229ef2deee160ec7bda016c897f24a79be32516d06e0fa8c | MATLAB | 432 | 17 | %% Preprocessing pipeline
% Prerequisite softwares
% 1. BrainStorm
% 2. EEGLab
% 3. EEGLab plugins
% Adjust
% Cleanline
% PrepPipeline
% clean_rawdata
%
% Running preprocessing
% 1. Run runPreprocDarpa.m
% 2. Remove ICs from Brainstorm (manual inspection)
% 3. Run preprocPostICA.mt
% 4. (option... |
a065e06c1713ca69c9ad1ac6ed77763d49ea7c5c4b8aff0a65ea2c82cb73ce63 | MATLAB | 435 | 26 | %
% units = getByteUnits()
%
% Description:
% get almost all possible units for information storage
%
% Input:
%
% Output:
% units - the cell array of units
%
% Copyright:
% 2017-2018 (c) USC Biomedical Imaging Group (BigLab)
% Author:
% Jian (Andrew) Li
% Revision:
% 1.0.3
% Date:
% 2017/05... |
3ddc8b81e76740df12a905f9537248c2348e171886b1526dfbe2d447c1c18079 | MATLAB | 436 | 12 | % Reshapes the input tensor X down to dim number of dimensions.
%
% Faster version of e.g. X(:,:,:), which is inexplicably slower than reshaping to 3 dimensions. Can
% flexibly specify the dimension dim above which all subsequent dimensions are concatenated into
% one.
function X = remould(X, dim)
sz ... |
e7e6f984689d3b068b037b86b46a75438679512730af8aa30f398293fd035cca | MATLAB | 436 | 15 | %% SAFEACOS acos() with safety against numerical precisions that may cause the argument to have magnitude slightly greater than 1
function angle = safeacos(angle, epsilon)
if nargin < 2
epsilon = 1e-6;
end
excess = abs(angle) - 1;
if any(excess(:) > 0)
valid = exc... |
d9678484089f9034755ac423ff76a4589642f93fd2bf23a74491fd6067a15235 | MATLAB | 437 | 20 | function [w, center] = doScreen
% Opens a full-screen window, sets text properties, and hides the cursor.
% Written by KGS Lab
% Edited by AS 8/2014
% open window and find center
S = Screen('Screens');
screen_num = max(S);
[w, rect] = Screen('OpenWindow', screen_num);
center = rect(3:4) / 2;
% set text properties
Scr... |
0ad462e09ebd07d7d5d0079e059869e35aac33deeb7a3ed5f6e6019369b61e26 | MATLAB | 440 | 15 | function runFile(script_filenames)
try
% Construct the command to run MATLAB script
cmd = sprintf('matlab -r "run(''%s'')"', script_filenames);
% Execute the command using the system function
status = system(cmd);
% Check if an error occurred during script execution
if status ~= 0
error(... |
2738ab11dbff3851a4e5100dbf13d030d2933aad53f0cc6e0debf367280d2921 | MATLAB | 441 | 12 | function [position] = findlast(array, varargin)
% FINDLAST Returns the index of the last item matching the given
% criteria. Zero is returned in case there are no matching items.
%
% Examples:
%
% findlast(array, value, [comparator = @eq], [outcome = true], [indexRange|veto = []])
% findlast(a... |
9d5400f177d526f10fc8411039f8fb83683fcf2dcb2b7a23fcad993771f7521b | MATLAB | 442 | 13 | %% Computes a linear scale factor within a given range
function scale = linscale(number, numberRange, scaleRange)
number = ( number - numberRange(1) ) ...
/ ( numberRange(2) - numberRange(1) ) ...
;
scale = scaleRange(1) ...
+ ma... |
8432517ceadda319f6c14fedc21ef87613832de5b2b49a51036011eea1fc2601 | MATLAB | 443 | 12 | function label = cblabel(handle, string, varargin)
label = get(handle, 'YLabel');
set ( label ...
, 'String' , string ...
, 'FontSize' , get(0,'DefaultAxesFontSize') ...
, 'Rotation' , -90 ...
... |
191a31383fe05ed02c9decd13285485afa9b4540fd2ecfb3376e425e4d3b8ed6 | MATLAB | 444 | 15 | function y = fullRectify(x, minX, maxX, sharpness)
y = nan(size(x));
sharpness = 10^sharpness;
scale = 1 / log(sharpness);
%% Softplus-like functional form for low end
sel = 2*x < minX + maxX;
y(sel) = minX + log( sharpness.^(x(sel) - minX) + 1 ) * scale;
%% Reverse... |
ff20c2b34c02d133cd44d014ebe9e50589e462de529c81cd8523552c55d2e18a | MATLAB | 444 | 13 | %% Computes a linear scale factor to represent area within a given range
function linScale = area2linscale(area, areaRange, scaleRange)
area = ( area - areaRange(1) ) ...
/ ( areaRange(2) - areaRange(1) ) ...
;
linScale = scaleRange(1) ...
... |
d51655596c819cc658b23a046595f493d4d0fc4f9ba0bf3728c775d2254f7c35 | MATLAB | 445 | 20 | classdef ImageArray
properties
data
headers
meta
waveform
acq_headers
end
methods
function self = ImageArray(data, headers, meta, waveform, acq_headers)
self.data = data;
self.headers = headers;
self.meta = meta;
... |
16195616616ae462382fe6bb13a521c3ec9256193d96ba1fb375c684fc858755 | MATLAB | 446 | 12 | function [position] = findfirst(array, varargin)
% FINDFIRST Returns the index of the first item matching the given
% criteria. Zero is returned in case there are no matching items.
%
% Examples:
%
% findfirst(array, value, [comparator = @eq], [outcome = true], [indexRange|veto = []])
% findfir... |
23aa15b3ae37435a3401aa8d948157d9d1c185a61ea6a63c15cad4e5471e3793 | MATLAB | 446 | 24 | %
% Map from image space to motor space
%
% Input
% pt: [n x 2] points (rows) in motor coordinates
%
% Output
% new_pt: [n x 2] points (rows) in image coordinates
function new_pt = space_img_to_motor(pt)
if iscell(pt)
new_pt = apply_to_nested(pt,@(x)space_img_to_motor(x));
return;
end
... |
371703ab5ee6d3e59d63eed87e3193c8312b6f387437e964b8956b082f88d286 | MATLAB | 449 | 24 | %
% Map from motor space to image space
%
% Input
% pt: [n x 2] points (rows) in motor coordinates
%
% Output
% new_pt: [n x 2] points (rows) in image coordinates
function new_pt = space_motor_to_img(pt)
if iscell(pt)
new_pt = apply_to_nested(pt,@(x)space_motor_to_img(x));
return;
end
... |
b75e812fe0aab680a485307103731a4716502861946831c32248c9a9fa1705f9 | MATLAB | 449 | 17 | %% Sets the units of all relevant graphics children to the given value.
function setUnits(parent, units, matchType)
if nargin < 3
matchType = '^(axes|uicontrol|uipanel|uitable)$';
end
children = findall(parent);
for iChild = 1:numel(children)
type = get(children(iChild), '... |
310f4a60e87ddedf2f51d3893c2eb4e418da4a09187fc815bac90e2c462d171e | MATLAB | 450 | 10 | function yeah = strismember(thing,setofthings)
% YEAHITIS=STRISMEMBER(STRING,SETOFSTRINGS)
% Returns true if the character vector STRING is a member of the
% cell array SETOFSTRINGS. This is generally faster than using
% ismember() -- about 2x as fast in recent versions, and up to
% 50x as fast in older ve... |
ad9cd82651a2411432510e8bdbad9757efadb851d0d8f1dbe93a83fa41e1d303 | MATLAB | 450 | 13 | %% Gergely Tarcsay, 2023. Function to read the minian dataset. c: raw ca trace, s: deconvolved signal, a: spatial footprint, unit_id: cell_id. All are coming from the minian pipeline.
function [c,s,a, unit_id] = ReadNCData(rootdir)
cd(rootdir)
c = ncread("minian_dataset.nc", 'C');
s = ncread("minian_d... |
b6f70a289b5b293112b31ac6d64639ef7a82f5cea28dd6e2091be7e49742e8d6 | MATLAB | 450 | 19 | %% function to cluster with k-means
function clusters = GetClusterKMeans(I, fieldBins, k, max_iter)
[idx,~] = kmeans(fieldBins, k, "MaxIter",max_iter);
%% create maps for individual fields
clusters = zeros([size(I) k]);
for i =1:k
clust_idx = find(idx == i);
for j = 1:l... |
730f42dc210993ba01c0c7393ca9a57c9570f0717e2c7fa05459f5ca9efcded1 | MATLAB | 451 | 17 | %% Return a list of struct field names that match the given regular expression pattern; see also regexp()
function names = fieldsmatching(S, pattern, invert)
names = fieldnames(S);
if iscellstr(pattern)
sel = ismember(names, pattern);
else
sel = ~cellfun(@isempty, regexp(names, pattern, 'o... |
0b9d0ee920404208a482c97c007af95362f2069ce2f351c66b29f4449f9d0a86 | MATLAB | 452 | 17 | function [trapz_ints] = delta_sigma_mod(data)
%% Calculates the integral between two points
%
% **Usage:** [trapz_ints] = delta_sigma_mod(data)
%
% Input(s):
% - data : Input data vector (BS data)
% Output(s):
% - trapz_ints : Integrals using the trapezoidal rule
%
% Author: R.M.D. Kock, Leiden University... |
f6d1f4ebb2653285c161286aaa9679f12ce90dde7cac3c9d4ea2893ed7c953bc | MATLAB | 453 | 22 | function y=nt_normpagecol(x,w)
% y=nt_normpagecol(x,w) - normalize each column of each page so its weighted msq is 1
%
% y: normalized data
%
% x: data to normalize
% w: weight
%
% Weight should be either a column vector, or a matrix (2D or 3D) of same
% size as data.
if nargin<2; w=[]; end
[m,n,o]=size(x);
i... |
0a2ba4653888ea0e68150e121303632c41c2f06958fff249c9cd382fa26410f3 | MATLAB | 455 | 12 | function tif2mat(fname) %function to convert segmented tif file to mat format
%fname is the path and name of the segmented tif file
imgInfo = imfinfo(fname);
N = size(imgInfo,1);
for i=1:N, eval(sprintf('channel%d = imread(fname,i);', i)); end
save([fname(1:end-4), '.mat'],'channel1','-v7.3')
if N>2
for i=2:N, save([... |
d910747f6c78cca8ab8a5a97fa7171f21ca96b6ab29a902bbcaf76885f1f7a0a | MATLAB | 457 | 14 | function [sf] = myCreateStringToWrite(input);
sf ='';
for i= 1:length(input)
if (length(input{i})> 1) && (isa(input{i}, 'char')~=1)
for j=1:length(input{i})
input{i}= input{i} * 1.000000001; % I do not know a clever way to have a uniform data format.
sf = sprintf('%s %s\t',sf, ... |
e03e7ba66e89762f6382d116b8187a12b13183f0a38f22ee3f14e69f054b406c | MATLAB | 457 | 8 |
s=readdfs('/home/ajoshi/coding_ground/bfp/supp_data/bci32kright.dfs');
[FaceNormal, FaceArea, FaceCenter, VertexNormal, VertexArea, SuspectFace, NumFacesEachVertex, Duplicated_Faces, Not_Twice_Faces] = tessellation_stats(s,1);
s=readdfs('/home/ajoshi/coding_ground/bfp/supp_data/bci32kleft.dfs');
[FaceNormal, FaceAr... |
c62114d24eacbb22612cfb92b2debc244a0d84807c998dab3c5aeef13a5a2a51 | MATLAB | 461 | 21 | %% From http://undocumentedmatlab.com/blog/controlling-callback-re-entrancy/
function flag = isMultipleCall()
flag = false;
% Get the stack
s = dbstack();
if numel(s) <= 2
% Stack too short for a multiple call
return
end
% How many calls to the calling function are in the stack?
na... |
7e60846c5d29504e348e9ecf1511ca09e5086728843d1888dd4d1fbe088a80c3 | MATLAB | 463 | 16 | function nt_mark(idx,labels,line_params,text_params)
% nt_mark(idx,labels,line_params,text_params)
if nargin<2; labels=[]; end
ylim=get(gca,'ylim');
for k=1:numel(idx)
line([idx(k) idx(k)],[ylim(1),ylim(1)+0.95*(ylim(2)-ylim(1))], 'color', 'r', 'linestyle', '--');
if ~isempty(labels)
if k<= numel(lab... |
7078cb559d8cf3cb91d26b767438b820129cfefeba36e092a74eadd95885e1bb | MATLAB | 465 | 16 | %function to get reward location
function RZ_Loc = GetRewLocation(trials, Correct, event, BinnedXY)
[~, ~, idxI] = intersect(trials,Correct(:,1));
RZ_frames = event{Correct(idxI,2),2}+1;
RZ_xy = BinnedXY(RZ_frames,:);
rewI_map = zeros(max(BinnedXY));
for i = 1:length(RZ_xy)
rewI_map(RZ_xy(i,2), RZ_xy(i,1))... |
2ac37a7f3d14cbb12a35ac42fce5d08797235c5537176885ca3db90d63be50e4 | MATLAB | 466 | 1 | function y=rms(x, dim)
%RMS - Root-mean-square
%
% y=rms(x): If x is a matrix the rms is calculated columnwise.
% y=rms(x,dim): calculate rms according to dim.
%
% see also nt_bsrms, nt_bsplot
%
% NoiseTools
% if row vector transpose to column
if size(x,1) == 1 ; x = x'; end
if nargin == 2
if dim == 0;
... |
0d78e4e71770055bb47c8271ccf7ba40e6201a21e1c96f309d7796a05582a2a3 | MATLAB | 468 | 19 | function U = upperTriangular(M, k)
%% Default arguments
if ~exist('k', 'var') || isempty(k)
k = 1;
end
%% Construct selection vector for one slice of the input tensor
mSize = size(M);
sel = triu(true(mSize(1:2)), k);
%% Apply selection to every slice of the input
M = resha... |
de1f6c0ab918c03264fe1c4170676b12e7bf5881aaa108f37db37ceffc79ba23 | MATLAB | 468 | 18 | %%
% Online computation of mean.
function [newMean, newWeight] = accumulateMean(currentMean, currentWeight, x, weight)
if weight == 0
newMean = currentMean;
newWeight = currentWeight;
else
newWeight = weight + currentWeight;
newMean = currentMean ...
... |
e22961fbbd2ccfd9a94681e762d4e1d02edda43f8bc1f763399e909b07aa3412 | MATLAB | 468 | 21 | %%
%
function [color] = desaturate(color, saturation, beta)
%% Default arguments
if ~exist('saturation', 'var') || isempty(saturation)
saturation = 0.5;
end
if ~exist('beta', 'var') || isempty(beta)
beta = 0;
end
hsv = rgb2hsv(color);
if ismatrix(hsv)
hsv(:,2... |
bad4d0f07988a974a01e555a3ba6372f9d55b0efa51e0a552fcf146c750384fe | MATLAB | 470 | 18 | % Make the mexhyp2f1 mex file;
% Siyi Deng; 10-10-2013;
mex -I. -largeArrayDims -c round.c
mex -I. -largeArrayDims -c gamma.c
mex -I. -largeArrayDims -c polevl.c
mex -I. -largeArrayDims -c psi.c
mex -I. -largeArrayDims -c hyp2f1.c
if ispc
mex -I. -largeArrayDims mexhyp2f1.c gamma.obj hyp2f1.obj pole... |
663b88ebb8436afd9549fcab707e08f7b7731351c6dc333e0fc0b08a1bcb59ea | MATLAB | 472 | 20 | function p = my_normcdf(x, mu, sigma)
%MY_NORMCDF implements the most common case of Matlab's NORMCDF.
%function p = my_normcdf(x, mu, sigma)
% ths function computes quantiles of the normal distribution
%input:
% x = point
% mu = mean of the distribution
% sigma = standard deviation
%
%output:
% p ... |
f2935569b1ac29da09b890dcc0ebd956125588d1035bfa90f62730a3788c2150 | MATLAB | 473 | 14 | %function to get firing pref - heading prob relationship (binned)
function [edges, MedianProbRew, ProbRew] = GetBinnedPrefProb(step, Firing_Pref, ProbReward)
edges = -1:step:1;
binned_pref = discretize(Firing_Pref,edges);
MedianProbRew = nan(length(edges)-1,3);
ProbRew = cell(length(edges)-1,1);
for b = 1:leng... |
cfe9a0ce5c69b1425744435deaee87c5e351b2ab3d5e1fb0b0767fa110262b54 | MATLAB | 474 | 11 | #!/bin/bash
#SBATCH --job-name=spyking-circus
#SBATCH --partition=bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=128G
#SBATCH --cpus-per-task=24
#SBATCH --output=/network/lustre/iss01/charpier/analyses/vn_pnh/slurm/%j_%A-%a-%x-output.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/vn_pnh/slurm/%j_%A-%a-%x-err... |
0800fbc9d8b43a2a252e094660e7106e01a7d92b908d3701d471c928772433c6 | MATLAB | 483 | 17 | function waveform = read_waveform(socket)
header = gadgetron.external.readers.decode_waveform_headers(read(socket, 40, 'uint8'), 1);
data = read_data(socket, header);
waveform = gadgetron.types.Waveform(header, data);
end
function data = read_data(socket, header)
N = header.number_of_sampl... |
6e6c2bd5a1338941fdc9a394e098c906e449ecb4d519783613395a2e365356e9 | MATLAB | 483 | 29 | function max_frame = get_ei_max_frame(ei, start_frame, end_frame, negative)
if nargin < 5
logscale=0;
end
if nargin < 4
negative = true;
end
if nargin < 3
end_frame = size(ei,2);
end
if nargin < 2
start_frame = 1;
end
max_frame = zeros(size(ei,1),1);
for e = 1:size(ei,1)
if ~negative
[... |
ff9b84a5c31197c18afc5b4a86ad021233d15aa4215ba72f46e49accd157ec3c | MATLAB | 483 | 21 | function outflag = hasipt()
% FLAG = HASIPT()
% Check whether the current installation has Image Processing Toolbox installed.
% State is persistent to reduce cost of repeated calls.
% Output is a logical scalar.
% for testing purposes
enable = true;
persistent hasIPT
if isempty(hasIPT)
hasIPT = license('test', ... |
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