sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cfeb516c72911e04037c802142f5f35fe2066baa1c0a2a598d89bb4f38fab141 | MATLAB | 702 | 29 | %%
% Returns the number of elements that are at least equal to or more than
% the given target values.
%
function [counts] = countAbove(sortedData, targets)
% Sanity check for inputs
if sortedData(1) < sortedData(end)
error('sortedData must be sorted in descending order');
end
if targets(1) >... |
c761b44db0e05f616c9b03cc37d9e5c0c579f89759d1a2d88be5dc5cb5ef68f2 | MATLAB | 703 | 19 | %% http://www.holoborodko.com/pavel/numerical-methods/noise-robust-smoothing-filter/
function smoothed = robustSmoothing(data, dim, degree)
% Smoothing kernel
if degree < 5 || mod(degree,2) == 0
error('robustSmoothing:degree', 'Invalid degree of smoothing %d, must be an odd integer >= 5.', degree);
e... |
0d72a42f74c04dca745e44ba4fd7ba5177ff4a60bbe03978b26478ea30da7239 | MATLAB | 704 | 31 | %% function to remove pixels that are not connected to the peak of the cluster
function clusters = CheckConnectivity(I, clusters)
[~,~,NClust] = size(clusters);
for clust = 1:NClust
% get peak of current field
[~, peak_idx] =max(I.*clusters(:,:,clust),[],"all");
[r,c] = size(I);
CC = bw... |
7983ef44eb2f3d6d45f52b1f02e77abad9248f3cc065cfdf594821f51a773525 | MATLAB | 705 | 30 | function [iMorton,toMorton]=nt_morton(nrows,ncols)
%[iMorton,toMorton]=nt_morton(nrows,ncols) - indices for Morton scan of image
%
% iMorton: matrix of indices in Morton order
% toMorton: indices to put pixels in Morton order
%
% nrows,ncols: dimensions of image
%
% NoiseTools
nt_greetings;
if nargin<2; error('!')... |
6ca62b916b27e8102d41a27162016bd3f9b0fe084420fb2015e288863f2596e2 | MATLAB | 706 | 20 | function firing_rate = getFiringRate(animal_name, spike_matrix, repeatCalc, save_data, output_folder)
% by Mattia 08.20
% helper function to compute and save firing rate
% spike matrix is assumed to be in ms
if exist(strcat(output_folder, animal_name, '.mat'), 'file') && repeatCalc == 0
load(strcat(output_folder, ... |
6178800ce83e6ee43709ade34cf879004cb7f62876ead51f76765fd1fbe716c6 | MATLAB | 708 | 24 | function idx_shuffled = shuffledIndexByCategory(catArray)
% shuffledIndexByCategory
% X = categorical({'A','A','B','B','B','C','C'});
% idx = shuffledIndexByCategory(X);
% X_shuffled = X(idx);
arguments
catArray (:,1) categorical %vertical
end
% 1. get unique category order
[~, firstId... |
1e01af4a67cd2c2ff3a442cf7fa35f1ed30a3653523fc7cb5ebafc7b89f0942b | MATLAB | 709 | 29 | %% function to save examples of drifting and non-drifting cells
type = ["Non-drift", "Drift"];
for i = 0:1
file_name = strcat(out, type(i+1), ".pdf");
delete file_name
idx = find(IsDrifting == i);
if N_example < length(idx)
y = datasample(idx, N_example);
else
y = idx... |
8f41ad90bee9b75735b11d4ca89bc50e250fa572b5b9081a82f4885c221552c1 | MATLAB | 711 | 28 | function [DSDeltaF, DTs, DFs] = DownSample(Signal,Fs,varargin)
%Signal-- the Delta F/F or Raw signal to be processed
%FS--The sampling frequency
%Variable Input Arguments:
%1-Size of Sample Group--median of n samples will be taken in order to
% downsample the data. New sampling frequency = old Fs/n. Default is 1... |
46a003958e25336c2f7938ae3e1bb1af56aa5a214ced47f3113f882da9faea39 | MATLAB | 713 | 26 | function nt_colorlines(h,permutation)
%nt_colorlines(h,permutation) - apply different colors to lines of plot
%
% h: handle to plot (default:gca)
% permute: permutation to apply to colors
%
% Colors are applied to children of h in reverse order (ie in order of plot
% commands). May produce unexpected results if ther... |
e10dc49c65329018c27f5cd6fa8963cd8e60724510bac9467d519de0863b42cf | MATLAB | 713 | 21 | function [colorchans alphachans] = splitalpha(inpict)
% [COLOR ALPHA] = SPLITALPHA(INPICT)
% Split an image into its color and alpha channels.
%
% INPICT is an I/IA/RGB/RGBA/RGBAAA image of any standard image class.
% Multiframe images are supported.
%
% Output class is inherited from the input.
%
% Example o... |
f6789e68643a46d5c720f0c6e9c852dd3177ed49a881b64d24d08a33b6881491 | MATLAB | 713 | 33 | function CBIG_znormalize(input_file, output_file, mask_file)
% Znormalize the input nifti file along 1st dimension.
%
% CBIG_znormalize(input_file, output_file, mask_file)
% Input:
% input_file : input file
% output_file : output file
% mask_file : mask file
%
% Written by CBIG under MIT lice... |
c26b5522d61337e6507e7f6f1d1a9265851d37c8b40d98a2a8cce37ab025b425 | MATLAB | 714 | 33 | function varargout=nt_spect_plot(x,varargin)
%nt_spect_plot - plot power spectrum
%
% The power spectral densities of all columns (pages, etc.) are calculated
% and added. The result is divided by the number of columns and either
% plotted or returned.
%
% See pwelch for syntax.
if numel(x)==0; error('!'); end
N... |
f34ecb4e5e7e93abe893d93751b0d487725a493aba6eebfb7ebdd4e148f266d8 | MATLAB | 714 | 21 | function out = mdSpatialScramble(md, area, vertord);
% out = mdSpatialScramble(md,area);
% Spatial scrambling of md data. Area is a vector with
% three numbers that define the range within which the
% random trajectory locations are chosen
%vertord = 0 ->retain vert layout; vertord = 1 ->scramble vert layout... |
20bb8628774cdb53bb122c98bed97cded93e9207a9e6ec635726e93a8659ea7d | MATLAB | 717 | 21 | % Compute the 1-sigma interval about the mean along a given dimension, using quantile-based
% statistics for robustness. NaN entries are ignored. Specifying useQuantile = false will use std()
% instead of quantile() for calculating the 1-sigma width of the distribution.
function [stdDev, mu] = meanStdDev(X, dim, use... |
0e00d95563b031f54d26910be76a2a4f454acacf7c4b8ebd6a5eb2a86e74eb57 | MATLAB | 718 | 26 | function inpict = iminv(inpict)
% OUT = IMINV(INPICT)
% Return the inverse (complement) of an image. Make dark
% things light; make light things dark. This is functionally
% the same as IPT imcomplement(). I just hate long names.
%
% INPICT is an image of any size or numeric/logical class.
%
% See also: imc... |
4f6c899d75497ccca2728c07c19eac4f34cbd01c05a3e9fd24a00d88dd775e49 | MATLAB | 720 | 28 | %% PARSEPATH Consistent file path/name/extension parsing across operating systems.
function [path, name, ext] = parsePath(path)
tokens = regexp(path, '^(.*?)[/\\]*([^/\\]*?)([.][^/\\.]*)?$', 'tokens', 'once');
if ~iscell(path)
if isempty(tokens)
path = '';
name = '';
ext = '... |
995e3c62bb3efe9d7724bada9a87a76c31e56b9649aa801cdf7f2c2ee7ad5633 | MATLAB | 720 | 29 | %
%reads the raw timestamps from a neuralynx CSC file.
%
%urut/april04
function [timestamps,nrBlocks,nrSamples,sampleFreq,isContinous,headerInfo] = getRawCSCTimestamps( filename )
disp(['reading ' filename]);
isContinous=false;
FieldSelection(1) = 1;%timestamps
FieldSelection(2) = 0;
FieldSelection(3) = 1;%sample fre... |
1e9e368a60e7aea30bd1259adea4b41ea05b9a212a83be7e865345e055120a7f | MATLAB | 722 | 30 | function CBIG_WriteToReferenceVolume(input_file, ref_file, output_file, exit_flag)
% Write input volume to reference nifti file.
%
% CBIG_WriteToReferenceVolume(input_file, ref_file, output_file, exit_flag)
% Input:
% input_file : input file
% ref_file : reference file
% output_file : output... |
4490dccf14b8decda629a2e78d5f890cbbff923ca37553f0c400503c6b7a7a6c | MATLAB | 723 | 18 | function out = fft3(x, N1, N2, N3)
% Function that computes the 3D Fourier transform of the input array x,
% along the first three dimensions, with optional size specification.
%
% Input parameters:
% --x: 4D array of size [N1, N2, N3, Nc], where N1, N2, N3 are spatial
% dimensions and Nc is the number of ... |
ed1fb9a264a29ae7455a89fde6de381fc8554f5392eaddf9ff3c5a0dcf26fb5d | MATLAB | 723 | 24 | % Like diag() when applied to convert diagonal elements to a square diagonal matrix. Slices (3rd and
% higher dimensions) are supported in that the diagonal matrix is assembled independently per slice.
function D = todiag3(A, k)
if nargin < 2 || isempty(k)
k = 0;
end
%% Deduce size of matrix
... |
8a03e2fe6f94875fdcddbcd15db6e5dc5fa512c4cd06b1e69478f8ef60963733 | MATLAB | 725 | 27 | function makeLegendsByDummyPlot(labelList,colorList,options)
arguments
labelList (:,1) string
colorList (:,3) {mustBeNumeric}
options.Marker = 'o';
options.MarkerEdgeColor = 'none';
options.MarkerSize = 12;
options.LineStyle = 'none';
options.FontSize = 12;
end
NList = length(labelList);
hol... |
99d73e09774aed0635784049c3a80bfb7ead978c52ea685bb309bbf15cf498a4 | MATLAB | 726 | 32 | function z = mutInfo(x, y)
% Compute mutual information I(x,y) of two discrete variables x and y.
% Input:
% x, y: two integer vector of the same length
% Output:
% z: mutual information z=I(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... |
be1a7c450f6af02de34025b1042a4720fd5a3a999d3032263be5cde5b1c4d4ee | MATLAB | 726 | 36 | function y=nt_squeeze_all(x)
%y=nt_squeeze_all(x) - squeeze structs and cell arrays
%
% x: object to squeeze
%
% y: result of squeezing
%
% If x is a struct, all fields and subfields will be concatenated. If x is
% a cell array, all elements will be concatenated.
VERBOSE=1;
x=squeeze(x);
if isnumeric (x)
y=... |
9a73b07c73aecf21c0dece46ec7a92414a51f8ced1c1a5d2cf1a929cb7eb315a | MATLAB | 727 | 20 | clc;clear all;close all;restoredefaultpath;
addpath(genpath('/home/rcf-40/ajoshi/aaj/git_sandbox/bfp'));
% Configuration file
configfile='/home/rcf-40/ajoshi/aaj/git_sandbox/bfp/supp_data/hpcconfig.ini';
%T1 and fMRI images in NIFTI-1 format (nii.gz)
lst=dir('/home/rcf-40/ajoshi/aaj/Beijing_Zang/sub*');
for jj=1:leng... |
031f47eec12b415852d558f3b29f537e60b15d5aa6d8f13defb7f76cc53e0190 | MATLAB | 730 | 26 | function write_array(socket, array, type)
dimensions = size(array);
gadgetron.external.writers.write_vector(socket, dimensions);
switch type
case 'complex64'
write_complex_array(socket, array, 'single');
case 'complex128'
write_complex_array(socket, array, 'doubl... |
0c7dcbcedd5d0c62fba647c4f4505c0790730a5541bbe7d0b8e891a2e32ec5ee | MATLAB | 730 | 20 | function [brain_index, non_brain_index] = CBIG_GetBrainIndices
% Get Freesurfer brain indices.
% Reference: $FREESURFER_HOME/FreeSurferColorLUT.txt
%
% [brain_index, non_brain_index] = CBIG_GetBrainIndices
% Output:
% brain_index : column vector, brain index
% non_brain_index : column vector, non brain... |
29d48641defc60289199e10ebdb19e06bcf675e512c5dd7f3dcba1e05f7ac178 | MATLAB | 730 | 23 | %%
% Convenience function to convert a variable number of inputs into cell
% arrays. Note that the first argument is the dimension, unlike
% num2cell(). It is possible to specify a dimension per array input by
% making this first argument a cell array.
%
function [varargout] = num2cells(dimension, varargi... |
49ada6c99ed1a402c0a8e0b0286d68d24b43a08e23f3dfa5b3e877d0df0ba2e0 | MATLAB | 730 | 23 | function outpict = gray2rgb(inpict)
% OUTPICT = GRAY2RGB(INPICT)
% Convert an image with a single color channel to one with
% three color channels by simple channel replication.
% If given an RGB image, pass it without complaint or alteration.
%
% INPICT is an I/IA/RGB/RGBA/RGBAAA image of any standard image clas... |
2f9acde54bbe6c145baa412f9a4f60427ae87f9e63bf29729a80ae0a69619b3b | MATLAB | 731 | 26 | function [y]=nt_xprod2(x1,x2,dsratio)
%[y,ind]=nt_xprod(x1,x2,dsratio) - form all crossproducts
%
% y: crossproducts
%
% x1,x2: data (time*channels*trials)
% dsratio: ratio by which to downsample cross-product.
if nargin<3 || isempty(dsratio); dsratio=1; end
if nargin<2 ; error('!'); end
if ndims(x1) ~= ndims(x2... |
08aa8a8cc64cd660004e71cc294363f9e82207a4aa60cf734c7e8473e2735cf6 | MATLAB | 733 | 29 | function [yes] = approx(x, y, tolerance, epsilon)
% APPROX Approximate equality of numeric objects; exact for other types.
%----- Input parsing
if any(ischar(x)) || any(ischar(y))
yes = strcmpi(x, y);
return;
elseif any(~isnumeric(x)) || any(~isnumeric(y))
yes = ( x == y )... |
9686b774c077a847fa821d5c8ce8468c62b84eb1adc64fe951808c677528e541 | MATLAB | 734 | 29 | % Apply a function (fnc) to the lowest level of a
% nested cell array.
%
% input
% dataset: nested cell arrays, where the bottom level is
% a non-cell array (like the vector of a stroke). Any
% nesting structure works.
% fnc: function handle to apply
%
% output
% ndataset: same nesting structure as th... |
90c79c3d25bfcc030975879ff02789c4d218c18ef9dd55ab9f09a8ae65dbbefa | MATLAB | 736 | 28 | function [padded] = padto(input, targetSize, padwith, direction)
% PADTO Pad the given input array so that it has the target size.
excess = targetSize - size(input);
if nargin < 3
padwith = 0;
end
if nargin > 3
if strcmpi(direction, 'pre')
padLeft = excess;... |
654e46cb331a343ba807913e0d3c0594a3e63232c4766049eeebf0dab42711fb | MATLAB | 737 | 20 | function [gray_index, non_gray_index] = CBIG_GetGrayIndices
% Get Freesurfer gray matter indices.
% Reference: $FREESURFER_HOME/FreeSurferColorLUT.txt
%
% [gray_index, non_gray_index] = CBIG_GetGrayIndices
% Output:
% gray_index : column vector, gray matter index
% non_gray_index : column vector, non g... |
8333246deb2d9e5ee65bbb793d1be83f75c891081b5cc465196360cf6556ce36 | MATLAB | 737 | 18 | SpikeWaveforms{ipart}.(markername){icluster}
itemp =1 ;
cm = parula(100);
figure; hold;
y = cat(1, SpikeWaveforms{ipart}.window{itemp}.trial{:});
avg_waveshape = mean(y, 1);
for itrial = 1 : size(SpikeWaveforms{ipart}.window{itemp}.trial, 2)
lh = plot(SpikeWaveforms{ipart}.window{itemp}.time{itrial}*10... |
3eca437cc79a5c70c7425eb29220cb90f68c9738a47b828c6cd31df9c937072d | MATLAB | 742 | 31 | %% function to measure whether a cell's calcium trace is drifting or not during recordings
function [Mins, IsDrifting] = DetectDrift(c, segments, ms_framerate, DriftParams)
[N_points, N_cells] = size(c);
step = segments*ms_framerate*60;
N_segments = floor(N_points/(step));
Mins = zeros(N_cells, N_segments);
I... |
7d3b20611d57dbdf713e340df7ef953e9356c05c6db853652e370432b5c6d85a | MATLAB | 742 | 17 | %% function to shuffle events and recalculate RVL
function RVL_distribution = ShuffleCaEvents(CaMatrix,repeat, minShift, framesToUse, binned_HDir, HDirOccupancy, Nbins, binCenter, edges)
[N_cell,Nframes] = size(CaMatrix);
maxShift = Nframes-minShift;
K = randi([minShift maxShift], repeat,1);
RVL_distribution=zer... |
d68f82412a24eacba67783b01bd7a73c91c5f913d230953d865c972d3d84f691 | MATLAB | 742 | 39 | %
% dataSm = laplaceBeltramiSmooth(LBO, data, sigma)
%
% Description:
% Laplace Beltrami filtering
%
% Input:
% LBO - Laplace Beltrami operator structure
% data - data to be smoothed
% sigma - Gaussian sigma
%
% Output:
% dataSm - filtered data
%
% Copyright:
% 2016-2017 (c) USC Biomedical I... |
cf7805868929df8af6052fa83dc76d9d80434db1379bc21768c98a2c52b0724e | MATLAB | 744 | 27 | function [ output_args ] = ciftisavereset(cifti,filename,caret7command)
%Save a CIFTI file as a GIFTI external binary and then convert it to CIFTI
tic
save(cifti,[filename '.gii'],'ExternalFileBinary')
toc
%unix(['/media/1TB/matlabsharedcode/ciftiunclean.sh ' filename '.gii ' filename '_.gii']);
%unix(['mv ' filenam... |
818663056803e9653c9c0a3a6094c681dafb68996a183928c62dac6e67a0fd00 | MATLAB | 746 | 23 | function arr = read_array(socket, type)
switch type
case 'complex64'
arr = read_complex_array(socket, 'single');
case 'complex128'
arr = read_complex_array(socket, 'double');
otherwise
arr = read_simple_array(socket, type);
end
end
function arr = read... |
c8458ada918b55868ade8586cdec24568cb392e045e1e546d59700b6e0d9df79 | MATLAB | 747 | 22 | function cbresize(axisHandle, cbarHandle, widthScale, heightScale)
axisPos = get(axisHandle, 'Position');
cbarPos = get(cbarHandle, 'Position');
newPos = cbarPos .* [1 1 widthScale heightScale];
deltaPos = newPos - cbarPos;
switch get(cbarHandle, 'Location')
case 'north... |
ec4f1109efc11e63cdc805e8e48f34a28d7b4711d6a0c17fa1bc6717546ad4f4 | MATLAB | 747 | 24 | function SN = rotateSpatialMaps(SN)
% SN = rotateSpatialMaps(SN)
%
% Code to rotate spatial maps to beter align or visualize them.
%
% 2019 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Rotate all the spatial maps
if iscell(SN)
for ll = 1:numel(SN)
SN{ll} =... |
8f79463ff1d0e810c2f5f3987efe955aa805f7ca2e3ae92e9b1fea07a2fd3e5d | MATLAB | 748 | 29 | %
%reads the raw timestamps from a neuralynx CSC file.
%
%urut/april04
function [timestamps,nrBlocks,nrSamples,sampleFreq,isContinous,headerInfo] = getRawCSCTimestamps( filename )
disp(['reading ' filename]);
isContinous=false;
FieldSelection(1) = 1;%timestamps
FieldSelection(2) = 0;
FieldSelection(3) = 1;... |
9a7ffbec51b628255d8df58d14a732e5e381ac17686ad153d147a4cbdbd4aae4 | MATLAB | 748 | 19 | clear, clc, close all
wlen = 32; % window length (recomended to be power of 2)
h = wlen/4; % hop size (recomended to be power of 2)
k = 5*wlen; % overlap-add span
win = hamming(wlen, 'periodic'); % window
s = zeros(k, 1);
for k = 0:h:k-wl... |
b0e53c33050e2e0f2485a0a03808e6825b3f5541d1c57e4d17152622268d0f31 | MATLAB | 751 | 31 | %%
function [p, s] = demo4plots()
close all ;
[p,s]=makePanels(4,'hi','hohohoho','LegendColumn',10,'TwoSided',true);
selectPanel(p,1,s);
draw([1:10; 2:11; 5:14]*10, 'ValueRange', [0,80]);
xlabel('xxxxx_{xxx}');
ylabel('yyy_{yyyy}');
title('hello cruel world');
selectPanel(p,2,s);
... |
dc18188b13c6725128e9180ba0809ba82ecac02e057f3ef25079dd7bb76e81f7 | MATLAB | 751 | 25 | function subj_list = CBIG_SPGrad_read_sub_list(subject_text_list)
% this function will output a 1xN cell where N is the number of
% subjects in the text_list, each subject will be represented by one
% line in the text file
% NOTE: multiple runs of the same subject will still stay on the same
% line
% Each cell will co... |
e3dd724d7e0d2096a08e0c21d67f06b88a7480a32b91f8aaa632284cd7acc7c1 | MATLAB | 751 | 21 | function [MI, rows] = getMI(values1, values2)
% by Mattia, 09/20
% simple helper function to compute modulation index (normalize "paired" values in the -1 to 1 range)
% inputs: - values1 & 2 -> vector with values to use to compute MI
% output: modulation index for the given values
% important: - if the inputs take neg... |
9f33831816b35488ea9d8cba205970b61d16c6fc40ad052fd333e8d54aff7c02 | MATLAB | 752 | 31 | function isdir_or_mkdir(p)
% ISDIR_OR_MKDIR Checks that a directory exists, or if not, creates the directory and
% all its parent directories.
%
% See also FOPEN_OR_ERROR
if~isfolder(p)
ft_notice('creating directory %s', p);
mkdir(p);
end
% add trailing file separator (slash or backslash)
p = char(p);
p_full... |
65a35169cdee3f25bba4947d687279e327d236c274f64aa84352de66eaa14b1a | MATLAB | 753 | 22 | %% function to decide whether cell's HD and spatial tuning is at the same reward location
function IsMisMatchTuning = GetHDSpatialRewardTuning(All_d)
IsMisMatchTuning = nan(length(All_d.HasRewardField),2);
for i = 1:length(All_d.HasRewardField)
if ~isnan(All_d.HasRewardField(i))
HD_rew = All_d.Re... |
f27e780a0770dd4fc38fe0557a9066f2d404bbe95cecb0420db7cce60e3f4780 | MATLAB | 755 | 24 | function CBIG_shiftimdim(input_file, output_file, shiftdim1, shiftdim2, shiftdim3)
% Circle shift a 3D nifti file.
%
% CBIG_shiftimdim(input_file, output_file, shiftdim1, shiftdim2, shiftdim3)
% Input:
% input_file : input file
% output_file : output file
% shiftdim1 : shift number in dimensi... |
a95227d491e9bcb4837490cf60454dd748c76d1197a3af41474149e66a5d78bf | MATLAB | 756 | 36 | %
% parProgressTracker(mode, num)
%
% Description:
% Track progress for parallel loop
%
% Input:
% mode - 's' - start, 'p' - progress or 'e' - end
% num - total number of iterations, only needed for mode 's'
%
% Output:
%
% Copyright:
% 2016-2018 (c) USC Biomedical Imaging Group (BigLab)
% Author:
%... |
8965967a58cdc8bb9ce4c686ea2535eebbb5b1fb6ef4761606e57e2894d8fcc2 | MATLAB | 757 | 33 | disp('test example for nt_zapline()');
disp('MEG, epoched data');
clear
fname='../data/example4/data3.mat';
% check for NoiseTools
try, nt_greetings; catch, disp('You must download NoiseNools from http://audition.ens.fr/adc/NoiseTools/'); return; end
% check for data
if ~exist(fname, 'file');
disp([fname, ' not ... |
d89f1f8321dbe5ec3dbf4ad4f4a7d84dc6cad7e4e4beb7691eca330dd67b303c | MATLAB | 759 | 28 | % Like image(), except with nonuniform grid spacing
function [handle, x, y] = imagexy(axs, x, y, C, varargin)
%% Default arguments
if isnumeric(axs) && ~ishghandle(axs)
%% Allow for non-specification of the axis to draw in
C = varargin{1};
varargin(1) = [];
y = ... |
2ba3fac1689406bd612e94e477b1e0015ff32d1e3d60b48fefa84df3e734b72f | MATLAB | 760 | 24 |
path_in = 'D:\Datasets\Test\sample10_128\';
path_out = 'D:\Datasets\Test\sample10_128_scale_ver\';
fname = 'mnist_0_scale16_0001.aedat';
[allAddr,allTs,ISI,monTime] = loadaerdat(fname, path_in);
for th = 50:5:100
for scale = 1:10
disp(['th = ' int2str(th) ', scale = ' int2str(scale)]);
... |
1eb7c4cd426ef1185a827f322e195ad5d13df7d40980af74dbee9c69a7cab579 | MATLAB | 761 | 24 | % Returns a list of linear indices for the k-th diagonal elements of A. Slices (3rd and higher
% dimensions) are included by concatenating the indices for diagonal elements of each slice of A.
function indices = diagIndex(A, k)
if nargin < 2 || isempty(k)
k = 0;
end
%% Ensure that we have a s... |
70283f51d9d1d0923c593f6b0357e2e01f014b65fff120ae6720dc04c238e495 | MATLAB | 764 | 33 | function z = nvi(x, y)
% Compute normalized variation information z=(1-I(x,y)/H(x,y)) of two discrete variables x and y.
% Input:
% x, y: two integer vector of the same length
% Output:
% z: normalized variation information z=(1-I(x,y)/H(x,y))
% Written by Mo Chen (sth4nth@gmail.com).
assert(numel(x) == numel(y));... |
97111d1bd9659713d55cb52d96dc90baa2f3482fe4c0e53d62eee1e68b84c5d6 | MATLAB | 765 | 25 | %%
% Expands the given range by the requested left/right scale factor.
%
function [range] = expandrange(range, dim, leftScale, rightScale)
%----- Parse input
narginchk(3, 4);
if nargin < 4
rightScale = leftScale / 2;
leftScale = leftScale / 2;
end
if size(range, dim) ~= 2
er... |
05cc6bac32cc4c04aa761938ee597d78b8a9963ecaca7c8b2df6495a469bf807 | MATLAB | 766 | 28 | function [B_boot, r_boot] = performRegression_kfold(X, y, n_folds, random_seed)
% ---- 10-fold cross-validation ----
%n_folds = 10;
rng(random_seed);
cvp = cvpartition(size(X,1), 'KFold', n_folds);
y_pred = nan(size(y));
r_boot = zeros(n_folds, 1);
for f = 1:n_folds
train_idx = tr... |
cd1e5df5bfaabbd66e524e3cdc697ba803d9f70d702fa534ca6388956e8d7bff | MATLAB | 767 | 21 | function corr_mat = CBIG_corr(s_series, t_series)
% Calculate correlation matrix between each column of two matrix.
%
% corr_mat = CBIG_corr(s_series, t_series)
% Input:
% s_series: T x N1 matrix, T is number of frames, N1 number of voxels
% t_series: T x N2 matrix, T is number of frames, N2 n... |
8bde8c88c7d81aeed0e65ff556298801fcb72280a4d2837d12239e2931217660 | MATLAB | 768 | 34 | % Toggles logarithmic scale on the given axes (y by default, otherwise specify xy = 'x' or xy = 'xy')
function logscale(xy, axs, force)
%% Default arguments
if nargin < 1 || isempty(xy)
xy = 'y';
end
if nargin < 2 || isempty(axs)
axs = curraxes;
end
if nargin < 3
force = [];
... |
0ae1229575d3365931889590ed0c7ace28cf5055010c97d074301d88b9a14b7c | MATLAB | 769 | 27 | function generateVolGOrdfMRI(GOrdVolIndFile,subbasename,fmri,GOrdVolFile)
load(GOrdVolIndFile);
invmap=load_nii_BIG_Lab([subbasename,'.svreg.inv.map.nii.gz']);
invmapx=invmap.img(:,:,:,1);
invmapy=invmap.img(:,:,:,2);
invmapz=invmap.img(:,:,:,3);
ind=~isnan(bci_vol_ind);
t1=load_nii_BIG_Lab([subbasename,'.bfc.nii.g... |
3327db255e2c79550d0e294758dd4e221bba4f073872cfa8aff26e9d56da231d | MATLAB | 770 | 42 | function [res,resd] = bpassW(arr,lnoise,lobject)
%
% bandpass filter.
%
% Written by Pei-Hsun Wu,
% Post-doc associate, @ JHU, IMBT.
%
% PW 211016,, imfilter --> use symmetric
% PW 240101 , suposition at filter level., reduce the costly imfilter step
arr=double(arr); % make sure this is double
b = double(... |
afa241619b4ab51c29143c2612eeaa8f13f5eb23e2f4cc5dd2261b559f90074a | MATLAB | 770 | 31 | function CBIG_DilateMask(input_file, output_file, dist, exit_flag)
% Dilate a binary mask.
%
% CBIG_DilateMask(input_file, output_file, dist, exit_flag)
% Input:
% input_file : input binary mask
% output_file : output file name
% dist : threshold for Euclidean distance aft... |
195971dc5f076374c224231f63dc02a83a76171969e60aa916334f8624356ee3 | MATLAB | 773 | 25 | function RGB = gmcmyk2rgb(CMYK)
% RGB = GMCMYK2RGB(CMYK)
% Convert a CMYK image to RGB.
% Note that this is in no way intended for print preparation.
% No profiles are used. This is a direct replication of the
% method used by GMIC cmyk2rgb -- specifically for the purpose
% of replicating GMIC code that depende... |
61b5ea1a63cc2ed7fc95148a7908a40db3d5b9f5b69482b1072d73a5a795562f | MATLAB | 773 | 32 | disp('test example for nt_zapline()');
disp('MEG data with large near-DC fluctuations');
clear
fname='../data/example3/data1.mat';
% check for NoiseTools
try, nt_greetings; catch, disp('You must download NoiseNools from http://audition.ens.fr/adc/NoiseTools/'); return; end
% check for data
if ~exist(fname, 'file');
... |
fd0425f998a5fd72e6c26a1274e20a950f98a1ab3c5e3f397c8401cae823898f | MATLAB | 773 | 28 | %%
% Fast computation of atan(x) via look-up table.
function [f] = fastatan(x)
persistent FASTATAN_lookup_table;
if isempty(FASTATAN_lookup_table)
FASTATAN_lookup_table = arrayfun(@atan, 0:0.01:3);
end
if x < 0
f = fastatan(-x);
elseif x > 9
f = pi/2 - 1/x;
elseif x >... |
060c257e9e92b2efc1d6f128a9157c3e4b07d1b6732cec7fc146287a12a65cc2 | MATLAB | 776 | 18 |
function simple_recon(connection)
disp("Matlab reconstruction running.")
next = gadgetron.examples.steps.noise_adjust(@connection.next, connection.header);
next = gadgetron.examples.steps.remove_oversampling(next, connection.header);
next = gadgetron.examples.steps.accumulate_slice(next, connect... |
7803cfea443f4645099f6a184283234df71a696b02cbfeee6fa90937e35c63b8 | MATLAB | 778 | 27 | function icc = CBIG_fisher_icc(data1, data2)
% icc = CBIG_fisher_icc(data1, data2)
% Compute fisher's intraclass correlation between two vectors.(This function will exclude NAN)
%
% cc = CBIG_fisher_icc(data1, data2)
% Input:
% data1: N x 1 vector
% data2: N x 1 vector
% Output:
% icc : 1 x 1... |
e8f469d990b33b7f15f3add8f7b70d16b156731fade9336904f552c6d8b04c3f | MATLAB | 778 | 26 | function [header, ext, filetype, machine] = load_untouch_header_only_gz( file )
% wrapper around load_untouch_header_only to work with .gz files.
%
% 1. Extracts GNU zip files, if file is zipped.
% 2. Loads the data & returns it.
% 3. Deletes the unzipped file, if file is zipped.
%
% file - is a string with rel... |
0dc646d25bec6668911d042a21ae15e009065100d3f32933fad476246cd0d4ac | MATLAB | 779 | 25 |
function main()
% Workaround for occasional blank windows when Matlab run as root (as in container)
% https://uk.mathworks.com/support/bugreports/details/2794932
% Fixed in Matlab R2023a
setenv('MW_CEF_STARTUP_OPTIONS', '--in-process-gpu');
port = getenv('GADGETRON_EXTERNAL_PORT');
module... |
a258abc47e51a75321914f5305583dc491eee303098bcd0a1f4da147d7754cb2 | MATLAB | 779 | 23 | function CBIG_AnalyzeDirectAndIndirectCorrespondence
% CBIG_AnalyzeDirectAndIndirectCorrespondence
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
load lh.1000sub.FSL_MNI.ras.mat
indirect_ras = ras;
load lh.FSL_MNI.DIRECT.ras.mat
direct_ras = ras;
tmp = sqrt(sum((dir... |
ce86c65128b284f5a01af77371bfcf9767fb5171298561bd3aa36f90609bdd9c | MATLAB | 780 | 24 |
clear, clc, close all
%% Using CEC2005 for testing
Func_name = “F4”; % Test function name, can be modified to: F1-F23
[lb, ub, dim, fobj] = Get_CEC2005_details(Func_name); % Retrieve function variable upper/lower bounds, dimension, objective function handle
pop = 50; % Population size
maxIter = 600; % Maximum iterati... |
3558720d076dbbe28c881c20aa4495dff678c75adc4f3a9fa865d1dee28cd194 | MATLAB | 783 | 34 | function [cell_array, num_lines] = CBIG_text2cell(text_file)
% [cell_array, num_lines] = CBIG_text2cell(text_file)
%
% This function reads from "text_file" and return the content of each line
% to be an entry of "cell_array".
%
% Inputs:
% - text_file
% The input text file.
%
% Outputs:
% - cell_array
% ... |
64b2adc8a7f9c5700c1136e6d08fe5bf8e0f6e9d2caf9914f56ae17d03e57bef | MATLAB | 784 | 24 | %% from: https://fr.mathworks.com/matlabcentral/answers/444501-how-to-use-intersect-command-with-a-tolerance-value
function [AI, BI] = CommonElemTol(A, B, Tol)
A = A(:);
B = B(:);
nA = numel(A);
M = zeros(1, nA);
% Collect the index of the first occurrence in B for every A:
for iA = 1:nA
... |
0e85fd0320e9b1fb37805fd3f14cb66fc9ba1c8b9c91e08cb8778713e7b2f2a6 | MATLAB | 785 | 24 | function thisrange = imclassrange(classname)
% RANGE = IMCLASSRANGE(CLASSNAME)
% Get the nominal data range expected of a given image class
%
% CLASSNAME is a string/char specifying the class in question
% Supports: 'single','double','logical','uint8','int8','uint16','int16'
% 'uint32','int32','uint6... |
e7bf5ddafe1d3623c0cc1ed77addfc47b392a9aa99cf28ae0252aee86c38e5a5 | MATLAB | 787 | 31 | disp('test example for nt_zapline()');
disp('MEG, 5 line noise components');
clear
fname='../data/example6/fig_9_data.mat';
% check for NoiseTools
try, nt_greetings; catch, disp('You must download NoiseNools from http://audition.ens.fr/adc/NoiseTools/'); return; end
% check for data
if ~exist(fname, 'file');
dis... |
37b2dacab3eb166f9761a87667f711ed05fe9bd1703ae6c25fdddf7490388924 | MATLAB | 789 | 30 | disp('test example for nt_zapline()');
disp('FieldTrip example data: Monkey ECoG');
clear
fname='../DATA/example1/data.mat';
% check for NoiseTools
try, nt_greetings; catch, disp('You must download NoiseNools from http://audition.ens.fr/adc/NoiseTools/'); return; end
% check for data
if ~exist(fname, 'file');
di... |
557060c5764e68d3203b5dc2a3c1028beaaff60b4a1c08b5dc8b403216332a6d | MATLAB | 789 | 19 | function [MuseStruct_updated] = updateMarkers(cfg, MuseStruct_updated, labels)
% 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)
for label = string(l... |
85a2603da2342d3c22fe9d201c8f6f5ba89a6c9827d29321c1bef084a2b38905 | MATLAB | 789 | 34 | function varargout = aa_splot(varargin)
%AA_SPLOT replaces plot command and automatically changes color
%
% This function is a replacement for the plot command.
% It automatically changes the color with subsequent
% uses of aa_splot.
%
% Usage is exactly the same as for plot.
np = get(gca,'nextplo... |
6e3e1b6068b9813d36fa007f28306c539e6a3d7c6a87a837395bfb187eaf08b8 | MATLAB | 790 | 38 | %% function to plot place map and clustered fields
function PlotFieldClusters(I, clusters, cluster_Method, gm)
figure
tiledlayout("flow")
nexttile;
h= imagesc(I);
axis square
set(h, "AlphaData", ~isnan(I))
box off
axis off
if cluster_Method == "GMM"
[r,c]... |
f2a7e78c52d04206f89612894038f1943e1f2a53af829fffc50a1d093ab723ea | MATLAB | 795 | 31 | function [data, offset, scale] = normalizeToRange(data, range, minData, maxData, capToRange)
%% Default arguments
if nargin < 2 || isempty(range)
range = [0 1];
end
if nargin < 3 || isempty(minData)
minData = min(data(:));
end
if nargin < 4 || isempty(maxData)
maxData ... |
3ca49551cb3731f912dc7bd8c94a29b8c642136d8d9f689ac90e49dac9814c9b | MATLAB | 802 | 34 | function unitaxes(hax)
% UNITAXES({AXESHANDLE})
% Simple convenience tool to set up an axes on the unit square.
%
if nargin<1
hax = gca;
end
hstate = get(hax,'nextplot');
hold(hax,'on')
gc = [1 1 1]*0.8;
hp(1) = plot(hax,[0 1],[0 1],'-','color',gc);
hp(2) = plot(hax,[0 1],[1 0],'-','color',gc);
hp(3) = pl... |
a0710e7463a1c1259618a7b21a696d2295ab5ada8ac362ad1b875919ab188102 | MATLAB | 802 | 20 | function disp_text(window, text, textcolour, backcolour, rect)
%Setup boundary defaults
if ~exist('rect', 'var')
rect=Screen('Rect',0); % Window-coordinates, e.g. [0 0 1024 768]
end
%Get centre of writing area
xcenter=round((rect(1)+rect(3))/2);
ycenter=round((rect(2)+rect(4))/2);
%Measur... |
f93873cb9368264b3442923293ad746b717a9ab9872c75f3e00305e6631722d5 | MATLAB | 803 | 25 | % Check correspondence between images in items_classification.mat
% and data_evaluation.mat
addpath(genpath('..'));
fprintf(1,'Loading dataset...\n');
load('data_evaluation','drawings','images','names','timing');
load('items_classification','nrun','ntrain','ntest','cell_train','cell_test','cell_Y');
D = Dataset(draw... |
bdd80eba7a69a3973173933cd34c8ce2418eef404aaa126e1297c0d5a1f34d78 | MATLAB | 805 | 56 | clearvars;clc;
% Define parameters for the coupled model
% KNDy parameters
par.d1=0.2;
par.d2=1;
par.d3=10;
par.k1=4;
par.k2=40;
par.k01=0;
par.k02=0;
par.pr=0.008;
par.v0=25000;
par.KD=0.3;
par.KN=4;
par.Kr1=600;
par.Kr2=200;
par.theta=0.5;
par.k=10;
par.je=1;
par.I0=0.19;
% MePD parameters
n=3;
par.dl= n;
par.di= n... |
370ac662be2e1d8012b864e1e26f1539198728e1cf5de3cf6c3512da2ef45dcf | MATLAB | 806 | 22 | %% Creates a struct with fields corresponding to public properties of the given class object.
function s = class2structure(c, varargin)
s = struct();
members = metaclass(c);
members = members.PropertyList;
% Apply selection criteria if so provided
isSelected = strc... |
23f7a1c257e9ce75901e029f1f98161a607441abf379fbf72a8578e88b27d88e | MATLAB | 808 | 29 | function varargout=nt_whoss
%size=nt_whoss - total Gbytes used by variables
%
% size: number of Gbytes
%
% If nargout==0, display Gbytes used
s=evalin('caller', 'whos'); % lists variables in caller's workspace
x=cell(1,numel(s));
[x{:}]=deal(s.bytes); % transfer to cell array
size=sum(cat(1,x{:})); ... |
be148519c3cec8fbb40d65d3f5bc50b0da6e4a5fb5d87a36017e61f46c7c243f | MATLAB | 808 | 30 | %% Colorbar title
function [handle] = cbtitle(handle, label, varargin)
%---- Get the colorbar
narginchk(1, inf);
if nargin < 2
label = handle;
handle = cbhandle();
end
%---- Set title
hTitle = get(handle, 'Title');
origUnits = get(hTitle, 'Units');
set(hTitle, 'Units', '... |
128393b5251b3d97314cfebe669190b799b2ea324490a3f5653df7884fc789ea | MATLAB | 809 | 29 | %% RENAMEFIELD Replace field name(s) old with the corresponding name in new.
function s = renamefield(s, old, new, useRegexp)
if nargin > 3 && useRegexp
%% Regular expression replacement
new = regexprep(fieldnames(s), old, new);
old = fieldnames(s);
end
%% Multi- or s... |
61427030b2640925a834de4a70da8abc5f633c6328bd00f412f151837ce28441 | MATLAB | 811 | 26 | clear all;close all;clc;
restoredefaultpath;
addpath(genpath('/ImagePTE1/ajoshi/code_farm/svreg/src'));
addpath(genpath('/ImagePTE1/ajoshi/code_farm/svreg/3rdParty'));
load('../supp_data/USCBrain_grayordinate_labels.mat');
roilist=[1147,225, 373,247];%, 345,351];
s{1}=readdfs('../supp_data/bci32kleft.dfs');
%s{2}=re... |
398f4636ac30a5e2618470e81fc13c4f05d0384c8243032a49387f1e68ad0de6 | MATLAB | 814 | 28 | function PRB2folder(probetype, folder2save)
% by Mattia. moves the PRB file in the same file in which the .DAT file
% will be created
% INPUT:
% probetype - as a string. obviously need to add other probes here
% folder2save - string, where you also save the .DAT file
% the "PRBfolder" in which you have ... |
c65113477164fd919794fb8cdc38e8da3c904cc4b3ebbd50f972885c9bde768d | MATLAB | 814 | 32 | % Faster version of histcounts().
function [N, edges, bin] = histcountsFast(X, edges, includeOverflow, normalize)
if nargin < 3 || isempty(includeOverflow)
includeOverflow = false;
end
if nargin < 4 || isempty(normalize)
normalize = false;
end
%% Locate the bin in which t... |
03d2b21bc0db75486df096b7adf30b5fd51396f08b76d6a14617802f13da1a52 | MATLAB | 815 | 28 | classdef PairDataGenerationOptions
properties
NoiseLevel double {mustBeNonnegative}
DataType string % "PC" or "gene"
DataDimension double {mustBePositive}
RngSeed {mustBeInteger}
end
methods
function obj = PairDataGenerationOptions(noiseLevel,dataType,dataDimension,... |
4fada4683f86713ae9f4306106c0f56d2c15c19c70c45968ad96465b1a84bada | MATLAB | 815 | 24 | function cmap = fscol(res)
%
% cmap = fscol([res=360])
%
% Returns the FreeSurfer colour map (like MatLab colour maps) with the
% resolution res, which must be a multiple of 4. By default res is 360.
if nargin == 0
res = 360; % steps from one colour to the next
end
steps = res / 4;
% Colour peaks
R = [1 0 0];
... |
db7a8f537715736444455ffdb3b87bba14a7c9e00b4dadd261300b829be5af8f | MATLAB | 815 | 28 | function [divided_data] = seperate_sequences(sequence, sequence_length)
%% Seperates input data into multiple sequences of a chosen length
%
% **Usage:** [divided_phone] = seperate_sequences(sequence, sequence_length)
%
% Input(s):
% - sequence = data to be seperated into sequences (BS or Phone data)
% - sequence_l... |
a8a6fad311eb64e670b62af4e399a60acf6f9aecd19f4902fb2134b1474861a3 | MATLAB | 816 | 9 | function [mask, cluster_p, one_sample] = run_clustering_linear(LIMO_paths, significance_threshold, channeighbstructmat)
for current_beta = size(LIMO_paths, 2):-1:1
one_sample_tmp = load(fullfile(LIMO_paths{current_beta}, sprintf('one_sample_ttest_parameter_%d.mat', current_beta)), 'one_sample');
one... |
ed57698ddf5da8f9adf8897a81357640542ee1b54cee9414db948a308a9177fc | MATLAB | 818 | 23 | function data = cifftn(data, dims)
% The following code uses less peak memory and is much faster than
% gadgetron.lib.fft.cifft
% ifind "inverse find" - e.g. ifind([2:3 5], 6) -> [0 1 1 0 1 0]
% Ref: https://uk.mathworks.com/matlabcentral/answers/385217-bed-of-nails-from-vectors-inverse-of-find
ifind = @(indices, le... |
f799992ec20b0c9143e0c3e3414599f318811e6533e49179ac64d7278cbbebd8 | MATLAB | 818 | 29 |
function sock = listen(port)
server = java.net.ServerSocket(port);
server.setReuseAddress(true);
server.setSoTimeout(1000);
cleanup = onCleanup(@() server.close());
% Accept would block forever in previous versions, leaving Matlab
% unresponsive (process was blocked, so Ctrl+C was ignore... |
a48506e9be47af1f17aef7ef201864a06e29b74da2fe342d3eb1d54110ade04c | MATLAB | 822 | 28 | function CMYK = gmrgb2cmyk(RGB)
% CMYK = GMRGB2CMYK(RGB)
% Convert an RGB image to CMYK.
% Note that this is in no way intended for print preparation.
% No profiles are used. This is a direct replication of the
% method used by GMIC rgb2cmyk -- specifically for the purpose
% of replicating GMIC code that depend... |
00f51d0e39898eae389b6618b31c2c7c71fd2f921c430fa787c3cf126760e80c | MATLAB | 823 | 38 | function [biom_ch] = find_channel_img_SAP(biom, biom_set_folder)
%% Find image based on biomarker
% @author: speressotti
%%
if biom_set_folder == 'B1'
channel_order = {'hoechst','sox2','btub','gfap'}
if contains(fname,'hoechst')
biom_ch = 1;
elseif contains(fname, 'gf... |
05f5202713dd645870ae065c1de503cf4fd66381604227b7b17c96491b12c6be | MATLAB | 823 | 26 | function rename_add_suffix(path, suffix)
%% Rename LIMO saved files by adding suffix
%
% **Usage:** rename_add_suffix(path, action, suffix)
%
% Input(s):
% - path = path to saved LIMO file
% - suffix = suffix to add behind file name
%
% Author: R.M.D. Kock, Leiden University
%%
x = split(genpath(path),':');
for f... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.