sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
959e17ae256cfc99951531348f3f23dd75388964e0b227951688d00f38038645 | MATLAB | 2,819 | 82 | % UNIQUEF: Given a matrix containing group labels, returns a vector containing
% a list of unique group labels, in the sequence found, and a
% vector of corresponding frequencies of each group.
% Optionally sorts the indices into ascending sequence.
%
% Note: it might be necessary to... |
05855b0ce681b26e625bb9fe4dd4520849c35065f4e9c83c620bd201f2e70048 | MATLAB | 2,820 | 71 | function x = RemoveJumpsAndSmooth(x, max_allowed_flips, jitter_threshold, smooth_std,filter_def)
% Removes large jumps in data, smoothes the removed regions
% ARGUMENTS
% x a vector of something. NaNs may be used in place of
% known bad samples
% max_allowed_fl... |
609aa12e1def13a08e9d10ff60cd97f6a5e313fdc4ad2b8876a5da30db99f076 | MATLAB | 2,820 | 70 | function java_dnd(jObj, dropFcn)
% Set Matlab dropFcn for java object, like JavaFrame or JTextField.
% 170421 Xiangrui Li adapted from dndcontrol class by Maarten van der Seijs:
% https://www.mathworks.com/matlabcentral/fileexchange/53511
% Required: MLDropTarget.class under the same folder
if ~exist('MLDrop... |
ea44666cc7d42f95b33e371f40b81e2e626783ff9ef83cf7f541a163f8a5776a | MATLAB | 2,820 | 85 | % eeg_retrieve() - Retrieve an EEG dataset from the variable
% containing all datasets (standard: ALLEEG).
%
% Usage: >> EEG = eeg_retrieve( ALLEEG, index );
%
% Inputs:
% ALLEEG - variable containing all datasets
% index - index of the dataset to retrieve
%
% Outputs:
% EEG - out... |
254193fe9610fb53ea98be6ec00ffee3f8a3dde5a47b73829d3edb8425fba84e | MATLAB | 2,824 | 110 | function[N,B,E] = isi(data,T,err,Nbins,plt)
% Calculate the inter-spike-interval histogram
% Usage: [N,B,E] = isi(data,T,err,Nbins,plt)
%
% Input:
% Note that all times have to be consistent.
%
% data - structure array of spike tim... |
29e202019f87f25ae85f095ba2181e9590aeb887fdbb4b91c89cefcd2cb8ccb2 | MATLAB | 2,824 | 94 |
function updateExpFolder(inputFolder, outputFolder)
% Update experiment folder from Recording computer to Analysis computer
%
% USAGE
% updateExpFolder(inputFolder, outputFoder)
%
% INPUT
% inputFolder Experiment folder in recording computer, can be
% multiple folders
% outputFolder ... |
a57a2d795a340ec24c127b4bd6164c385c5826deeefb6999254e6ed5fb09ab45 | MATLAB | 2,824 | 63 | function index_changes = CBIG_gwMRF_save_index_trans_btwn2versions(new_dir)
% index_changes = CBIG_gwMRF_save_index_trans_btwn2versions(new_dir)
%
% This function generates a cell array to save the index changes for all
% Schaefer2018 parcellations.
%
% Input:
% -new_dir:
% Path of the new parcellation fol... |
0adf9ef3ea8732a7043d50e125219a2b18c3b2a80849413751cdafd977c0c443 | MATLAB | 2,825 | 79 | function setTightInset(ax, targetWH, anchorXY)
% Set axis Position so its full footprint matches a target size.
%
% This function adjusts ax.Position so that the *total footprint* occupied by
% the axes INCLUDING tick labels, axis labels, and title matches a specified
% width/height. It uses ax.TightInset (the extra sp... |
0f62728d99a04ff8ab2a42bbfe180131524fab526100b1dcb0f3aa2e77d07cf0 | MATLAB | 2,825 | 73 | function [all_erp_all_midi] = Trinh_MiniTrialMaker(data,midi_names,code_corresponding_to_midi,n_offsets,prestim)
%
% midi_names = cell with strings containing the names of the files of
% interest
% code_corresponding_to_midi = trigger codes, present in the FieldTrip
% data structure, associated to the midi_names (... |
1b2776210db7aaec8db757ad0ed190b24a58cff1123d829ba81c57984dcdfa42 | MATLAB | 2,825 | 54 | function obj = set_layout_options( obj , varargin )
% set_layout_options Change figure layout options
%
% 'name',value pairs:
% 'position': specify the position of the gramm plot in the figure, using
% normalized coordinates (between 0 and 1) [left bottom width height]
% Defaul... |
f7bf4a1b02798f81507ce3c1af4690e2e9843a100083eabda7a64cf9d31af269 | MATLAB | 2,825 | 92 | function [occupancy, xdim, ydim, pos_locs] = sOccupancy(self, xdim, ydim, mergeepochs, dim)
% Spatially scaled occupancy map
%
% Returns occupancy matrix of time spent in bins of dimension 3x3cm^2 be
% default. occupancy = root.Occupancy(xdim, ydim) where will return a matrix of
% dimensions xdim by ydim(:,2)
%
% Remem... |
796cb02826bdfc4024102ad21a9bb41923b9ee414510487f2f775a54096b31f4 | MATLAB | 2,827 | 87 | function AUC = ea_logit_regression(Ihat_train, Ihat, Improvement, training, test)
% Fit logit model, compute ROC and find the optimal threshold.
% Compute confustion matrix for the test set (can be the same as training)
% if Ihat_train was not provided, then we have in-sample analysis
if Ihat_train == 0
Ihat_trai... |
ffbd8cd52d15c8523f88c177ec4d59d46dd01242ab29cf4081a8a55420924223 | MATLAB | 2,827 | 86 | function c = ea_colorlover(n,plot)
% Version 2.0
% c = colorlover(palette_number,plot);
% c is a matrix with 5 colors in matlab color codes
% e.g. plot(x,y,'color',c(1,:)) will plot in color 1 from the matrix
% if n is empty a random palette will be chosen
if ~exist('plot','var')
plot = 0;
end
if ~exist('n','var... |
32f7e39802323bcc73dea69cda60f937b16b06e08854271153acbdc05c692023 | MATLAB | 2,828 | 103 | function [rescaled_mat, rescale_range] = G_Rescale( mat, rescale_range, varargin)
% Re-scale a mtrix to a new range
%
% Input
% mat, matrix to rescale
% rescale_range, [lo_boundary, hi_boundary] range the input will be re-scaled to
% varargin{1}, margin in percentage [0, 0.5)
%
% modified from http://stackoverf... |
7bf251a1bc7497e717b3496f89537241775107256613ff63167401e66ba1d816 | MATLAB | 2,828 | 68 | function obj=facet_grid(obj,row,col,varargin)
% facet_grid Create subplots according to factors for rows and columns
%
% Example syntax (default arguments): gramm_object.facet_grid(row_variable_column_variable,'scale','fixed')
% This function has two mandatory arguments: the variable used
% to separate data by rows of ... |
b19c1c90ed3ffda7a42c3e93cefab665f7a351481cd229990839fa33e37218ce | MATLAB | 2,828 | 77 | function [node,elem,face]=cgals2m(v,f,opt,maxvol,varargin)
%
% [node,elem,face]=cgals2m(v,f,opt,maxvol)
%
% wrapper for CGAL 3D mesher (CGAL 3.5 and newer)
% convert a triangular surface to tetrahedral mesh
%
% http://www.cgal.org/Manual/3.5/doc_html/cgal_manual/Mesh_3/Chapter_main.html
%
% author: Qianqian Fang (fangq... |
e88073367924c7dbd02350e933d61867de00b05ef9081cbde85570f6e2e36cc1 | MATLAB | 2,828 | 83 | function [mask,Xdiff]=plotsigdiff(X1,X1err,X2,X2err,plt,t,f)
% Function to plot significant differences between two time-frequency arrays X1 and X2
% given errors X1err, X2err.
% Usage: mask=plotsigdiff(X1,X1err,X2,X2err,plt,t,f)
%
% X1 err and X2err contain upper and lower confidence intervals for X1 and X2
% The plo... |
ad729a905cdcc812998235f8c89bcf7c284515abbf863eb297b45f2bd4981db3 | MATLAB | 2,829 | 82 | function [concentrations, factor] = calcConcentrations(T,data_counts,BMD,intervene_matrix,numReplicates,keep_species)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologic... |
6fd4bbde9d9c413a6bb622ccf71d52cd21e244cc58adbe4ae08ec38840369f50 | MATLAB | 2,831 | 91 | function [a,succ] = palm_nextperm(a)
% Given a sequence of integers "a", returns the next lexicographic
% permutation of this sequence. If "a" is already the last possible
% permutation, returns a vector of zeros of size(a).
% Note that to shuffle vectors, they must be supplied as
% column vectors (N by 1).
%
% Usage:... |
7470b701aec88d2ef504d203505d61b410dc7bfa01a385204d4ae1731e9d97b5 | MATLAB | 2,834 | 59 | function Obj = SOFAaddVariable(Obj,Name,Dim,Value)
%SOFAaddVariable
% Obj = SOFAaddVariable(Obj,Name,Dim,Value) adds a user-defined variable
% to the SOFA structure OBJ. NAME must be a string with the variable name
% ('API', 'PRIVATE', or 'GLOBAL' are not allowed). DIM is a string
% describing the dimens... |
b2aefcfd7331f9c0848236feb3d23673fec2dfafa755f8ec3b59038cf0b4742b | MATLAB | 2,834 | 74 | % std_precomp_worker() - allow dispatching ERSP to be computed in parallel
% on a given cluster.
% Usage:
% >> feature = std_precomp_worker(filename, varargin);
%
% Inputs:
% filename - STUDY file name
%
% Optional inputs:
% Optional inputs are the same as for the std_precomp function. No... |
f6844ecc3c24fc33374131093bcf00485d9afa0c161ff206b51386b6b08245c1 | MATLAB | 2,835 | 120 | function testspecgram(data)
%cd 'C:\Documents and Settings\Admin\Desktop\';
%data=wavread('bird109_26519_on_Aug_19_16_33.wav');
params.tapers = [3 5];
params.fpass = [100 20000];
params.Fs = 44100;
params.pad = 2;
max_time =10; % seconds per run
max_tapers = 150;
increment = 1.5;
profile on
nsamples = 1000;
if 1
s... |
788415c5357cd8296b49124e500ecdb5625eeafdca3a5cf31c998b09fc8e6448 | MATLAB | 2,836 | 70 | % Simplified version of flirtmat2worldmat removing the various dependencies
% to SPM. Instead using PaCER's Nifti Classes which in turn rely on the
% Nifti Toolbox. Thus it works with .nii.gz files too and has a lot less
% dependencies in general.
% 2017 Andreas Husch.
%
% Based on flirtmat2worldmat by Ged Rigway. See... |
b35b59385eee1c89956ac7d65f22179980e05081b153184bef77dd96138e4ca9 | MATLAB | 2,836 | 80 | function enigma_scatter(ax, x, y, varargin)
% Usage: enigma_scatter(ax, x, y, varargin)
%
% REQUIRED INPUTS
% ax = figure axis
% x, y = two maps (ndarray)
%
% OPTIONAL INPUTS
% scatter_color = color of data in scatter plot, default is black
% linear_fit = add linear fit on top of scatter, ... |
2bee7c4d0fe284055dd26ea6c99a9b589a335d63885258f5703a034c4263c76a | MATLAB | 2,838 | 70 | function analyzeCalciumExperiment(headpath,fileexpnum,imskip,expskip,correction,fluor,copy,savemode)
%give this function the experimental path you want to start in
%and the filename and experiment number (ie vt019532_f3e4)
%correction if the motion correction needs to be done, fluor if the dff
%hasn't been extracte... |
f5e54f54951fa32ab0622a3e750a4f30fd76e37ab1d810fb730589b24d44fc93 | MATLAB | 2,840 | 89 | function PlotCSD(csd,varargin)
%PlotCSD - Plot current source density.
%
% USAGE
%
% PlotCSD(csd,<options>)
%
% csd current source density (see <a href="matlab:help CSD">CSD</a>)
% <options> optional list of property-value pairs (see table below)
%
% =======================================... |
27a970d2722cf9a25054eaf0063880195bbad5bd9fce83942d8538b0cb3ef250 | MATLAB | 2,842 | 76 | % std_selsubject() - Helper function for std_erpplot(), std_specplot()
% and std_erspplot() to select specific subject when
% plotting channel data.
% Usage:
% >> data = std_selsubject( data, subject, setinds, allsubjects);
%
% Inputs:
% data - [cell array] mean data for each ... |
adbc48259c771f532090e3df8f7c7184067397e0503fa9377437bd9ea0c81958 | MATLAB | 2,842 | 86 | function mov=videoread(fname,varargin)
%VIDEOREAD Read an video file in a mannter compatible with Matlab's
% built-in AVIREAD function, but using a videoReader object to do
% the work instead.
%
% MOV=VIDEOREAD(FNAME)
% Read the video file FNAME into the Matlab movie structure MOV. MOV
... |
bbaf0ec6604c036dee1a8ac764d3f113cf5613023c02df4c07510d737ab0210c | MATLAB | 2,844 | 88 |
function header = constructNPYheader(dataType, shape, varargin)
if ~isempty(varargin)
fortranOrder = varargin{1}; % must be true/false
littleEndian = varargin{2}; % must be true/false
else
fortranOrder = true;
littleEndian = true;
end
dtypesMatlab = {'uint8','uint16','uint32','uint64','int8','int16'... |
df067ae677c0273dcd1fc6b56923f89f9cada86b745d8b0afe76c9ea87780682 | MATLAB | 2,846 | 120 | function y = geo_mean( x, dim, w )
narginchk(1,3);
%GEO_MEAN Internal cvx version.
%
% Size check
%
try
if nargin < 2, dim = []; end
[ x, sx, sy, zx, zy, nx, nv, perm ] = cvx_reduce_size( x, dim ); %#ok
catch exc
rethrow( exc )
end
%
% Third argument check
%
if nargin < 3 || isempty( w ),
w =... |
fffd842ead6405d8f39f50735906f4812ad2c8914fe5956946e30cc704ac694e | MATLAB | 2,846 | 59 | function [param, qMetric, fractionRPVs_allTauR] = loadSavedMetrics(savePath, saveTSV)
% JF, Load saved quality metrics
% ------
% Inputs
% ------
%
% ------
% Outputs
% ------
qMetric = parquetread(fullfile(savePath, 'templates._bc_qMetrics.parquet'));
fractionRPVs_allTauR = parquetread([fullfile(savePath, 'templates.... |
c566fee00e9cf55b1e18de6f400c38caedc883fc9715157aa739b7e2b4866f56 | MATLAB | 2,848 | 84 | function [img, v2smap]=surf2vol(node,face,xi,yi,zi,varargin)
%
% [img, v2smap]=surf2vol(node,face,xi,yi,zi,'options',values,...)
%
% convert a triangular surface to a shell of voxels in a 3D image
%
% author: Qianqian Fang (fangq <at> nmr.mgh.harvard.edu)
%
% input:
% node: node list of the triangular surface, 3 colum... |
f00154440a15af736b7f9e130f38413da99a0554f4075264c6063af0b1b93985 | MATLAB | 2,848 | 77 | % pop_compareerps() - Compare the (ERP) averages of two datasets.
%
% Usage:
% >> pop_compareerps( ALLEEG, datasetlist, chansubset, title);
% Inputs:
% ALLEEG - array of datasets
% datasetlist - list of datasets
% chansubset - vector of channel subset
% title - plot title
%
% Author: Arnaud De... |
11896dbaa7de65ef2aa4c9e2785fb1117a2884e485b70f9501534a967a11da45 | MATLAB | 2,850 | 70 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
4e475a3030c240c55377c8fb212b3e019f95913d985a1f19485c7b58e0fe8d00 | MATLAB | 2,850 | 95 | function y = vsmooth(x,frame,mode)
%VSMOOTH Smooth a vector using mathematical functions
%
% Y = IOSR.DSP.VSMOOTH(X,FRAME) smooths the input vector X by calculating
% the running RMS over a series of frames. FRAME specifies the frame
% characteristics; it can be set to:
%
% a scalar - this will be used ... |
749c42800fb5a623a7d83dfdb1e777a0b4a7ab71b3c90a6a8be49c5158bd1351 | MATLAB | 2,850 | 77 | % getipsph() - Compute "in place" (m by n) sphering or quasi-sphering matrix for an (n by t)
% input data matrix. Quasi-sphering reduces dimensionality of the data, while
% maintaining approximately the "original" positions of the axes. That is,
% quasi-sphering "rotates back" a... |
21e0673d706a8e7482d374365df6bfb1cd92175d87b0add8637ad3265524f8b8 | MATLAB | 2,851 | 111 | function S = ea_cleartune_generateSfile(rightsets,leftsets,S,volcur)
% rightsets - [amplitude;k1, k2, k3,...], e.g. [2.0; 0.0,-100.0,0.0,0.0]
% -cathodic 2 mA stimulation via the second contact
%
% volcur - 1 for voltage-controlled, 2 for current-controlled
rightsets(isnan(rightsets)) = 0;
leftsets(isnan(leftsets)) ... |
33d58d31d1336a7f93f94733a26c48c43ab36e911736ed1ad799f6ab593e8fdb | MATLAB | 2,851 | 67 | function [hM,meta,stimPar]=SOFAconvertSOFA2ARI(Obj)
% OBJ=SOFAconvertSOFA2ARI(hM,meta,stimPar) converts the HRTFs described in hM, meta, and
% stimPar (see ARI HRTF format) to a SOFA object.
%
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences;
% Licensed under the EUPL, Versi... |
990bd24565263a619df328f14f5dbcd9ac57b3175a3150ff93ced856d816d050 | MATLAB | 2,851 | 114 | function Y=ea_detect_edges_3d(varargin)
%% function detect_edges_3d for Nii-Images
% Andreas Horn, 2014
% in: X (image matrix), alpha (threshold), useimgtoolbox (use image toolbox
% or replacement function).
X=varargin{1};
alpha=varargin{2};
if nargin==3
useimgtbx=varargin{3};
else
useimgtbx=0;
end
Y=X;
dime... |
b35dc1d713ceb30aed272a11414bd1d31e2e2ebbd42ffcadfda189e202afc1f8 | MATLAB | 2,851 | 112 | function y = prod( x, dim )
% Disciplined geometric programming information for PROD:
% PROD(X) and PROD(X,DIM) are vectorized versions of multiplication
% so in most cases it would be incompatible with DCPs. Therefore it
% has not been implemented to support DCPs. DGPs however support
% pr... |
19f9d8d898a6f649f4c0e8bbd5ac3859c8f743a79262e9f681abb2b81f3a51d9 | MATLAB | 2,853 | 86 | function topo = get_adj_mat(V, C)
% GET_ADJ_MAT Build the full topology (adjacency) description of the
% vertex model tissue from its vertices and cell-vertex lists.
%
% topo = GET_ADJ_MAT(V, C) computes the vertex-vertex, vertex-edge,
% cell-vertex, and cell-edge adjacency matrices, plus the edge list,
% from t... |
b707d333ef01883a0bbb10dbcd4ce7c199d6e929ab30cfdc3494606e53bf2c08 | MATLAB | 2,853 | 99 | function [y,ii]=stkProj(stk,range,dim,type)
% Usage ... [y,ii]=stkProj(stk,range,dim,type)
%
% Range is the start-end indeces for the desired
% dim dimension to take the projection of
% default is max in all directions. select option only works
% in 1 direction
%
% Ex. zMax=stkProj(data,[14 70],3,'max'); or zMax=stkPro... |
19be9811fa90ae9886ba92ad373535f48b1a588ef1f58591b801103d23e847d5 | MATLAB | 2,854 | 84 | function outputfile = inflate_file(inputfile)
% INFLATE_FILE helper function to uncompress a compressed file of arbitrary
% compression type. Returns the full path to the extracted file or
% directory, which will be located in a temporary location.
% Copyright (C) 2012 Eelke Spaak
%
% This file is part of FieldTrip, ... |
d7374201c319ea7251c312e69131d5d46e404f1b201b698b50a8d7f2640f8c01 | MATLAB | 2,854 | 61 | % This script is only valid because I confirmed that the red and green
% channels are equally affected by the optic flow stimulus when the gain is
% equal across both channels. Moving forward I will endeavor to keep the
% gains the same so that I don't have to do this bs
[fs,frs,fds] = combineFluordata('67A04_aug05... |
d2a29fd2663d4d7489edf1a491972acde437aca0b3ae81d2935bf9a752cb91c5 | MATLAB | 2,855 | 110 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% demo script for surface smoothing
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% preparation
% user must add the path of iso2mesh to matlab path list
% addpath('../');
% user need to add the full path to .../... |
cd1d19710e440a470914c831f649c191e2b641bf5a24793a76ea52d823d4cdd8 | MATLAB | 2,856 | 69 | function [y, m] = std(varargin)
%STD Standard deviation.
% For vectors, Y = STD(X) returns the standard deviation. For matrices,
% Y is a row vector containing the standard deviation of each column. For
% N-D arrays, STD operates along the first non-singleton dimension of X.
%
% STD normalizes Y by N-1 if N>1... |
5215d1ad7f993bd1922bd81e880fad78ca0ca9578546889df8a99d0b25783bcc | MATLAB | 2,859 | 134 | % Figure 6.2: Penalty function approximation
% Section 6.1.2
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX Argyris Zymnis - 10/2005
%
% Comparison of the ell1, ell2, deadzone-linear and log-barrier
% penalty functions for the approximation problem:
% minimize phi(... |
c81e9ba4766143c5e78aa21de40c3ef4f714ebabe83a832aba0517f2a0046fbc | MATLAB | 2,859 | 85 | function varargout = tsvread( varargin )
%[data, header, raw] = tsvread( file ) reads in text file with tab-seperated variables. default value for data is nan.
%alternative input/output option is suppluying header strings
%[col1, col2, col3, ..., header, raw] = tsvread( file, header1, header2, header3, ... )
%header is... |
ad98c1b5ddfec39ca8ded69d509941587bcaf3662f82308b76dc62ea82c7690e | MATLAB | 2,860 | 76 | function [ ] = calc_simulation( cfg )
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically relevant behaviors of the ecosystems.
% Copyright (C) 2015 Vanni Bucci, Georg G... |
092b0651e1270d56c124428c3cae795dbdbe7aafccbfd46a195144bd80d1444c | MATLAB | 2,861 | 91 | function derivative = bz_Diff(samples,timestamps,varargin)
%Diff - Differentiate.
%
% USAGE
%
% derivative = Diff(samples,<options>)
%
% samples data to differentiate
% measured in number of samples (default = no smoothing)
% <options> optional list of property-value pairs (see ... |
1664f4b63e346ccbaec8b7d7a5b1e59ef4b479a184f8eb38bd278f82ea68fc73 | MATLAB | 2,861 | 112 | % Figures 6.8-6.10: Quadratic smoothing
% Section 6.3.3
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX Argyris Zymnis - 10/2005
%
% Suppose we have a signal x, which does not vary too rapidly
% and that x is corrupted by some small, rapidly varying noise v,
% ie. x_cor =... |
fac5921b7b2a1ca080602b07f355b5e1275d6058e836c385f1dfcc406cfc2180 | MATLAB | 2,861 | 112 | function PipeRaster(cellin, varargin)
% Scatters the time course of a single element on ydim with the pipe '|'
% character. Existing plot must be 'held'
% PipeRaster(cellarr_in, ['color'], 3xN matrix of color values, ['ys'],
% N array of y indeces for each row, ['ydim'], num)
% ARGUMENTS:
% cellin is the only requir... |
2a7107b1af8c383ba38c511d895f52cd608d4acbfa65486e22047e60ac2715be | MATLAB | 2,862 | 64 | %%PEAK AMPLITUDE
%Vessel Diameter (rr1a)
tstart=1;
tstop=2;
rr1a_percentmeansC=[];
rr1a_percentmeans=[];
rr1a_percentmeansSM=[];
rr1a_percentsemC=[];
rr1a_percentsem=[];
rr1a_percentsemSM=[];
%Capillary(StimCombined.m, stimAllTrials.mat)
rr1a_percentmeans=nanmean(all_rr1a_percent(tt>=tstart&tt<... |
bace761eba51d2e48b7aff1748c7b11df617f1c431cec79e939eae6c97ba80fa | MATLAB | 2,863 | 71 | %% Step 2 Tiny Dancers: Epoching and artefact rejection
clear all
clc
addpath 'C:\Users\tnguyen\OneDrive - Fondazione Istituto Italiano Tecnologia\Documenti\MATLAB\functions'
addpath(genpath( 'C:\Users\tnguyen\OneDrive - Fondazione Istituto Italiano Tecnologia\Documenti\MATLAB\toolboxes/Giac_ToolBox/'))
addpat... |
b8cf9f465011d54eeb5cd23184fae1f588eabb2ad307862d59d9a8e4b597e727 | MATLAB | 2,865 | 90 | % fast_t1 - Computes a 2D matrix of one sample/repeated measures t-tests
% relatively quickly.
%
% Usage:
% [p_values, t_scores, mn, stder]=fast_t1(data,tail,verblevel);
%
% Inputs:
% data - 2D matrix of data
%
% Optional Inputs:
% tail - [1 | 0 | -1] If tail=1, the alternative hypothesis is that ... |
c74ed28b20dacc9f1c6512886a32ce2f3e61563b9cfa96a38f3aa2d9296f742a | MATLAB | 2,866 | 63 | % Example 6.3: Optimal input design
% Section 6.3.2, Figure 6.6
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 09/26/05
%
% Consider a dynamical system with scalar input sequence u(0),u(1),...,u(N)
% and scalar output sequence y(0),y(1),...,y(N) related ... |
6d0e19344f1fddc896b70e4c033dcd0ca2a4e310fd6fff37003fa204470c2b1c | MATLAB | 2,867 | 107 | clear;
close all;
clc;
addpath(genpath('../functions/'));
SUBINFO_FILE = '../../subInfo/rid_sex_mDoB_yDoB_mExam_yExam_ageExam_dx_icv_bl.csv';
GMICV_FILE = '../../vbm_810bl/gmVolAndICV/rid_gmVol_icv_bl.csv';
% !!!!!!
% '_memRegEF' for regressing out each other; '' for not
tail = '';
%% MMSE baseline
cd('../jointGLM... |
62b1f5fa3345f65445b85a082444ce8e254b265c2fbcc6eb7c9e901c08a751cb | MATLAB | 2,868 | 63 | function plotbox(ax, data, axloc, color, alpha, bxw, lw, msize, plotY)
% Makes a boxplot
hold(ax, 'on');
% Get values
md = median(data);
qtls = quantile(data, [0.25 0.75]);
iqrange = iqr(data);
outmx = qtls(2) + 1.5*iqrange;
outmn = qtls(1) - 1.5*iqrange;
outinds = data > outmx | data < outmn;
outs = data(outinds);
mx... |
b9530ae891b240ce4827b1485671bbd52c19bd7b3e09d364c17406162d6bd393 | MATLAB | 2,869 | 86 | function ext = palm_checkprogs
% Test whether some external programs or toolboxes
% are available, namely, FSL, FreeSurfer, SPM and
% Jimmy Shen's NIFTI toolbox.
%
% ext = checkprogs
%
% 'ext' is a struct containing one field for each
% of these applications, each being containing
% a 0 (false) or 1 (true) depending o... |
2729ba0687f798d18222495d58e750fb796282dff0c50446afe866b25c82bb4c | MATLAB | 2,870 | 72 | function [Cxy, F] = cmtm(X,Y,NW,Fs)
%CMTM Coherence function estimate using the multitaper method.
% Cxy = CMTM(X,Y) estimates the coherence between two equal length
% vectors vectors X and Y using Thomson's multitaper method. The
% coherence is a complex function of frequency, with magnitude betwee... |
cf1af0fa9c53064869c83533f50e2fb2a146bbedf736f374d61d380d5a692e0b | MATLAB | 2,870 | 82 | function [fig, varargout] = draw_surface_bluewhitered(surface_to_plot, data_to_plot, hemisphere, medial_wall, with_medial)
% draw_surface_bluewhitered.m
%
% Draw data on surface using blue-white-red colormap for
% negative-zero-positive values
%
% Inputs: surface_to_plot : surface structure with fields
% ... |
d26f6ce040173722e274bad95579cc2219e279b330bc7dabd2bc1ccc52778d4b | MATLAB | 2,871 | 101 | function newmap = bluewhitered(m)
%BLUEWHITERED Blue, white, and red color map.
% BLUEWHITERED(M) returns an M-by-3 matrix containing a blue to white
% to red colormap, with white corresponding to the CAXIS value closest
% to zero. This colormap is most useful for images and surface plots
% with positiv... |
1b45779f23c1cb2483db77fc9a68bf51fc6fc6d65d5a2b8f621e4aeb82e09cde | MATLAB | 2,875 | 83 | function [dat, lo, hi] = maskToSignificant(stat_vec, sig)
% maskToSignificant Prepare a statistic vector so a range threshold keeps only
% the significant voxels.
%
% [dat, lo, hi] = maskToSignificant(stat_vec, sig)
%
% Returns stat_vec with the NON-significant voxels moved to a sentinel value
% below lo, togeth... |
87947b204bc899866136601a0abdda9874de9b8d5220dec866b80910f32a66e9 | MATLAB | 2,875 | 68 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
754110c5745d5841c20e7541416f32424abdb632833915bd5a636f9eac92dda7 | MATLAB | 2,876 | 101 | function [y, se] = predict(varargin)
% Interpolate a fit produced by locfit().
%
% predict(fit) produces the fitted values at locfit's selected points.
% predict(fit,x) interpolates the fits to points specified by x.
%
% Input arguments:
% fit The locfit() fit.
% x Points to interpolate at. May be a matr... |
e71c15adad2a4567b04664d84432a5c16abeadacb1296ad17656e852d74219b1 | MATLAB | 2,876 | 114 | % windows() - Returns handle to window function or window
%
% Usage:
% >> h = windows(t);
% >> h = windows(t, m);
% >> h = windows(t, m, a);
%
% Inputs:
% t - char array 'rectangular', 'bartlett', 'hann', 'hamming',
% 'blackman', 'blackmanharris', or 'kaiser'
%
% Optional inputs:
% m - scalar window len... |
31133c163ff0781cb98ee880dfb2a9363a5de618552735b74db9a3155be228ba | MATLAB | 2,877 | 83 | function [status, version] = bfCheckJavaPath(varargin)
% bfCheckJavaPath check Bio-Formats is included in the Java class path
%
% SYNOPSIS bfCheckJavaPath()
% status = bfCheckJavaPath(autoloadBioFormats)
% [status, version] = bfCheckJavaPath()
%
% Input
%
% autoloadBioFormats - Optional. A boole... |
e1ee7c9e7fba9788a39fda5955f410f310c7a88c25d0ea7a164e9e94d8d1f1dc | MATLAB | 2,878 | 62 | function [coords_mm,trajectory,markers] = ea_runpacer(options)
[tmat,ctnii] = ea_getrawct2preniimat(options);
niiCTSPM = NiftiModSPM(ctnii); % load nifti using SPM instead of PaCER default Nifti Toolbox
if ~isfile(options.subj.recon.rawCTMask)
ea_genctmask(options);
end
switch options.prefs.reco.mancoruse
cas... |
da779237b78071b2595fb927be3a6b2654ee3614942d600de25b78c7e158f2cd | MATLAB | 2,881 | 94 | classdef ( Hidden ) Node < dynamicprops
%uix.Node Node
%
% n = uix.Node(o) creates a node for the handle o.
%
% Node is a helper class for managing trees of objects and associated
% listeners.
% Copyright 2009-2015 The MathWorks, Inc.
% $Revision: 1165 $ $Date: 2015-12-06 03:0... |
3560b001cf14c092db88126570fc47549e03051564e99571d2ee18728ee53c29 | MATLAB | 2,884 | 69 | function CBIG_ASDf_plotConjunctionUniqueMaps_wrapper(output_dir)
% CBIG_ASDf_plotConjunctionUniqueMaps_wrapper(output_dir)
%
% Wrapper function to plot conjunction and unique maps for RSFC factors
%
% Input:
% - output_dir:
% Absolute path to directory where output results will be saved
%
% Example:
% ... |
3a537e3c38131e35d6928f515a553a2d273d9e18265111da60792c9a5771cb2b | MATLAB | 2,884 | 110 | function [nameStr, errStr]= get_unique_str(entriesCell, defaultStr, nameGenFlag, strucFlag, forceDialogFlag)
%function [nameStr, errStr]= get_unique_str(entriesCell, defaultStr, nameGenFlag, strucFlag, forceDialogFlag)
%
%
% Bjoern W. Kreher
% 03/04
%
% UNIX
% Set default flags
if ~exist('defaultStr') || isempty(def... |
ba102e7d545a21aebe7f35139fd21f5fc3d3652ccc871a624e3548d4c0585a2d | MATLAB | 2,884 | 86 | function varargout = sort_dicm(srcDir)
% Sort dicom files for different subjects into subject folders.
%
% subjects = SORT_DICM(dicmFolder);
% The optional input is the top folder containing dicom file and/or subfodlers
% which may contain dicom files and/or subfolders.
%
% Optionally, it returns subfolder na... |
d7d656c4cc927cfa21b2bcd07d80a9af28cdfcf0656471224e232a56e3f88296 | MATLAB | 2,884 | 80 | function [outputImg,outputImgArray] = convCoord2Img(coord, imageSize, imageType, bgType)
% CONVCORD2IMG convert x-,y- positions to a 2D image
%
% SYNOPSIS: outputImages = convCoord2Img(coord, imageSize, imageType, bgType)
%
% INPUT: coord : (matrix) x-,y-positions, with x in 1st col, y in 2nd col
%
% imageSi... |
fbe9ceace51e1bb5532c8dbc66001ec7e77eed7e3c6fcf0fd48abf260286e733 | MATLAB | 2,886 | 83 | function surf = SurfStatWriteSurf1_nonorm( filename, surf, ab );
%Writes coordinates and triangles to a single .obj or FreeSurfer file.
%
% Usage: surf = SurfStatWriteSurf1( filename, surf [,ab] );
%
% filename = .obj or FS file name. If extension=.obj, writes a .obj file
% (ASCII or binary), els... |
3e9b732b175e9a35925e858eeeccf2bc5cf4877eb1d5cd3de7e824c7c98a2179 | MATLAB | 2,888 | 113 | %CompareRecordingPC1.m
datafolder = '/Users/dlevenstein/Dropbox/Research/Datasets/BWData/';
figfolder = '/Users/dlevenstein/Code Library/SleepScoreDevelopment/StateScoreFigures/';
%Make List of all Recordings in data folder
recordings = dir(datafolder);
recordings(strncmpi('.',{recordings.name},1)) = []; %Remove en... |
ddd48d5ed70e13ecb18d7b7d22be8336da9038dab50fa88f2dfc8f068c522683 | MATLAB | 2,888 | 66 | function r = cvx_remap( varargin )
%CVX_REMAP CVX expression type map generator.
% This is an internal function used to help filter CVX expressions by type.
% Classifications:
% 1 - negative constant
% 2 - zero
% 3 - positive constant
% 4 - complex constant
% 5 - concave
% 6 - real affine
% 7 -... |
f75d89e74f068c38e3a519128693954859b53da66d8b1bc1d7be3f4743c1a086 | MATLAB | 2,889 | 111 | function [n, nm, nl, ts, names, m] = nex_marker(filename, varname)
% nex_marker(filename, varname): Read a marker variable from a .nex file
%
% [n, nm, nl, ts, names, m] = nex_marker(filename, varname)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% varname - variable name
%
% ... |
4d428af9976f706501f778f193673c4116c0757f90a820e09e71dcfcbe911bc1 | MATLAB | 2,890 | 68 | function Obj = SOFAgetConventions(sofaconventions,flags)
%SOFAgetConventions
%
% List = SOFAgetConventions() returns a list with supported conventions.
%
% Obj = SOFAgetConventions(sofaconvention) returns a SOFA object
% with all metadata and data for the corresponding sofaconvention. Obj
% will be ... |
eb61d77db69f4269ccc993a527813b1fd2a5f6c5fb6192da86da058065018874 | MATLAB | 2,890 | 60 | function [crp, crpH] = rel_phase_cont(data1,data2,samprate)
% RELPHASE - calculates the relative phase between two segments, joint
% angles, coordinates, etc. It is calculated using the atan2 function in
% order to preserve the quadrant in the phase portrait. The sign of the
% relative phase is determined from segmen... |
c428a18dd26f2715f7ce27356a7ec79bd536131354583497757d2b14aee26f45 | MATLAB | 2,892 | 69 | function sigma = nonst_stat(data,A,sumV,params)
% Nonstationarity test - continuous process
%
% Usage:
%
% sigma=nonst_test(data,A,sumV,params)
% Input:
% Note units have to be consistent. See chronux.m for more information.
% data (1d array in samples) -- required
% A quadratic coefficient matrix - (Co... |
6b5cdc4daf61e02810447336ef5bf91ac9905e677dff23a284c5ec264d7584b6 | MATLAB | 2,893 | 81 | function [R,Rperm,Rnaned,Rpermnaned,h]=ea_partialRmap(varargin)
% creates a correlation nifti file given a set of images and a
% regressor ("R map" in Horn 2017 AoN)
% ea_Rmap(fis,regressor,outputname,mask,sk,corrtype,covariate) % sk can be 'k','s','sk'
% for smoothing and normalization options. Mask only necessary if... |
9c4bc16b00ada85063c8afdb2cb99957d328d5589329db8199966335efddd5dd | MATLAB | 2,894 | 73 | function out = LaBGAScore_combat_apply(dat, batch, est)
% Apply ComBat parameters fitted on a training set to held-out data
%
% :Usage:
% ::
% out = LaBGAScore_combat_apply(dat, batch, est)
%
% :Inputs:
% **dat:** p x n data matrix (features x subjects) to harmonize
% **batch:** n x 1 batch/site labels for ... |
c20bc28a208f34dfa5cae61ef17fdd92160b58718441bd1096237b79fe440d55 | MATLAB | 2,894 | 86 | %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%This scipt is for cleaning 60, 120, 180Hz noise from LFP1000 downsampled signal.
%Inputs: animal ID, numchans of your probe
%Output: add a LFPvoltage_notch to LFP1000 files together with original LFPvoltage
%Writen by SF, 8/1/2021
%%%%%%%%%%%%%%%%%... |
ced47ef4b2f840f3cbc80faffc8a82a628a2596921912e58ec3cb944949c7051 | MATLAB | 2,894 | 119 | function k=ea_concavehull(XYZ,thresh)
% This function tries to convert the convexhull generated by Qhull into a
% concave hull. Equally, output is in format k [n x 3] which defines n
% triangles as rows in XYZ. If the function finds a triangle that has 2
% sides whose midpoints are further away than thresh from another... |
b448cd623d7f1ac1dd837e9b495732e2b5a05bc4757c719a663de45e6f80d14b | MATLAB | 2,895 | 81 | % eeg_dipselect() - select componet dipoles from an EEG dataset with
% reisdual variance (rv) less than a selected threshold
% and equivalent dipole location inside the brain volume.
% Usage:
% >> selctedComponents = eeg_dipselect(EEG, rvThreshold, selectionType, depthThreshold)
... |
5f14c528dc09d58fd585beb3809b7e99761529c79fcd9340d1700a41cc321b02 | MATLAB | 2,897 | 76 | % pop_fileiodir() - import directory into EEGLAB using FileIO
%
% Usage:
% >> OUTEEG = pop_fileiodir; % pop up window
% >> OUTEEG = pop_fileiodir( folder );
%
% Inputs:
% folder - [string] folder name
%
% Optional inputs:
% 'channels' - [integer array] list of channel indices
% 'samples' - [min max] sam... |
7b35344e39fbe0af6637f2cceae3db6550e927be71c46e9973087d42d8a13de3 | MATLAB | 2,897 | 80 | function output = SOFAdefinitions(varargin)
% SOFAdefinitions
%
% SOFAdefinitions returns a struct containing definitions like the time
% format used in the API.
%
% SOFAdefinitions('dateFormat') returns the date format
%
% SOFAdefinitions('APIName') returns the APIName
%
% SOFAdefinitions('dimensio... |
c95e472126e1808eb9f995dbc8823822e4a5001b905ba0acd898fe41ea0aea08 | MATLAB | 2,897 | 87 | function [ydata,D] = tsne(X, labels, no_dims, initial_dims, perplexity)
%TSNE Performs symmetric t-SNE on dataset X
%
% mappedX = tsne(X, labels, no_dims, initial_dims, perplexity)
% mappedX = tsne(X, labels, initial_solution, perplexity)
%
% The function performs symmetric t-SNE on the NxD dataset X to reduce its ... |
86ed4a3e91ba13d7318c1d27ac523e764d8d561895f84a318f3fe0d84cb78814 | MATLAB | 2,898 | 86 | % readegilocs() - look up locations for EGI EEG dataset.
%
% Usage:
% >> EEG = readegilocs(EEG);
% >> EEG = readegilocs(EEG, fileloc);
%
% Inputs:
% EEG - EEGLAB data structure
%
% Optional input:
% fileloc - EGI channel location file
%
% Outputs:
% EEG - EEGLAB data structure with channel lo... |
8c6739359f3c0d8823ac8aff5f531ba9c017af82afbe579755152e0302d81248 | MATLAB | 2,898 | 91 | function Store(variable,name,varargin)
%Store - Store variable in memory to avoid redundant computations.
%
% This function is useful in the following scenario. When processing data
% in batches, a function is called repeatedly with different parameters.
% Because not all parameters change every time, some computat... |
1c3eb3df32ff993f5d7e0dd38161796e4e30775c99b91a53e364844f238178a4 | MATLAB | 2,899 | 71 | function ea_save_fixed_weights(stimfolder, opt_weights, fixed_weights_values, slider_name, pos_and_neg)
% save weights that should not be changed during optimization (fixed weights)
% opt_weights - adjustable weights or 0 (all fixed)
% fixed_weights_values - from the sliders in ClearTune
% slider_name - corresponds t... |
c90c15a51302b6a70e37c618914da7697715bcd0ecb357ff99823dd2b4798012 | MATLAB | 2,901 | 92 | function DBAddVariable(v,eid,name,parameters,comments,mfiles)
%DBAddVariable - Save variable in current database.
%
% Save variable and code used to compute it.
%
% USAGE
%
% DBAddVariable(v,eid,name,parameters,comments,mfiles)
%
% v variable
% eid experiment ID (identifier string)
% ... |
62c256aa2aa35628138e15dfbda50afe4c524f09eede77370857b43364dc62a9 | MATLAB | 2,903 | 111 | function [V,t,Err] = evoked(data,Fs,win,width,plt,err)
% Function to calculate the evoked response given continuous data in the
% form time x channels
% Usage [V,t,Err] = evoked(data,Fs,win,width,plt,err)
%
% Inputs
% Note that all times can be in arbitrary units. But the units have to be
% consistent. So... |
d607a50231a43bf04d05838ee41eb8ea99f3d4113223ac3b1b01e4148a7a8359 | MATLAB | 2,903 | 95 | function splitNSx(splitCount)
% splitNSx
%
% Opens and splits an NSx file in smaller pieces, timewise.
%
% Use splitNSx(splitCount)
%
% All input arguments are optional. Input arguments can be in any order.
%
% splitCount: Defines the number of splits.
% DEFAULT: Splits the file in 2 pieces.
%
% ... |
f83ef287ba64b857311e936db8e93490ab0983edd2e111f61e3cc1ba663133b4 | MATLAB | 2,904 | 106 | function [ probs ] = AssociationLDA2( WP , BETA , W1 )
%% Function WriteTopics
%
% works on single samples as well as multiple samples
if iscell( WP )
% we are dealing with multiple Gibbs samples. Need to average
% predictions over these samples. Note that the WP samples do not have
% to contain the ... |
5c99b966779a9a5f6841f8d61d8666ec6650fd0f52e8624c26f58d9147c12f73 | MATLAB | 2,905 | 73 | % [kcMap,A0Map] = getLocalDcorr(im,tileSize,tileOverlap,r,Ng,figID)
% ---------------------------------------
%
% Estimate the image local cut-off frequency based on decorrelation analysis
%
% Inputs:
% im 2D image to be analyzed
% tileSize Size of a tile in pixels
% tileOverlap Spatial overlap between tw... |
45f1fbfe6cf3f55fb199ef35a634f851dee4e6079f0c9bc82de93109e1627870 | MATLAB | 2,906 | 99 | function VisualizeDocs( DP , ALPHA , S , NCHARS , MAXLINES );
%% Function VisualizeDocs
%%
% Visualize documents in a 2D map
%%
% |visualizedocuments( DP,ALPHA,S,NCHARS,MAXLINES )| takes the document
% strings in |S| and the document-topic count matrix |DP| where |DP(i,j)|
% contains the number of times a word i... |
9a1147f6fe71968afa3ad38db58018484ab59d11b6955b7ca68e16506be620d0 | MATLAB | 2,906 | 81 | function [ xi, R ] = cvx_orthog_structure( xi, clean )
%CVX_ORTHOG_STRUCTURE Constructs an orthogonal structure matrix.
% CVX_ORTHOG_STRUCTURE(X), where X is an M x N matrix from CVX's
% matrix structure facility, determines an orthogonal structure: that
% is, a matrix Z of size (N-rank(X)) x N such that X ... |
be19df993a852239a867e9581125e63008b83e74288a569903599f1d02327384 | MATLAB | 2,906 | 106 | function [ probs ] = AssociationLDA3( WP , BETA , W1 )
%% Function WriteTopics
%
% works on single samples as well as multiple samples
if iscell( WP )
% we are dealing with multiple Gibbs samples. Need to average
% predictions over these samples. Note that the WP samples do not have
% to contain the ... |
8049c531328625a34083216b24f8a7a5c953f897a625819dd320e249bfb3c9d1 | MATLAB | 2,910 | 93 | function cvx_optpnt = semidefinite( sz, iscplx ) %#ok
%SEMIDEFINITE Real symmetric positive semidefinite matrices.
% SEMIDEFINITE(N), where N is an integer, creates a symmetric matrix
% variable of size [N,N] and constrains it to be positive semidefinite.
% Therefore, given the declaration
% variable ... |
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