sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fe51bc9e0e887aa1f1ce192528f078913e39dc7a0c187dbf0936c191343f817b | MATLAB | 4,184 | 116 | function [Header] = w_ReadDF(Header)
%function [Header] = w_ReadDF(Header)
% Read image header to get DF
% ------------------------------------------------------------------------
% Input:
% Header - The Header of image data, use y_Read.m to get it.
% The elements in the structure are:
% Header.fname - the filen... |
3f5898693831479f24cc6a91fcb6b3663939f82850be2b5a2d28d8784264e707 | MATLAB | 4,185 | 88 | %% List all the 100 subjects and loop through them
current_dir=pwd;
list_subj_ID=dir('/home/andrea/miplabsrv2/HCP/*');
list_subj_ID(1)=[];
list_subj_ID(1)=[];
%min_length_task={1000,1000,1000,1000,1000,1000,1000};
min_length_task={176,253,316,284,232,274,405};
load('min_size_tasks_regressors.mat')
%min_size_tasks_regre... |
9b7ec6a64ff8f24480a0fe03db9d355e02b4cc2ba2b9a9ff01ac2cc57f35259d | MATLAB | 4,185 | 101 |
function WriteImageBoutonsAndROIs(Image,FileNameAndDir,BoutonROIArray,MaskBouton,ROIs)
OS=computer;
if strcmp(OS,'MACI64')
dc='/';
else
dc='\';
end
if length(FileNameAndDir)>260
error('Shorten Name and or dir...')
end
% Image=double(TempContr... |
f93b895af53e7a615d8a2ead6381afdf88de733465852b5a5ac8a80745391c37 | MATLAB | 4,185 | 122 | % FADE-SAME: Table 3
% clear
% close all
%%% Step 1: load data %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% load results file
FADE_file = '../FADE_scores/FADE_SAME_scores_2021_01_11_FADE_only.xls';
[num, txt, raw] = xlsread(FADE_file);
clear num txt
% specify inference
conf_lvl = 0.9;
% extract variable... |
f2c2425e44f3bfb43a18450f6db079544e7786abe6e4b881b6805d947110e0ee | MATLAB | 4,187 | 170 | function wlPlot_plotEventScatterMulti(cfg, eventseries, ...
freqrange, durrange, amprange, figtitle, filelabel)
% function wlPlot_plotEventScatterMulti(cfg, eventseries, ...
% freqrange, durrange, amprange, figtitle, filelabel)
%
% This function makes a scatter-plot of burst amplitudes and burst durations
% (in pe... |
43091f6012b7c12fdcc50b9632c6f8c8729f60c636013138997f21c388b63318 | MATLAB | 4,188 | 115 | function extract_spikes_samples
%extracts sample indices of spikes. calls subroutine extract_kwik_file(kwikfile,tet_number)
cluster_data.spikes.SUA=[];
cluster_data.spikes.MUA=[];
if exist('raw')==7
cd('raw');
end
disp('folder: ')
pwd
tetrode_list= dir('*.kwik');
for i=1:length(tetrode_list)
st= strfind(tetrod... |
9e1635a3daad637a4d47fb166fa6121811e369cfbad1159b3f029f0efae85a71 | MATLAB | 4,188 | 102 | function plot_ICs(params,EEG)
% Recording ids
s_ids = cellfun(@(x) regexp(x,'.*(?=_eeg.set)','match','lineanchors'),{EEG.filename});
% Check that the number of channels is the same for all the recordings
etc = {EEG.etc};
if range([EEG.nbchan]) ~= 0
error('Different number of total channels in at least one recordin... |
6e19a4f1bc26d34998e82c7b72c7e104ec67d979a69d059e4b73c87be80c9dbe | MATLAB | 4,189 | 138 | %% test_choose_orientations
MINVEL = 3;
MINANGLEDIFF = 3*pi/4;
MINANGLECHANGE = 3*pi/4;
MININTERVALLENGTH = 5;
velocity_angle_weight = .05;
max_velocity_angle_weight = .25;
WINDOWRADIUS = 100;
tag = 'movie20071007_165047';
path = '/home/kristin/FLIES/data/walking_arena/highres/';
ext = '.fmf';
moviename = ['/media/da... |
83b5ac69ac7d3a5d612fae81df95f60eb6214f012bf8f250666d521c9f7ac902 | MATLAB | 4,189 | 525 | %% SH suggested flyID2rm
flyRmCalib = [
90
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];
%%
fl... |
9250959f7d7ad85b6236bd666c8caf3849dc9b7305a31a070c8a7f021446e9b8 | MATLAB | 4,189 | 117 | function [spkZ, spkMapZ, spkViewZ, spkZnan, spkMapZnan, spkViewZnan] = normDat(spk, spkMap, spkView, par)
% Normalize firing rates based on mean and std of activity between 200 and
% 600 ms after motion onset during RDM discrimination trials
% Inputs
% - par = basic information about the recording session and p... |
066fc7d989a6fa8490866a2c2887d8e89f3a6ed529f2f29e449f9d3ee4aa39fc | MATLAB | 4,195 | 178 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
44231beda6dff05d111c8819c840dd46cd8f9c10f62811d0afaff829b761bcd9 | MATLAB | 4,195 | 112 | classdef LabelROI
methods (Static)
function s = new(n)
if nargin < 1,
n = 0;
end
% s.id = ...
s.verts = nan(4,2,n);
s.f = nan(n,1);
end
% Barebones add/edit API for now. Can improve over time if nec
function s = setF(s,v,f)
% set/replace all rois for frame ... |
6c0cf8df7936f7987f645bc982abeeae60838c0cc94a89ea9d7a1d0c2fd75ba7 | MATLAB | 4,195 | 168 | function y = recurrentQuadratureFilter(x,lambda,omega,tau,n,RIC,deltaT)
% Feb 2023
% y = recurrentQuadratureFilter(x,lambda,omega,tau,n,RIC,deltaT)
%
% x: 3D input signal with time in the 1st dimension (real or complex
% valued)
% y: output signal (real or complex valued: see RIC)
% omega: preferred tempora... |
b867efb8a6df5dfd7910eeffd3ed07a6878fe384cc39b294d4e576caf77c213b | MATLAB | 4,195 | 138 | function [Theta0,Re0] = lme_mass_fit_EMinit(X,Zcols,Y,ni,maskvtx,nit,prs)
% [Theta0,Re0] = lme_mass_fit_EMinit(X,Zcols,Y,ni,maskvtx,nit,prs)
%
% Starting values at each location for the linear mixed-effects iterative
% estimation. These starting values are based on the ordinary least squares
% estimators plus some fa... |
305a785cb642f1bdb5d0dccb44bf954fc7517d8e751fe3654669ebaf3431d60b | MATLAB | 4,197 | 125 | function [P]=ExpandBoundaryBufferZone(t,p,P,shell_normals,density,DELTA,llc)
% Expands each triangular facet of the boundary by a factor (depending on
% local mesh density) and then extrudes a prism out of the expanded
% triangle. Then checks for all the pixels that are within this prism and
% tags them as buffer pixel... |
d7819fcaf54c8633b8c44d5eb86f68b577de14d7b607c00df15e84b59cd5131d | MATLAB | 4,197 | 187 | clear
clc
% close all
%%% This script reproduces panel d of Figure 5.
%%% It is also used to reproduce panels c and d of Ext. Data Fig. 8.
rat_names={'P049','P055','P059','P095','P100','P101','P102'};
%%% load results of logistic regression
load data/logistic_regression_results_ephys_rats
%%% (generated by compute_... |
2f7eb1131dbf34910073483373ae7da8792f701a2b94cf410426f782ac83ec68 | MATLAB | 4,198 | 106 | % FT_POSTAMBLE_SAVEVAR is a helper script that optionally saves the output
% FieldTrip data structures to a *.mat file on disk. This is useful for
% batching and for distributed processing. This makes use of the
% cfg.outputfile variable.
%
% Use as
% ft_postamble savevar data
% ft_postamble savevar source mri
%
% ... |
b55f413f7a96025a6abc19b392cdc788fd9fbb93720cece5f64d7c8992a764ab | MATLAB | 4,198 | 107 | % SearchDir=ParentDir3
% Destination=['Z:\Temporary QuaSOR File Backup'];
SearchString='_MiniEvoked_SOQA_Data2.mat'
SearchDir='/Volumes/Time Machine Backup/Enterprise Image Analysis 3/'
Destination='/Volumes/Zach/Temporary QuaSOR File Backup/'
function Search_and_Destroy_or_Save(SearchDir,SearchString,Destination)... |
059d2c9549e460c6aa74a86be4c6ecb4808d101928b1e784b6f8d4e92ad6b918 | MATLAB | 4,201 | 215 | clear
clc
load('Sfast_G1.mat');
load('Sfast_G2.mat');
load('Sfast_G3.mat');
load('Sfast_G4.mat');
load('Sfast_G5.mat');
load('Sfast_G6.mat');
load('Sfast_G7.mat');
load('Sfast_G8.mat');
load('Sfast_G9.mat');
G1_corrected = Sfast_G1(:, 6:10);
G1_corrected(:,6:10) = Sfast_G1(:,1:5);
Sfast_G1 = G1_corrected;
G2_correc... |
8acb36b92bd52d29ade1883f025e85008cd23b3c34017a047dbc7e5f9decfc3c | MATLAB | 4,202 | 89 | function detector = acfModify( detector, varargin )
% Modify aggregate channel features object detector.
%
% Takes an object detector trained by acfTrain() and modifies it. Only
% certain modifications are allowed to the detector and the detector should
% never be modified directly (this may cause the detector to be in... |
a81fe2f8ecadcdef420bf06030a686c6487d353c0c492377f2d325d2686a4878 | MATLAB | 4,202 | 123 | function [eeg] = read_ns_eeg(filename, epoch)
% READ_NS_EEG read a NeuroScan 3.x or 4.x EEG File
%
% [eeg] = read_ns_eeg(filename, epoch)
%
% filename input Neuroscan .eeg file (version 3.x)
% epoch which epoch to read (default is all)
%
% The output data structure eeg has the fields:
% eeg.data(..) ... |
b303443003ec1087f47e0e025171eb176929cc390634cff6ac98269d5b011489 | MATLAB | 4,202 | 152 | function [HL,CLIN] = cmlines(varargin)
% CMLINES Change the color of plotted lines using the colormap.
%
% SYNTAX:
% cmlines
% cmlines(CMAP)
% cmlines(H,...)
% [HL,CLIN] = cmlines(...);
%
% INPUT:
% CMAP - Color map name or handle to be used, or... |
239f2625a65f2715f8ff3bdd4e94fede3c4e0ba50358d8cf2e6b69cc46d903d0 | MATLAB | 4,204 | 139 | %GHOSTSCRIPT Calls a local GhostScript executable with the input command
%
% Example:
% [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript was installed into. The resulting path
% is stored for future reference.
%
% Once ... |
d481a5682f6a3641c4797c701bb0cd54449328709a7c6aefe01bb76632ec5489 | MATLAB | 4,205 | 144 | % DELCODE-SAME, Table "FADE SAME dc"
% _
% original paper: Soch*, Richter* et al., HBM, 2022
% Table 3: Within-subject ANOVAs for FADE-classic and FADE-SAME scores
%
% DELCODE paper: Soch et al., medRxiv, 2023
% Table S3: Effects of diagnosis group and fMRI contrast on single-value scores
%
% written by Joram Soch ... |
dbff286bc0bda0fbc0aa87775f83285f5dc93d5028559d19efb64651b9ef4de0 | MATLAB | 4,206 | 70 | function params = initPhotoreceptorParams(modelType)
% Initialize parameters for different photoreceptor models.
% Default values (could be adjusted based on needs)
params.sigma = 22; % receptor activity decay rate (1/sec)
params.phi = 22; % phosphodiesterase activity decay rate (1/sec)
params.eta = 2000; % pho... |
1434825221898ae7d8c2d6eeae27642c0eadd6566416dd320eb7cd8e30a40660 | MATLAB | 4,207 | 151 | % fourieeg Single-Sided Amplitude Spectrum of your continuous dataset
%
% [ym f] = fourieeg(ERP,ch,f1,f2) returns the module (magnitude) ym of the FFT output
% of your dataset, evaluated at channel ch, between the frequencies f1 and f2 (in Hz).
% f contains the frequency range.
%
% [ym f] = fourieeg(ERP,ch,f1) returns ... |
5470bb7f2cd6a883a924f9c33889ffff29989b525e59f737289a22755712e093 | MATLAB | 4,209 | 82 | %% Description
% This example shows the use of the helper functions MCmatlab.plotAzFz()
% and MCmatlab.plotRadialReflectanceTransmittance(). They generate plots
% similar to those made by MCML, available at omlc.org. Use the log scale
% button to see the details in the wings of the distributions.
%
% The radially reso... |
c67eb1b7aa6b17f218c4b45db16e6f3ff9d346e23bbba631dd7294e25fa7e19e | MATLAB | 4,210 | 87 |
ind = 1;
data = dir('/DATAPOOL/ERRORMONITORING/SEM_mri_data/P*');
%%
for i = 1:size(data,1)
data_func = dir([data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/nifti/func/run*']);
fprintf(data(i).name);
runs = [1:size(data_func,1)];
for j = runs
dir_folder... |
a3cdb2e6d5b7465906f95043215facf0c6e85eac410f5e39464450b1c80679c0 | MATLAB | 4,211 | 141 | function [gmdmproduct] = y_gmdmp(tensor1, d1, tensor2, d2)
%GMDMP General Multi Dimensional Matrix Product.
%C = GMDMP(A, d1, B, d2) Computes the product
%C(i[1],...,i[d1-1],i[d1+1],...,i[m],j[1],...,j[d2-1],j[d2+1],...,j[n]) =
% A(i[1],...,i[d1-1],k,i[d1+1],...,i[m]) * B(j[1],...,j[d2-1],k,j[d2+1],...,j[n])
%(Sum ... |
496f6ec0167fe040956df2d6e3e600a48238f6ed430a24b65993015677393138 | MATLAB | 4,212 | 213 |
function runAutomateAction(self)
menu_items = self.handles.menu_name(4).Children;
% go over all the files and load them
[~,~,ext] = fileparts(self.file_name);
allfiles = dir([self.path_name '*' ext]);
n_files = length(allfiles);
switch self.automate_action
case crabsort.automateAction.view_only
channel = self... |
29c61ba6644ea1f46a3d181d693161a79d72838bff87472cc19318aba315f7a6 | MATLAB | 4,213 | 133 | function vol = dilate3d(vol, dop, r, res)
% dilate3d - perform 3D dilation with operator
%
% FORMAT: vol = dilate3d(vol [, dop, r, res])
%
% Input fields:
%
% vol 3-D boolean volume
% dop dilation operator with odd size ! (default 3x3x3 cube)
% r 1x1 double radius, wei... |
ae5c7ca00c1d1a8f39c0af0003c955dbd433f4ed1add18a3bca67eb5598e5a45 | MATLAB | 4,214 | 146 | function [Theta0,Re0] = lme_mass_fit_init(X,Zcols,Y,ni,maskvtx,prs)
% [Theta0,Re0] = lme_mass_fit_init(X,Zcols,Y,ni,maskvtx,prs)
%
% Starting values at each location for the linear mixed-effects iterative
% estimation. These starting values are based on the ordinary least squares
% estimators (OLS).
%
% Input
% X: O... |
a318fac8d2d874782fe1e6685bfcba79031f3efe2c454302d96eb554aa096c63 | MATLAB | 4,215 | 58 |
function replay_decoding_split_events
%splits each replay event approximately in half, based on when the MUA is
%lowest in the middle third of the event. This is used to seperately analyze the
%first and second half of long duration replay events
% Load parameters
parameters = list_of_parameters;
load('decoded_repla... |
f62aaff919dd368e27525a0ae243d331b8eba43f942ccf7d39aae41abe2afd68 | MATLAB | 4,215 | 96 | % Correlation table all NTs all Freqbands
% Prerequisites, parcellation image, input image - smap/fmap, wjn toolbox
addpath C:\Code\wjn_toolbox-master
addpath C:\Code\spm12
addpath(genpath('C:\Code\leaddbs'))
%
% Atlas_dir = 'C:\Users\ICN_guest\Charité - Universitätsmedizin Berlin\Interventional Cognitive Neuromodula... |
312601d251f1b58f2c84812d11b0afe1d541e8b0dd474b29bd615298507569d3 | MATLAB | 4,216 | 127 | function [missing, extra, copyProblems, missingExtra] = pmlOrganizeCode(bookSource, dest, demosOnly, includeCodeSol)
% Organize the PMTK code files referenced in PML into folders
% according to the chapter in which they are referenced. If a file is
% referenced in more than one chapter, the first chapter is used unles... |
3e0aae73f67557499ca5a17093eb03d4a70ac634163566db4558f958906905ab | MATLAB | 4,217 | 148 | clear all
trialCOUNT = 1;
b = [0, 0.4470, 0.7410];
o = [0.8500, 0.3250, 0.0980];
y = [0.9290, 0.6940, 0.1250];
p = [0.4940, 0.1840, 0.5560];
g = [0.4660, 0.6740, 0.1880];
a = [0.3010, 0.7450, 0.9330];
r = [0.6350, 0.0780, 0.1840];
%% DATA with rule biased towards depression (with no plastic F -> VIP)
external_sti... |
47a37a041e986a581b5668eed6aaeae3f099380984bed67d309188f1c857f777 | MATLAB | 4,217 | 123 | function [tfr,t,f] = tfrbj(x,t,N,g,h,trace);
%TFRBJ Born-Jordan time-frequency distribution.
% [TFR,T,F]=TFRBJ(X,T,N,G,H,TRACE) computes the Born-Jordan
% distribution of a discrete-time signal X, or the
% cross Born-Jordan representation between two signals.
%
% X : signal if auto-BJ, or [X1,X2] if cross-BJ.
% ... |
5e04f9b17645c59e4757bcf25816d8adcecd03a099c29cdfe1d36f708759d0c4 | MATLAB | 4,217 | 114 | function [th,boot_values] = limo_ecluster_make(bootf,bootp,alphav)
% ECLUSTER_MAKE creates a multivariate, cluster based, statistical threshold based
% on bootstrapped F tests. The function operates along the last dimension of the
% input data. For each bootstrap, independently at each electrode:
% (1) signi... |
9f2213bae9258b5cd2021ba6e5c24f5e9cb28ae7762757d6f9dfeb883ad0b94d | MATLAB | 4,217 | 145 | function [minPos,fmin] = polyinterp(points,doPlot,xminBound,xmaxBound)
% function [minPos] = polyinterp(points,doPlot,xminBound,xmaxBound)
%
% Minimum of interpolating polynomial based on function and derivative
% values
%
% In can also be used for extrapolation if {xmin,xmax} are outside
% the domain of... |
b90d3aece6329712681cb75a4da376d47a50b70bbc25a2e9fc78eb83cbd76968 | MATLAB | 4,217 | 122 | % FADE-SAME: Table S4
% clear
% close all
%%% Step 1: load data %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% load results file
FADE_file = '../FADE_scores/FADE_SAME_scores_2021_01_11_FADE_only.xls';
[num, txt, raw] = xlsread(FADE_file);
clear num txt
% specify inference
conf_lvl = 0.9;
% extract variabl... |
1ae33e83a8b44354e300f5881823768397223e9bf740ae5b6e56380a6f85a8ef | MATLAB | 4,218 | 182 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
43c74f282917e550c9d535c1b165ceeb5ceb2399027bd5595075a109bd5d8aaf | MATLAB | 4,219 | 88 | function SOFAplotGeometry(Obj, index)
% SOFAplotGeometry(Obj) plots the geometry found in the Obj.
%
% SOFAplotGeometry(Obj, index) plots the geometry for the measurements
% given in the index.
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences;
% Licensed under the EUPL, Version 1... |
a9d164c57334f18eb836e70febf2aece7451da2f2c954e842763584f2f2d1b43 | MATLAB | 4,221 | 118 | classdef MouseVocImporter < FeaturesImporter
properties
end
methods(Static)
function n = typeName()
n = 'Mouse Vocalization';
end
function ft = possibleFeatureTypes()
ft = {'Vocalization'};
end
function... |
3298acd4072ef44af8bf41fe993e21eb80ae1c05dae0292cda2453d4c880f0b3 | MATLAB | 4,222 | 133 | function h=plotgauss2d(mu, Sigma)
% PLOTGAUSS2D Plot a 2D Gaussian as an ellipse with optional cross hairs
% h=plotgauss2(mu, Sigma)
%
% This file is from pmtk3.googlecode.com
h = plotcov2(mu, Sigma);
return;
end
%%%%%%%%%%%%%%%%%%%%%%%%
% PLOTCOV2 - Plots a covariance ellipse with major and minor axes
% ... |
51e3c9a967ac337779d209ad05c0980ab10d98ea8f2665a32bd7363ad4b5985e | MATLAB | 4,222 | 105 | function y_Call_DPABISurf_VIEW(SurfUnderlay,SurfOverlay,Flag_LR, N_Min,P_Min,Surf_Mask,Surf_Mask_Rule,ColorMap,N_Max,P_Max)
%This is a function which is used to display the result by DPABISurf_VIEW.
%FORMAT y_Call_DPABISurf_VIEW(SurfUnderlay,SurfOverlay,Flag_LR, N_Min,P_Min,Surf_Mask,Surf_Mask_Rule,ColorMap,N_Max,P_Max... |
868db0a470f115e6c8a22fb5c1c30ff0ffe198ccbf0bcf110dea9865aeb9a3e8 | MATLAB | 4,222 | 134 | function vol = erode3d(vol, eop, r, res)
% erode - perform 3D erosion with operator
%
% FORMAT: vol = erode3d(vol [, eop, r, res])
%
% Input fields:
%
% vol 3-D boolean volume
% eop erosion operator with odd size ! (default 3x3x3 cube)
% r 1x1 double radius, if given, ... |
939a2401ca25226161044fed56762e246e8da3b88fab53717765774f2d9b81d7 | MATLAB | 4,222 | 196 |
local = true;
if ~local
ldir = '/localhome/kabram/Dropbox (HHMI)/PoseEstimation/Stephen/18012017_trainingData/justHead/';
Q = load('/groups/branson/bransonlab/mayank/PoseTF/headTracking/FlyHeadStephenCuratedData.mat');
else
Q = load('/home/mayank/work/poseTF/headTracking/FlyHeadStephenCuratedData.mat');
ldir ... |
920ae27b89bdd5ca046111885b1b04dea9cbbe2fed0a78e1165d571ee487b890 | MATLAB | 4,224 | 119 | %% TODO: turn this into a function, rather than script
%%
%Plot the basic elements of a linear model that accounts for neural firing
%as a function of the subject's choice and the cued action. From this
%dataset it appears that there is no significant tuning prior to the action
%cue suggesting some type of heir... |
dcf7f912932adf3bf772ec9eab279ac04160a8f1634c49bc1cad7b2b9ab9b62d | MATLAB | 4,224 | 152 | function [img, Vto] = scn_map_image(loadImg, sampleTo, varargin)
% This function takes an image name in loadImg
% and loads the data, resampling to the space defined
% in the image sampleTo. The resampled image will retain
% the data type of the input image.
%
% :Usage:
% ::
%
% [imgData, volInfo_mapto] = scn_map_i... |
27230ea987ed91a86cc37490d64ce2dbb853776069d3405d577b1ad95ee08ad7 | MATLAB | 4,225 | 122 | function [mappedX, mapping] = npe(X, no_dims, k, eig_impl)
%NPE Perform the Neighborhood Preserving Embedding algorithm
%
% [mappedX, mapping] = npe(X, no_dims, k)
% [mappedX, mapping] = npe(X, no_dims, k, eig_impl)
%
% Runs the Neighborhood Preserving Embedding algorithm on dataset X to
% reduce i... |
7d7253ac96d43281bc89fea056c5e26990f9c4a35fa55ac98baa0638d84db9ec | MATLAB | 4,227 | 141 | % AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Provided by the Herzenberg Lab at Stanford University
% License: BSD 3 clause
%
classdef CellB... |
a7c121e6c0ddcfe6dcd4d016b98a40c177099bff33628d224cc3b0676b6cbfae | MATLAB | 4,227 | 144 | classdef ParameterVisualizationMemory < ParameterVisualization
properties
% If true, a prop for this pvObj is currently selected, and we are
% successfully initted/displaying something.
initSuccessful = false;
hArgs = {'Color','k','LineWidth',2};
propPrefix = '';
imsz = [];
net... |
ee0fb701b8373be8046785af065446f249c36eb8386a110e4469b22964f3e5cf | MATLAB | 4,229 | 106 | function machine = train_rbm(X, h, eta, max_iter, weight_cost)
%TRAIN_RBM Trains a Restricted Boltzmann Machine using CD1
%
% machine = train_rbm(X, h, eta, max_iter, weight_cost)
%
% Trains a first-order Restricted Boltzmann Machine on dataset X. The RBM
% has h hidden nodes (default = 30). The training is performed... |
832bd4581f930327bbc196972233198207a88c7d2bbfc04b71e93990a66fdf31 | MATLAB | 4,231 | 164 | function [samecost, sameassignment] = testassignment
%TESTASSIGN Test and compare the assignment algorithms
% [SAMECOST, SAMEASSIGNMENT] = TESTASSIGN randomly generates distance
% matrices and solves the assignment problem using different algorithms.
% Edit the header of this file to change the simulation parame... |
798326a0abe281030152693a497ebb453670498d167d50d1e2c28dbb493d1391 | MATLAB | 4,232 | 142 | function [] = LogScale( whichaxis,logbase,varargin)
%LogScale(whichaxis,logbase) renames the tick labels on your axes for a
%logarithmically scaled variable.
%
%INPUT
% whichaxis which axis did you log scale (can be 'x' 'y' or 'xy')
% logbase base of the logarithm you used for your points (ex 10)
%
%EXAMPLE
%... |
397cc20fb02628a797a665934a3cd15551e632c618acdd26cfce346a4be2ff4c | MATLAB | 4,233 | 115 | % Second-kind integral equation on the unit cube, Laplace single-layer.
%
% This is basically the 3D analogue of IE_SQUARE2.
%
% Inputs (defaults are used if not provided or set empty):
%
% - N: number of discretization points in each dimension (default: N = 32)
% - OCC: tree occupancy parameter (default: OCC = 512... |
8fe277022e11e4691f7e2d5bcd2769125c7411a9c41096d1424737e80cda6935 | MATLAB | 4,233 | 103 | function C = normxcorrn( T, A, shape, Tm )
% Normalized n-dimensional cross-correlation.
%
% For 2 dimensional inputs this function is exactly the same as normxcorr2,
% but also works in higher dimensions. For more information see help on
% normxcorr2.m. Also see Forsyth & Ponce 11.3.1 (p241).
%
% Also, it can take ... |
f9d52c44e399f91370f2e8475660b92f09a5c31e78b1683a99ab12a1cab1c62f | MATLAB | 4,233 | 140 | function [e,p,nodemap,elemap,dim,nnpe]=read_nod_elm(infn,tetgenflag)
% [e,p,nodemap,elemap,dim,nnpe]=read_nod_elm(fn,tetgenflag) reads the node/elm list
% from a file whose format is as follows. fn should not have any extension.
% The format of .nod header is:
% <# of points> <dimension> <# of attributes> <# of bounda... |
ed514391240b3d4f1712c04f61e18aea9b5d6a338bf8228e8b4b80f0bc830ad6 | MATLAB | 4,234 | 106 | function plot_badchannels(params,EEG,single_path)
% Recording ids
s_ids = cellfun(@(x) regexp(x,'.*(?=_eeg.set)','match','lineanchors'),{EEG.filename});
% Check that the number of channels is the same for all the recordings
etc = {EEG.etc};
if range([EEG.nbchan]) ~= 0
error('Different number of total channels in ... |
d71d03461f534f1adc3b3acef784cbafafd03da02261f658a4f6b275c57de207 | MATLAB | 4,235 | 115 | % Second-kind integral equation on the unit cube, Laplace single-layer.
%
% This is the same as IE_CUBE2 but using HIFIE3X.
%
% Inputs (defaults are used if not provided or set empty):
%
% - N: number of discretization points in each dimension (default: N = 32)
% - OCC: tree occupancy parameter (default: OCC = 512)... |
3c9bb2d826e70a4dffdc38c950b712513f7e900bce9773883c9f2009d6dc8ae2 | MATLAB | 4,236 | 109 | function [event] = read_shm_event(filename, varargin)
% READ_SHM_EVENT reads the events in real-time from shared memory
% this is a helper function for READ_EVENT
% Copyright (C) 2007, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% ... |
e0cd932f8128423e774c1d1fb146034dd91025b04480962efa291b3e143d1b47 | MATLAB | 4,236 | 133 | %% choose sessions
datRoot = '/Volumes/LaCie/Farries recordings/';
rat = 'IM1261';
sesList = dir([datRoot rat '/20*']);
sesList = arrayfun(@(x) x.name, sesList, 'UniformOutput', false);
sorted = cellfun(@(s) exist([datRoot rat filesep s filesep 'unitDat.mat']), sesList) == 2;
behav = cellfun(@(s) exist([datRoot rat fil... |
6b3c1876f386be247d2338401bf62717224b74d51c457f3edd0ebca89a13b41f | MATLAB | 4,239 | 137 | function [hmm,Gamma,Xi,vpath,LL,datat] = hmmdual_FK(data,T,hmm,Gamma,Xi,residuals)
%
% Dual estimation of the HMM, first Gamma and then the HMM structure
%
% INPUTS:
%
% data observations - a struct with X (time series) and C (classes; optional)
% T Number of time points for each time series
% hmm ... |
aef52eb438e7942624c52fa6196b82b81cb8f6106227fe3e69d1bb575687b05f | MATLAB | 4,240 | 65 | psthPara.binsize = 10; psthPara.binstep = 10; % ms
psthPushPara.binsize = 50; psthPushPara.binstep = 5; % ms
cwStr = ["correct", "wrong", "all"];
if contains(protStr, "duration")
devStr = "devDur";
end
for cwIdx = 1 : length(cwStr)
switch cwStr(cwIdx)
case "correct"
%% (cwStr(cwIdx)... |
7b2abdf5760a71f51cb13587918049394c0a7306d3db16e747daf18ef7b3371e | MATLAB | 4,241 | 181 | %***********************************************************
% imsjm - imagesc tool with a few better features. 18-5-05
% % 11-8-08: beefed up version
% % 10-9-08: use proper cartesian axes w/ 'xy'
% % 22-10-08: flip second axis for corrct orientation wrt scanner
% extra arguments:
% phase or p - ph... |
cf32f965ffbcee4baf28b9fa98b0acfc593a04496214707c6bb84340234b38e4 | MATLAB | 4,241 | 128 | %%% Simple linear unmixing script for Guo et al (Science Advances) manuscript submission.
%%% Written by Chetan Poudel, Ziyu Guo, and Joshua Vaughan. (2024)
clear all
% Enter path to the analysis script.
script_path = 'A:\MATLAB scripts\';
cd(script_path)
% Select region of interest (ROI) for unmixing (eg... |
a6f35a1927502dd6774e52244a5b47bcefca4cb058f2f016e4755f72dc5d7d9b | MATLAB | 4,243 | 115 | function [select] = parameterselection(param, data)
% PARAMETERSELECTION selects the parameters that are present as a volume in the data
% add that have a dimension that is compatible with the specified dimensions of the
% volume, i.e. either as a vector or as a 3D volume.
%
% Use as
% [select] = parameterselection(... |
c20b8fd18502fb81332004262c36c5b747570485e72f1217e7c5829776abf73f | MATLAB | 4,243 | 176 | function plotmesh(mesh, isPlotFiducials)
% PLOTMESH Allows fast and easy viewing of meshes in NIRFAST format.
%
% SYNTAX:
% PLOTMESH(MESH)
% PLOTMESH(MESH, ISPLOTFIDUCIALS)
%
% PLOTMESH(MESH) MESH is NIRFAST mesh structure.
% PLOTMESH(MESH, ISPLOTFIDUCIALS) MESH is the NIRFAST mesh structure.
% ISPLOTFIDUC... |
f17853c621b145657c95aa5ff46d3baa59c53c2424886757c0d0fb0e0a3a1aa6 | MATLAB | 4,243 | 125 | %% make a plot avg LFP for each animals, raster of all detected waves, and a histogram
clear;clc;close all
%paths to dta files for each animal
dataPaths{1} = 'D:\InVivo\S1-Baclofen\2022-04-19_Baclofen\3-baseline';
dataPaths{2} = 'D:\InVivo\S1-Baclofen\2022-04-21_Baclofen-Attempt\1-baseline';
dataPaths{3} = 'D:\I... |
e9b200c96d60b908712461f22f6702aa186f1c6660de97433eeda95076f3f323 | MATLAB | 4,246 | 146 | % topo2sph() - convert a topoplot() style 2-D polar-coordinate
% channel locations file to a 3-D spherical-angle
% file for use with headplot()
% Usage:
% >> [c h] = topo2sph('eloc_file','eloc_outfile', method, unshrink);
% >> [c h] = topo2sph( topoarray, method, unshrink );
%
% Inputs:
%... |
cbf5cae450063b312e001d516d4eb0dd5bc9963b10da79c9a943d833da1ae340 | MATLAB | 4,248 | 103 | function [BlockdemonDispFields,myPool]=SmoothDemonField(myPool,BlockdemonDispFields,DemonSmoothSize,DynamicSmoothing,IsDFTMoving,CircularFilter,CircularFilterFrames,...
PixelBlockSize,TotalSmoothingArea,VerticalPixels,HorizontalPixels)
% PixelBlockSize=10;
% TotalSmoothingArea=Intermediate_Crop_Props.Bou... |
3155550fe2ee430bc5144f0f2e9d77a6ad70a31a0d789c846b286e21332462dd | MATLAB | 4,252 | 99 | % MATLAB code provided by Seyed Mohammad Ali Rahmati
% Affiliation: Biomechanics and Motor Control Lab, Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA.
% Description:
% This script computes a sensitivity analysis of the mean maximum muscle-tendon (MT) moment to changes in
% muscle para... |
c38f8c5121216b2714e3dfe57c3e6d3c6b2e4838fc21dcdde68d75bbce26edbd | MATLAB | 4,253 | 110 | %{
Copyright (c) 2025 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
classdef LegacySupport
%LEGACYSUPPORT This is a static class that contains resources for
%loading old style Axis Data
properties(Constant)
P200D30S_PLATE_TYPE = hex2dec('0400001... |
b656b135b1a2d575413a4b5b024ce7f74321b287ef67e7bfb0ee1d101f008cff | MATLAB | 4,254 | 121 | %% permtest_tsdata_to_mvgc
%
% Calculate null distribution for conditional time-domain MVGC from time series
% data, based on a permutation test
%
% <matlab:open('permtest_tsdata_to_mvgc.m') code>
%
%% Syntax
%
% FP = permtest_tsdata_to_mvgc(U,x,y,p,bsize,nsamps,regmode,acmaxlags,acdectol)
%
%% Arguments
%
% See al... |
deda9c685ff1c1d7941be2057437b8616a2a64e786706c1a57bcc43e3a53c64b | MATLAB | 4,255 | 121 | function write_edf(filename, hdr, data)
% WRITE_EDF(filename, header, data)
%
% Writes a EDF file from the given header (only label, Fs, nChans are of interest)
% and the data (unmodified). Digital and physical limits are derived from the data
% via min and max operators. The EDF file will contain N records of 1 sampl... |
18df9cac6756eccea6978e10dc502374cc3a87309ff2a38aa9eb14c05fd585cf | MATLAB | 4,256 | 129 | function [spike] = read_neurosim_spikes(filename,headerOnly)
% READ_NEUROSIM_SPIKES reads the "spikes" file that is written by Jan
% van der Eerden's NeuroSim software. The output is represented in a
% structure that is consistent with the FieldTrip spike representation.
%
% OUTPUT
% spike: A FieldTrip raw spike stru... |
738f639b7109aba884585033752c1419d8cd75b3a46df3366e5cb4b74faf697a | MATLAB | 4,257 | 182 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
e3b829e2134eb4ee8939ad5354f17b57bd4c4f86e57322325a2f5c499048955e | MATLAB | 4,257 | 131 | function [int_dat,mask_vol,outname] = iimg_intersection(varargin)
% Make a mask of the intersection of n image files (pos or neg values)
% If 'name' followed by an image file name is entered, writes output to
% that image
%
% :Usage:
% ::
%
% [int_dat,mask_vol,outname] = iimg_intersection(name1, name2, etc.)
% ... |
feb9347e3527710d748bfcdbb6054086f63ee4637637f23b471ba4410802f10e | MATLAB | 4,258 | 182 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
673f54b3e6ff7bb5961b25ec706c3c5dd62913b3be32c16b4c76da75a1ef8a51 | MATLAB | 4,259 | 129 | function [spike] = read_neurosim_spikes(filename,headerOnly)
% READ_NEUROSIM_SPIKES reads the "spikes" file that is written by Jan
% van der Eerden's NeuroSim software. The output is represented in a
% structure that is consistent with the FieldTrip spike representation.
%
% OUTPUT
% spike: A FieldTrip raw spike stru... |
7fcbee84638723a1a961966aedf65306607da0153cb652c3972ffbf2f3f32aa8 | MATLAB | 4,260 | 134 | function COR = modelr1(COR,cfg)
% <*LAN)<]
% v.0.0.1
%
%
%
% Realiza modelos usando R
% COR estructura de datos
% .cfg configuraciones
% .model = formula del modelo segun R
% 'rt ~ BETA'
% .command = comando a utilizar
% 'lme' linwae mixed effect model
% ... |
1993803311c951f05c8645a5abc059d1040fa945992ad8a9b002bd9331a9aa3b | MATLAB | 4,261 | 112 | % Step 2-3: Keypoints and Descriptors
% Calculate the SIFT Descriptors for a subset of subvolumes of the experiments
% as dictated in the loadExperimentParams.m script.
%
% INPUTS:
% sample_num is the index of the tissue sample to register
% run_num is the index of the experiment for the specified sample
% start_idx an... |
e6834c0daca94d6b0434942cd29fcc1bb104a0fc7d0d29444b37560fd83573f4 | MATLAB | 4,261 | 104 | function [masks,keepLocs] = maskGaussians( siz, M, width, offset, show )
% Divides a volume into softly overlapping gaussian windows.
%
% Return M^nd masks each of size siz. Each mask represents a symmetric
% gaussian window, the locations are evenly spaced throughout the array of
% size siz. For example, if M=2, the... |
1ffd9a8980eb2830033bd05cb90c38dda411221ec6601d1ec1207725a0c42bd0 | MATLAB | 4,262 | 118 | function basis=legs(x,n)
% usage: [basis,gradbasis]=legs(x,dir,n)
%
% returns the values and directional derivatives of (n+1)^2
% spherical harmonics at locations given in x and, for the
% gradients, for (in general non-normalized) directions given in dir.
%
% input: x set of N locations given as an Nx3 ma... |
bec04b4299ea0e356f5f324fb678991c31b252482f724deb3f08cc3f88b0de02 | MATLAB | 4,262 | 125 | function socialnetworks_convert_logfile_to_prt(logfile_to_convert, output_prt_filename, template_prt_file)
% A function for conversion of presentation logfiles to BrainVoyager protocol (PRT) files
% Open and read the log file
fid = fopen(logfile_to_convert);
text = textscan(fid,'%s');
text = text{1};
fclose(f... |
64d4bd53d9f7c595f269421b20ef671cad7df0955d17e393cb50e601b82a57f8 | MATLAB | 4,263 | 145 | % df = readtable("U:\users\ryanh\projects\hpc_ctx\sessions_v2.csv",'Delimiter',',');
% df = df(contains(df.use,'TRUE'),:);
df = table()
df.basepath = {pwd};
check_original_states = true;
% visual of current edges (states) for linearized pos
% gui labeled as this:
% ___ ___
% | 1 | 4 |
% |2 |0 |5
% |__ | __|... |
3e437a69fb563bc3fdf989fb7acf4f4db5bbdb0c752fb49e0e3620a2c7cd3c25 | MATLAB | 4,264 | 182 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
394b8ab62b79291a60c37533b21dd1e83e1b2327d703ecf3a5075d29dd169fee | MATLAB | 4,267 | 159 | %% Create the adjacency graph of a portion of the Web.
% [U,G] = surfer(root,n) starts at the URL root and follows Web links
% until it forms an adjacency graph with n nodes. U = a cell array of n
% strings, the URLs of the nodes. G = an n-by-n sparse matrix with
% G(i,j)=1 if node j is linked to node i.
%
% Example: ... |
7f9f1f6b4921c525457721b5242a134c966bec0117293ef20b1bd53bbc587c57 | MATLAB | 4,267 | 151 | function [stat,out] = RFT_GLM_contrast(X,y,c,type,u,verbose)
% applies RFT to GLM-based contrast inference
% function [stat,out] = RFT_GLM_contrast(X,y,c,type,u,verbose)
%
% In brief, this function uses RFT to test linear mixtures of effects,
% under the general linear model (GLM):
% y = X*beta + e
% where y is the d... |
5c286e7d153d38b35238a1ac5da3b27e51aaffd57eba5e460cd4c92d428b52b9 | MATLAB | 4,268 | 129 | function [spike] = read_neurosim_spikes(filename,headerOnly)
% READ_NEUROSIM_SPIKES reads the "spikes" file that is written by Jan
% van der Eerden's NeuroSim software. The output is represented in a
% structure that is consistent with the FieldTrip spike representation.
%
% OUTPUT
% spike: A FieldTrip raw spike stru... |
daa7bdeb2280395aedb9874aaf079339c78283757af03ce7747d6f438e6be3d0 | MATLAB | 4,268 | 151 | function [ peak, clus, clusid ] = SurfStatPeakClus( slm, mask, thresh, ...
reselspvert, edg );
%Finds peaks (local maxima) and clusters for surface data.
%
% Usage: [ peak, clus, clusid ] = SurfStatPeakClus( slm, mask, thresh ...
% [, reselspvert [, edg ] ] );
%
% slm.t = ... |
3f9d508165233d5f951a4ff73939d0921f1c073863c884edf3469ae5ee50fe98 | MATLAB | 4,270 | 144 | function gtdata = GT3DReconstruct(gtdatain,gtinfo,varargin)
[isshexp,istime] = myparse_nocheck(varargin,'isshexp',false,'istime',false);
nviews = numel(gtdatain);
% run on all cells of networks
if isstruct(gtdatain{end}) && ~all(isfield(gtdatain{1},{'pred','labels'})),
gtdata = gtdatain{end};
netfns = fieldnames(... |
99641d21c13927731173c43cc736e3c7983c2d400aa757f59a99db089ac0ed23 | MATLAB | 4,270 | 195 | % Normalize
% throught the 3th or 2th dimention
%
% Method 'z'
% for z-score
%
% Method 'm'
% for mean substraction
%
% Method 'mdB'
% for decilBell : 10*log(signal/baseline)
%
% Method 'bz'
% for bootstrapping z-score (Revisar por que esto es absurdo)
%
%
%
% V 1.7
%
% Pablo Billeke
%
% 17.03.2015 ad... |
6d8d9470797d83afb2f88f214ab21947b5d239037e325b676ca25b8077670082 | MATLAB | 4,271 | 132 | %% Orig "truncated lbl" file from Mayank
%
% note, lbl.labeledposMarked doesn't have expected number of els compared
% to .labeledpos and .movieFilesAll. So we ignore this field entirely as we
% cannot even know the correspondence of labeledposMarked to the other
% fields.
%
lbl = load('f:\aptStephenCPRInvestigate201... |
b9748b1e1899372cb70b3fee51fb67ead175c2eadca8dec82ca64c5f25722bd7 | MATLAB | 4,274 | 133 | function CBIG_VK2019_example_wrapper(out_dir)
% Written by Valeria Kebets and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
CBIG_CODE_DIR = getenv('CBIG_CODE_DIR');
current_dir = fileparts(mfilename('fullpath'));
pos_v = strfind(current_dir,filesep);
root_dir = fullfile(current_... |
83a4fb78a3407c65fac6a45764675465b6942c771016c5b0a8209f7dcc085f3c | MATLAB | 4,275 | 182 | % This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
997b5e0d0be83b16e0550ca5362a5aef203ce1a95caaa196cebfde92588c858d | MATLAB | 4,275 | 90 | classdef (Sealed) AdjMatrixParams
% defines the available parameters for an adjacency matrix
properties (SetAccess = private, GetAccess = public)
Type = adjmatrix.NetworkTypes.SqrLatt; % network type
N = 400; % number of elements
L = [ 20 20 1 ]; % linear dimension (sqr latt: number of e... |
f6375ca5450378d1e3d471fd75fb6ac76b05e153081dd1b62e6dee379e24478b | MATLAB | 4,275 | 126 | function obj = TLprep1l(obj,Y_grayMatter_mask,V_grayMatter_mask)
for i=1:length(obj.MPfile_name_run)
obj.run(i).td.MPs=readmatrix(obj.MPfile_name_run{i});
end
for i=1:length(obj.MPfile_name_run)
obj.run(i).name=['run' num2str(i)]; %auto generate the run names
end
obj.run(1).p.def... |
edfd859aa32e225b2746c09e503f9d69d7b017433baee5d883831e126198ddca | MATLAB | 4,276 | 89 | function [Obj, log] = SOFAcompact(Obj)
%SOFAcompact
% Obj = SOFAcompact(Obj) compacts the unique value to singleton dimensions
% of variables where possible.
% Current limitation: Variables with 3 dimensions will be only compacted
% when the third dimension is the compressible one.
%
% SOFA API - function SO... |
7d96f7518e7299bf35210f82bf7529189afc3f015874bc32c4ba8ea2c300a45f | MATLAB | 4,278 | 151 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
function figure_singleTrial_cca(condition, srmr_nr, isubject, ...
c_axis, iscolorbar, trial_number, is_norm)
% set path
savepath_ga = getenv('GADIR');
% condition info
cond_info = get_conditionInfo(condition, srmr_nr);
cond_name = cond_info.cond_name;
nerve = cond_i... |
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