sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7b612d04ab9173175cc0a1d947a846cbc59f21e1274f08c29002eecb04d958c2 | MATLAB | 1,704 | 51 | function c = tapas_softmax_2beta_config
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Contains the configuration for the softmax observation model for multinomial responses and
% different betas for rewards and punishments. NOTE: this model is acausal in situat... |
833763ea43b7f511169d7459ecbe0d63904f8558cf58ffc2a48c2d5a5172cbbc | MATLAB | 1,704 | 62 | %% h = sepia_handle_panel_qsm_myMethod(hParent,h,position)
%
% Input
% --------------
% hParent : parent handle of this panel
% h : global structure contains all handles
% position : position of this panel
%
% Output
% --------------
% h : global structure contains all new and other h... |
b4af315bc29a1832834fddeb714c185e2d247a78c40b997de700949e9c315136 | MATLAB | 1,704 | 55 | function [channels,groups] = GetChannels(groups)
%GetChannels - Get list of channels for one or more spike groups.
%
% USAGE
%
% channels = GetChannels(groups)
%
% groups one or more optional electrode groups (default = all groups)
%
% EXAMPLES
%
% all = GetChannels; % list all channels
% ... |
3d32d380acad6d967a9b2f3a225da9581c90478278f33b6c04b435695a1146ca | MATLAB | 1,705 | 40 | function Mppe = localCorrelationMap(movie,tilesize)
distMat = zeros(tilesize^2,tilesize^2);
for i = 1:tilesize^2
for j = 1:tilesize^2
[x1, y1] = ind2sub(size(distMat),i);
[x2, y2] = ind2sub(size(distMat),j);
distMat(i,j) = norm([x1 y1]-[x2 y2]);
end
end
mask = 1./(distMat+1);
mask = ma... |
06e3333266d403d294175de36d6ffed8b4104580f58cedff8e7d802a8967ac22 | MATLAB | 1,706 | 61 | function [y_fit, x_fit] = datafit_smoothingSplines(x, y)
% fits smoothing splines, estimates the smoothing coefficient such that the
% R-square value => 0.90
% (c) Jiri, Dec16
assert(size(x,1) == size(y,1));
%% settings for fitting
rSq_lim = 0.50;
rSq_tol = 0.01;
%% initial fits
% upper bound
pSm_hi = 1.0; % para... |
243184028bf60a36639c1afe3bb9f1afa0bd81808a2c7722e87c45580368d68f | MATLAB | 1,707 | 48 | %% tol = sepiatest.tolerance_for_method(category, methodName)
%
% Description: returns the numeric tolerance to use when comparing a
% method's output stats (sepiatest.mask_stats) against its saved
% reference (sepiatest.compare_to_reference). Deterministic closed-form
% methods get a tight tolerance; iterative solvers... |
5dc7a1153c1f39f82bf5e61f23f1b52cc4fb7dff5af98a6cfcf944b14631ef94 | MATLAB | 1,707 | 50 | function C2 = mahiem_trialwise(dat,theta,thetabasis)
if nargin < 3
thetabasis = -pi:pi/8:(pi-pi/8);
end
thetabasis = thetabasis(:); %make sure the basis set locations are in a column vector
nChan = length(thetabasis); %number of virtual channels of output
nsens = size(dat,1); %number of M/EEG sensors
ntrl = size... |
d04d6fbdb257b66cf912fea2c996c1d8832c30b9d49ee51c212f3652d0cc5b86 | MATLAB | 1,707 | 57 | function outputImage = imerode(this, structureElement, nD)
% Erodes image clusters slice-wise; mimicks imerode in matlab functionality
%
% Y = MrImage()
% dilatedY = Y.imerode(structureElement, nD)
%
% This is a method of class MrImage.
%
% IN
% structureElement
% morphological structuring element for d... |
fcaccc46bdc4233ceaec1c48ea45766dac453a282d8c4b0f1904233b4bbe28b6 | MATLAB | 1,707 | 54 | function [] = create_comparison_image(sim,bin,sim_domain)
% %@create_comparison_image Creates a good looking image that compares a
% %simulation (sim) with a real binary tumor (bin).
% % Detailed explanation goes here
% sim, bin and sim_domain must have the same size (182 x 250)
brain_contour = bwperim(sim... |
571c4ee4bb388f4793d0c6727b3fde24503fb49ae980fa762644397c07cc887a | MATLAB | 1,708 | 55 | function y = vl_nnrelu(x,varargin)
%VL_NNRELU CNN rectified linear unit.
% Y = VL_NNRELU(X) applies the rectified linear unit to the data
% X. X can have arbitrary size.
%
% DZDX = VL_NNRELU(X, DZDY) computes the derivative of the block
% projected onto DZDY. DZDX and DZDY have the same dimensions as
% X and ... |
a4087a1feae04c36e1b4c802ab5e91475499e61254e72ad6dd70fed0d2b4780a | MATLAB | 1,709 | 42 | %% =============================
% PALM Analysis: REEXT CS×TUS×EXP
% =============================
% --- Locate repo root (relative to this script)
thisfile = mfilename('fullpath');
[scriptdir, ~, ~] = fileparts(thisfile);
cd(scriptdir); % Ensure consistent working dir
% stats/permutation_tests/palm_code/<thisfile>... |
33abbe7c5bdeefc6422965ed456876e124813b76b49fd6ca22005dceead43659 | MATLAB | 1,710 | 59 | function wpt = modwt_custom(data, wavelet_type, level)
% Usage:
% wpt = modwt_custom(data, wavelet_type, level)
%
% Inputs:
% data - (Samples x Channels) matrix
% wavelet_type - 'haar' (currently only 'haar' supported for manual implementation)
% level - Decomposition level
%
% Output:
% wp... |
40a7a13bca58972349662bd6ae9aa8b2b8e7ab03c6d166ccfc1b36be09386185 | MATLAB | 1,710 | 55 | function tapas_rdcm_compile()
% tapas_rdcm_compile()
%
% Compiles integrator for DCM. Assumes that source code file
% 'dcm_euler_integration.c' is in the same folder as this function
% and places the compiled mex-file in the same folder.
%
% Input:
%
% Output:
%
%
% -----------------------------------------------... |
b7d4dd71dabcfb87d2e1957ebf6906fe6ffe6b56c67a83e425bc179a66552f29 | MATLAB | 1,710 | 37 | function [I,Ie,Ii,Ix] = atttRec_compute_input_current(Wrr, Wrf, Jrr, Jrf, r, r1, Ne, Ni, Nx, Ke, Ki, Kx)
% Vectorized computation of input currents from excitatory and inhibitory neurons
N = Ne + Ni;
I = zeros(N, 1); % Output current
% Excitatory connections
idx_e = 1:(Ne*Ke); ... |
a342d8f58874148617b3f66cbaf55aee2f531de07f94aa0439109aebd0d8e8db | MATLAB | 1,711 | 59 | function plotEventTimeDistributions(eventInfo, eventName, yLim, zeroLabel)
% Plot the distribution of the desired event as a box plot
% Make figure
fig;
hold on;
axis off
ax = gca;
% Box plotting parameters
lw = 0.5;
bxw = 0.25;
alpha = 1;
spacing = [1,1.75];
buff = 2.5;
axlocs = [spacing; spacing + buff; spacing + b... |
274267a1cf920d83501fb322c532f2a6a74130be9b337e44de15969b4aea6bbe | MATLAB | 1,712 | 68 | function obj = centre_latent(obj)
N = numel(obj.data);
D = prod(obj.lat);
% ---------------------------------------------------------------------
% Centre
z0 = sum(obj.Z,2)/N;
obj.Z = bsxfun(@minus, obj.Z, z0);
obj.ZZ = obj.ZZ - N * (z0 * z0');
% ---------------------------------... |
2ec1fb13f724e01f99c78d20f42cef1927887e6c8875a38ddbdf3c0079a4f2ec | MATLAB | 1,712 | 44 | function [neuronid,idthr,ens_cel_corr,sur_cel_cor] = find_core_cells_by_correlation(raster,ens_raster,nsur,p)
%
% [neuronid,idthr] = find_core_cells_by_correlation(raster,ens_raster,nsur,p)
%
% Detectes the core neurons of a given raster. A core neuron is defined as
% a neuron that whose correlation with an ensemble is... |
4473cd7f9aded502e91e021dff7bf209940d149c60791cd05cd470505d1de0a8 | MATLAB | 1,712 | 47 | %% Downlaod example CSV and data
if ~isdir('ExampleData')
mkdir('ExampleData');
end
availableDataSource = {'HarvardDatabase', 'Dropbox'};
downloadSource = 'Dropbox';
app.MEANAPStatusTextArea.Value = [app.MEANAPStatusTextArea.Value; ...
'Downloading example matlab files...'];
pause(0.1);
fileNames = { ...... |
7afed0fee85be21e600ac34e8a80378224f74849937189bd836c92b82a1bdcce | MATLAB | 1,714 | 54 | %% Set up the analysis
% ------------------------------------------------------------------------
% Add the MKDA Toolbox with subfolders to your Matlab path:
% (Customize folder name for your computer)
g = genpath('/Users/tor/Documents/Code_Repositories/Canlab_MKDA_MetaAnalysis');
addpath(g)
savepath
% Create a direc... |
ae7ed7bd2ca71ad6281138d1879b77980bea0941ff9bde35395f6f45784dc3f5 | MATLAB | 1,714 | 97 | % plot_error
% Data dir
rootdir = [getenv('MATHOME') '/umeda_data/'];
datadir = [rootdir 'motion_unit_rate/'];
modeldir = [rootdir 'model_spr3/'];
errordir = [rootdir 'model_err/'];
dataname = 'motion';
modelbase = 'neuron_to_motion';
%modelbase = 'motion_to_neuron';
xy_mode = [1 3];
Nxyz = 6; ... |
110f12bf78227b3343714b73621287737c9c26a97b0d3de4d58cd59b5f864df1 | MATLAB | 1,715 | 67 | function pfxFileArray = tapas_uniqc_prefix_files(fileArray, pfx, isSuffix, isMixedCase)
%prefixes/or suffixes (cell of) files (incl. paths) with file prefix before file name
%
% output = tapas_uniqc_prefix_files(input)
%
% IN
% fileArray cell(nFiles,1) or single string of filenames
% e.g.
% '/LK215... |
49170ad5a7a50aa28fc95625d6afd3ed97e3d5ec97aae08918d3339d3d5252a5 | MATLAB | 1,715 | 50 | % setup circles lookup tables
% lookup tables are in files that are pointed to by a database table
% circles_lookup
% a unique file exists for a combination of width, height and radius
% if a previous file exists, it will be overwritten
% assumes datajoint is setup in the environment, and table definition is
% already ... |
d65695fc43c1380c191d7596e5c6a13f324fed4572f4ae60141565111e4ffe8d | MATLAB | 1,716 | 65 | function [betas,residuals] = massGLM(X,y,add_offset,rank_regression)
%function [betas,residuals] = massGLM(X,y,add_offset,rank_regression)
%efficiently calculates betas for mass univariate GLM
%
%inputs: X (design matrix) should be nTrials*nRegressors
% y (data) should be nTrials*nChannels*nTimepoints(*nFrequenc... |
a6d0e50dd62b6ff1b8ff94ad61a6af2b01e64ef5ed1ae03fe33020f949b6f333 | MATLAB | 1,717 | 56 | function c = tapas_gaussian_obs_offset_config
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Contains the configuration for the Gaussian noise observation model for continuous responses, with
% an offset lambda
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
23ff7b0506bee8e5edb4066644dbc4d47abbeffba57288822142c3dfef894199 | MATLAB | 1,718 | 43 | function outputCellCell = SUB_cell2cellcell(inputCell,delimiter)
% SUB_cell2cellcell Turn a cell of delimited strings into a cell of cells.
%
% Inputs a cell with some delimiter, and outputs a cell of cells using this
% delimiter.
% ------------------------------------------------------------------------------
% C... |
03ad89507cd1405a7be6686badf3f5c18c94da090795418688864274514ac5d1 | MATLAB | 1,719 | 41 | %{
monet.DriftTrial (computed) # noise drift trials
-> monet.DriftTrialSet
drift_trial : smallint # trial index
---
-> psy.Trial
direction : float # (degrees) direction of drift
onset : double # (s) onset time in rf... |
0e00ff8b1316540fe69ef8828faba1024ec08eb4aafc3b73ec639e7e759ce396 | MATLAB | 1,719 | 62 | function [fh, f, P1] = tapas_physio_plot_spectrum(t, y, hAx)
% Plots one-sided amplitude spectrum of a time series, following Matlab
% help examples
%
% [fh, f, P1] = tapas_physio_plot_spectrum(t, y)
%
% IN
% t [nSamples,1] time vector
% y [nSamples,nTimeseries] different signal time series, one per
% ... |
71ba4e16947838c50f465061c70836aea47a3349abade4b1000e593b0df20553 | MATLAB | 1,719 | 55 | function this = MrAffineTransformation_affineMatrix(this)
% Unit test for MrAffineTransformation computing the affine Matrix
%
% Y = MrUnitTest()
% Y.MrAffineTransformation_affineMatrix(inputs)
%
% This is a method of class MrUnitTest.
%
% IN
%
% OUT
%
% EXAMPLE
% MrAffineTransformation_affineMatrix
%
% See als... |
903182edbe857001ea014966dc6cec43e23512e9bb4d3fff3bbdc46130246434 | MATLAB | 1,719 | 57 | function [verbose] = tapas_physio_plot_iterative_template_creation(hasFirstGuessPeaks,...
t, c, cpulse1stGuess, nPulses1, nPulses2, cpulse2ndGuess, meanLag1, meanLag2, verbose)
% Plot refined heartrate templates
% (C) 2023 Johanna Bayer
stringTitle = 'Preproc: Iterative Template Creation Single Cycle';
if hasFir... |
e34783f7b4d0afab20bd0ca3c94c188291a2affcf7269a1610f4e8c2e05c8016 | MATLAB | 1,719 | 72 | % op_zeropad.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_zeropad(in,zpFactor);
%
% DESCRIPTION:
% Apply zeropadding (a.k.a. zero-filling) to MRS data.
%
% INPUTS:
% in = input data in matlab structure format.
% zpFactor = the factor by which the number of points in the fid will be
% ... |
91181688a70a6f98b939a47114c60da19c94cb012de49ffd681cc79e89754e20 | MATLAB | 1,720 | 57 | function [dvt,types,ids] = detector_vs_truth(hsi,det_out,filt,halo)
%function [dvt,types,ids] = detector_vs_truth(hsi,det_out,filt,halo)
%
% Gets detector confidence for each target, put it in a matrix vs ground truth fields
% for easy comparison
%
% outputs:
% dvt - n_targets x 6 - [detector_output | id | size | ty... |
a29e2b3573bd50c893790df2ed3dbc91ce36ec25c8a029e6fe6f89f42b82682b | MATLAB | 1,721 | 37 | function [pvec, pstruct] = tapas_hgf_jget_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2013 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% ... |
2d0a791dd28e29e626c9e8e788cff659c360ed61ba7d25994d447846c67b8952 | MATLAB | 1,722 | 41 | %!
% @brief This script transfers from json to deepsqueak
% @details This script converts from predefined json files to .mat file
% that can be used in deep squeak
files = dir("json/*.json");
for file = files'
jsontext = fileread(strcat(file.folder, "/", file.name));
json_data = jsondecode(jsontext);
% ... |
c1c88fa75aa976a461024ee799db7ed281b1f01ab88d0887789df2a0c5d274f3 | MATLAB | 1,723 | 37 | function [pvec, pstruct] = tapas_ehgf_jget_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2013-2020 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Pub... |
da944830fcffe3b1c77002a206ffe8e8cddcc2ff19dd5e352e61950744768c28 | MATLAB | 1,723 | 49 |
function npx_example_plotter(ex_unit1,raster_traces,sdf_all,t_pre,t_post,color_s)
trial_nr=size(raster_traces,1);
data={};data=raster_traces;
fig2=figure;set(gcf,'color','w');set(fig2, 'Position', [500, 800 ,700, 350]);t=tiledlayout("vertical");
t.TileSpacing = 'compact';t.Padding = 'compact';
nexttile;
ylim([0 10... |
e65bee150a4a8be206154090d050bdeaefea871e0af8ebf0ec2904bdf6e5e085 | MATLAB | 1,723 | 40 | %% The McsHDF5 Matlab tools
% This and the following documents gives a short explanation of the usage
% of the McsHDF5 Matlab tools.
%
%% Purpose
% The McsHDF5 Matlab toolbox can be used to import HDF5 files generated by
% software from Multi Channel Systems MCS GmbH. Importing the HDF5 files
% via this toolbo... |
4da77c187912885cd7b1c0b2ae2bb30f325ad3561c8614736df3417429741213 | MATLAB | 1,724 | 58 | function outputImage = imdilate(this, structureElement, nD)
% Dilates image clusters slice-wise; mimicks imdilate in matlab functionality
%
% Y = MrImage()
% dilatedY = Y.imdilate(structureElement, nD)
%
% This is a method of class MrImage.
%
% IN
% structureElement
% morphological structuring element f... |
1932b86cda57f4069930fc5c5b49a9e6a7be58d14ec55e8f103882bbecd264fa | MATLAB | 1,725 | 92 | function dt = DistanceTransform(b)
%DistanceTransform - Compute distance transform of a binary matrix.
%
% This function assigns to every point (x,y) in a binary matrix B the distance
% to the nearest point in B with value 1. It uses the Euclidean metric for
% computing distances. The code is based on the algorithm... |
959a0708c97c71238bcb4f535643acfa3318e98908e17f805c38909924756fbb | MATLAB | 1,726 | 47 | addpath('/Users/monaminishio/Downloads/nonfractal/m')
addpath(genpath('/Users/monaminishio/Downloads/wmtsa-matlab-0.2.6'))
lb = [-0.5,0];
ub = [1.5,10];
H_combined = readtable('Hurst_rat_alcohol.csv', "FileType","text");
%col457 = H_combined.H_combined157;
%col458 = H_combined.H_combined158;
%col459 = H_combined.H_com... |
a129cb0668a10309b48a00f8a09307147465127e90682bb1715f4e048299b255 | MATLAB | 1,726 | 47 | % function Z = ZG_rdiv(X,Y)
%
% row division: Z = X / Y row-wise
% Y must have one column
%
% Machine Learning Toolbox
% Version 1.0 01-Apr-96
% Copyright (c) by Zoubin Ghahramani
% http://mlg.eng.cam.ac.uk/zoubin/software.html
%
% ------------------------------------------------------------------------------
% The M... |
f7fabf345bd2eaacef6d2c59794ea10a58d1cc4135c86def73b890ff083a8173 | MATLAB | 1,726 | 61 | classdef Loss < dagnn.ElementWise
properties
loss = 'softmaxlog'
ignoreAverage = false
normalise = true
opts = {}
end
properties (Transient)
average = 0
numAveraged = 0
end
methods
function outputs = forward(obj, inputs, params)
outputs{1} = vl_nnloss(inputs{1}, inputs{2}, ... |
9b50d0b3d37a6dacf9898b96280574a8f159dae884d23856016c8260048edd65 | MATLAB | 1,727 | 56 | function tuning_summary
% summarizes the quality of mice
set(groot,'defaultAxesColorOrder', parula(4)*0.7, 'defaultAxesLineStyleOrder', '-|--|:')
von = aod_monet.VonMises & 'preprocess_id=3' & 'spike_inference=2';
keys = fetch(vis2p.Experiments & aod_monet.VonMises, 'exp_date', 'ORDER BY exp_date DESC');
scores = array... |
43a5a665e8851e3cd85004c1dc69990f3d91590e25cb31eb916ab41fb34156ce | MATLAB | 1,728 | 47 | function [neurons, config, M] = lockNeural4Classifier(R, M, config)
% Lock neural activity for classifier models
if ~isfield(config, 'goodTrials')
goodTrials = [R.success] & ~isnan([R.grabTimeC]) & [R.timeToContact] < 1000 & [R.liftRT] < 1000 & [R.goodDLC] == 1 & [R.liftRT] > 0 & [R.hasNeuralData];% & ~isnan([R.li... |
9a06b349ff0907a0ec3d66c3321b5e3a03f6da46bafafb1b965d4fe3e23d3bd4 | MATLAB | 1,728 | 83 | function [Wout,Weff] = make_test_weight(parm)
% Make output weigtht for test
% -Input
% parm.Ydim = Output dim
% parm.Xdim = Input dim
% parm.Meff = Effective Input dim
% parm.Tau = Lag time steps
% parm.Dtau = Number of embedding dimension
% parm.WXmax = maximum weight of X-dim
% parm.WYmax = ... |
cde1008ea13ab01421915c8b047194d968b953eeb940a923fb8ffb5fd178ae61 | MATLAB | 1,728 | 55 | function [intervals,subcycle,cycle] = FindSubcycles(angles,nSubcycles)
%FindSubcycles - Find timestamps for subcycles of an oscillating signal.
%
% USAGE
%
% [intervals,subcycle,cycle] = FindSubcycles(angles,nSubcycles)
%
% angles phase <a href="matlab:help samples">samples</a>
% nSubcycles numbe... |
d50989d548ca2b60eb3f2ff6820804c4796e85de33dcaaaf909d4c0535280604 | MATLAB | 1,728 | 68 | function [IXr, IEr, IIr, normX, normE, normI] = atttRec_calc_current_norm(weight_name,stats_name,J,optSave)
load(weight_name,'Wrr','Wrf',...
'seqindE', 'seqindI', 'seqindX');
temp1=load(stats_name);
if isfield(temp1, 'Stats1')
V1fr = temp1.Stats1.V1fr;
MTfr = temp1.Stats1.MTfr;
else
V1fr = temp1.V1fr;... |
2e8f6641c99f0868ac0ea718edc189146551b05309da209fc6b6328ca42b41e8 | MATLAB | 1,729 | 50 | %% Interface for batch spike detection - simple version
%{
This is the main script for running spike detection in multiple files ("in
batch") with most advanced settings hidden away to make this easier to use.
The things you need to modify are:
dataPath (str) : where your .mat files containing electrode recordings ar... |
9b7fe573f94866ab72fe8dbbc82053f91e48450bf08c88c04d1f2c28f31b35bc | MATLAB | 1,729 | 61 | classdef Loss < dagnn_bc.ElementWise
properties
loss = 'softmaxlog'
ignoreAverage = false
normalise = true
opts = {}
end
properties (Transient)
average = 0
numAveraged = 0
end
methods
function outputs = forward(obj, inputs, params)
outputs{1} = vl_nnloss(inputs{1}, inputs{2... |
c5df2972c657ff1df2e9078aa5e9d13eabb24e02bf57adf95eab7aaa33293c8a | MATLAB | 1,729 | 42 | function [R, keepers] = BF_RemoveNaN_DistMat(R)
% BF_RemoveNaN_DistMat Removes NaNs from an input distance matrix
% ------------------------------------------------------------------------------
% Copyright (C) 2013-2026, Ben D. Fulcher <ben.d.fulcher@gmail.com>,
% <http://www.benfulcher.com>
%
% If you use this c... |
c8c6e7f2bc15cbd74a49fc098cd212b7f7dc0ec8d7eef2d83a4ed62535a0e77f | MATLAB | 1,729 | 60 | classdef Crop < dagnn.ElementWise
%CROP DagNN cropping layer.
% This is a pecurial layer from FCN. It crops inputs{1} to
% match the size of inputs{2} (starting with a base crop amount).
% A future version
properties
crop = [0 0]
end
properties (Transient)
inputSizes = {}
end
methods
f... |
d0313bd220c0c56f04b74d10063a7e0238c346b07359b076384facc325340f80 | MATLAB | 1,729 | 25 | % Helper functions for FMAToolbox.
%
% Parameter testing.
%
% isastring - Test if parameter is an (admissible) character string.
% isdscalar - Test if parameter is a scalar (double) satisfying an optional list of tests.
% isdvector - Test if parameter is a vector of doubles sa... |
db684bf6d31e5151bcd2c346f3f2f6bb7e61764c3b88f32618f4c98e03ab02b9 | MATLAB | 1,729 | 45 | function exportCurrentFigAsPostscript(filespec,appendFlag,userOptions)
% exports the current figures to the file [filespec,'.ps'] in postscript
% format. if appendFlag is 0 any existing file [filespec,'.ps'] is
% overwritten. if appendFlag is 1 the figure is appended to the existing
% postscript file [filespec,'.ps']. ... |
082bbf2b747bcdd89b94ff32cab4c5e82c5817447f64d6d14fcbdbc8c5c450c2 | MATLAB | 1,731 | 71 | %{
%%%%%%% INPUT %%%%%%%
This function assume 32-Channel ECoG recording along with behavioral
TTL input representing Baseline versus OddBall stimuli
Need to specify: Fs, epoch length (begin&end times) as a 2 element vector
Extract and normalize each epoch based on the 2s baseline prior to the
stimulus.
%%%%%%% OUTPU... |
443ca3ad576a7b698a12d12795d4a62789cae255e30292195f4112b38270101f | MATLAB | 1,731 | 79 | function [folderpath_out,foldername,formatted_string]=getFolder(varargin)
% EXAMPLE USE WITH ARGUMENTS
% getFolder() - dialog
% getFolder(initial_folder_path) - folder to start
%
% This function prompts a window to choose a folder, whose path is passed
% as an output argument and corresponding matlab commands are form... |
5c455c52b62e7fda7c319d84552cb1ce9e75a577e0f78c77d3d138f60a0825d1 | MATLAB | 1,732 | 60 | classdef Crop < dagnn_bc.ElementWise
%CROP DagNN cropping layer.
% This is a pecurial layer from FCN. It crops inputs{1} to
% match the size of inputs{2} (starting with a base crop amount).
% A future version
properties
crop = [0 0]
end
properties (Transient)
inputSizes = {}
end
methods
... |
80537117c36651543299d63e7262cdbfc1dc43825b6eb7dc40d15fd81900eb20 | MATLAB | 1,732 | 64 | function bleach_rate = estimate_bleaching_rate(params)
timepoints_to_skip = 1000; % skip first 1 second
show_simple_plot = false;
show_fits_in_cftool = false;
% Load data
ts_fn = string( getFileName(params,'TS') );
load(fullfile(params.pth, "Analysis", ts_fn));
roi_fn = string( getFileName(params,'ROI'));
l... |
84d983bf47c73209ce90bda36060eb61a0e9e32e3c3a466240a7593d1e75fff3 | MATLAB | 1,732 | 58 | function [nel] = afni_nel_parse(nellcell)
%should really check that this is nel and not ngr ...
%assuming we have nel
%get the header part
cnel = char(nellcell); clear nellcell;
ncnel = length(cnel);
%break up into head and data
expr = '(?<head><(\w+).*?>)(?<data>.*)<';
%using expr =... |
a64b65a6aebe19ea9d5ed8a91e4ebdcb497c19102afce11196ec3f8aaacefdeb | MATLAB | 1,732 | 48 | function [K,dK] = covPoly(mode,par,d,hyp,x,z)
% Polynomial covariance function. The covariance function is parameterized as:
%
% k(x,z) = sf^2 * ( c + s )^d , where s = x*inv(P)*z is the dot product
%
% The hyperparameters are:
%
% hyp = [ hyp_dot
% log(c)
% log(sf) ]
%
% Copyright (c) by Carl Edward ... |
0a49978776df0d3ed6fafd373a8cca5b2d4632b27fb29ae6406619338333a5ee | MATLAB | 1,733 | 52 | % this function adds the pairwise copmparison bars to a figure; the 'hold on'
% should have been set before executing this function
% pairWisePs: an nxn pairwise comparison matrix. This is supposed to be
% sorted in descending order of average values (large to small heights)
% a horizontal bar would be displayed whene... |
1d87af4fc68d62efc3c3f761c4361e0e15e5c3946a6f8979f5dafc97cf33460d | MATLAB | 1,733 | 62 | function [RHSdiv, RHSdivx, RHSdivy, RHSdivz] = divergenceTerm3D(F)
% This function calculates the divergence of a field using its face
% average flux vector facevariable, which is a face vector
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE ALSO:
%
% Copyright (c) 2012-2016 Ali Akbar Eftekhari
%... |
3c7e8c6ede4d11b53e5b9b38692ae6c00c1ed70d27a23058d9090b88e3945cb4 | MATLAB | 1,733 | 42 | function slice_regressors = tapas_physio_split_regressor_slices(...
slice_regressors_concat, nSampleSlices)
% Splits a concatenated phase regressor into slice-wise regressors, one per
% column
%
% slice_regressors = tapas_physio_split_regressor_slices(...
% slice_regressors_concat, nSampleSlices)
%
% IN
% ... |
6c18045cc427fb62af416417212f3707e3e559d1780945ee92067db6a65d50d0 | MATLAB | 1,733 | 58 | function r = issubfield(s, f)
% ISSUBFIELD tests for the presence of a field in a structure just like the standard
% Matlab ISFIELD function, except that you can also specify nested fields
% using a '.' in the fieldname. The nesting can be arbitrary deep.
%
% Use as
% f = issubfield(s, 'fieldname')
% or as
% f = i... |
72ac6551590f3818fd05032f2748e86bef517c9688942562a564199bb39e2474 | MATLAB | 1,733 | 61 | close all
clear all
load('Z:\BCI\Data\NDNF_Opto\NDNF_07\062624_NDNF_07\Baseline_noopto\baselineMask_1.mat')
frames_tmp = sbxgrabframe('Z:\Scanbox\Data\NDNF\NDNF_07\062624_NDNF_07\062624_NDNF_07_000_009\062624_NDNF_07_000_009', 1, 24000);
frames_tmp = squeeze(frames_tmp); frames = frames_tmp(:,:, 1:2:end);
% writer... |
bed7612be119946eabeead9da440c67e4cffe854fc75f2ebb241a60d2f873bea | MATLAB | 1,733 | 56 | function vol=addBinaryMapToVol(vol, map, col)
% USAGE: vol=addBinaryMapToVol(vol, map, col)
%
% FUNCTION: to superimpose the binary map map to the true-color
% volume vol. where map==1 the corresponding voxel of volume
% vol is marked in the color col. all other voxels retain
% ... |
c00b1813b9fc6333109aea1ad85570eb871e153e5c5a108d2875c7b9950c9e51 | MATLAB | 1,733 | 51 | function run_current_noise_simulation(params, options)
% RUN_CURRENT_NOISE_SIMULATION - Run with current noise injection
%
% H1 Line: Execute simulation with additive current noise
%
% Syntax:
% run_current_noise_simulation(params, options)
%
% Description:
% Runs simulation with white noise current injection to ea... |
8f3657674b7b22c3e6cba619740fa017310e05bd14b596af8977676232900cbe | MATLAB | 1,735 | 46 | addpath('../Functional/modules/nonfractal/m')
addpath(genpath('../Functional/modules/wmtsa-matlab-0.2.6'))
lb = [-0.5,0];
ub = [1.5,10];
H_combined = readtable('Hurst_schaefer100.csv', "FileType","text");
col457 = H_combined.H_combined157;
col458 = H_combined.H_combined158;
col459 = H_combined.H_combined159;
IDs = str... |
cf6eca766b9e63cd12bf17faab677f29ced12f6ac43122cb98646b6e15e2b0ae | MATLAB | 1,735 | 47 | function [rez] = Waveform_T(rez,DATA)
M_T = length(unique(rez.st(:,3)));
temp = unique(rez.st(:,3));
nt0 = rez.ops.nt0;
Nchan = rez.ops.Nchan;
%calculate the average template of the merged clusters
template = zeros(rez.ops.nt0,Nchan,M_T);
sumaT = zeros(nt0,Nchan,M_T); %To calculate the average template
nb_spike... |
79b8bca3f79549ec66ab0b438039bc88efb79a2d4e9685462b197565180e7876 | MATLAB | 1,736 | 44 | function TMSmkC6(subjdir)
%% delete the noise of the DARTEL c6
%% 1. find t1 voxels with low intensity (e.g., arbitrary threshold 1000). This also highlighed within brain voxels, such as CSF
%% 2. only keep the largest cluster in the result map of step1. These were performed one slice by one slice in three dimentio... |
c796af1616a4cc691dcafe07df0f4271fdebe08be58dbc8b2c22c35e8db53df6 | MATLAB | 1,736 | 34 | %{
# 3-D volumes that compose this stack (usually tiled to form a bigger fov)
-> stack.StackInfo
roi_id : tinyint # same as ScanImage's
---
-> experiment.StackFilename
field_ids : blob # list of field_ids (0-index) sorted from shallow... |
43ad0543d6f4ec3ed76715ad4d5e0ede9524e7c2cc7dd6dc5ef87778abbe7783 | MATLAB | 1,737 | 30 | %-----------------------------------------------------------------------
% Job configuration created by cfg_util (rev $Rev: 4252 $)
%-----------------------------------------------------------------------
function TMSseg(T1dir)
matlabbatch{1}.spm.spatial.preproc.data = {T1dir};
matlabbatch{1}.spm.spatial.preproc.... |
a1db46ad781c3c33a6eb2650b604889abb9b3444832f3cd4ddefa1dac645fb01 | MATLAB | 1,737 | 48 | %% Installing the Toolbox
% Following these instructions is only necessary, if you have downloaded
% the Toolbox as a .zip file. If you are using the .mltbx file or have
% installed the Toolbox via Matlab's "Add-Ons" menu, there is no need to
% perform the steps in this document
%% Adding the package base bath
... |
bf11e2f4ddc0c2626a8e9d0c0ffbcc65d07bccbdeb9e4a01e15ec2278293f8c0 | MATLAB | 1,737 | 54 | classdef BatchNorm < dagnn.ElementWise
properties
numChannels
epsilon = 1e-5
opts = {'NoCuDNN'} % ours seems slightly faster
end
properties (Transient)
moments
end
methods
function outputs = forward(obj, inputs, params)
if strcmp(obj.net.mode, 'test')
outputs{1} = vl_nnbnor... |
fedf73b2b4ae48d638f056085a03e8fd665b52cb7a4805692d9208df8f47d8ab | MATLAB | 1,737 | 80 | function [r,c,V] = findnearest(srchvalue,srcharray,bias)
% Usage:
% Find the nearest numerical value in an array to a search value
% All occurances are returned as array subscripts
%
% Output:
%
% For 2D matrix subscripts (r,c) use:
%
% [r,c] = findnearest(srchvalue,srcharray,gt_or_lt)
%
%
% To also output the f... |
108afcb8ded86c63ed3b12e6f0b2dccde806a97be7ac214511d24edacf0278a5 | MATLAB | 1,738 | 79 | function status = GE_convertVolume(inDir,runnum,outName)
%
% status = GE_convertVolume(inDir,runnum,outName)
%
%GE_convertVolume
%
% Version 3.1
%
% Converts a series of GE slices into Analyze format for SPM.
% inDir is the name of the directory containing the first file of
% the series, e.g. 003
% runnum is the run nu... |
5adf1c418eaf979f5e44cac9ff6fa52f3ab83a8377a5ae9f60b2556ed37a488b | MATLAB | 1,738 | 52 | function [ screen ] = tapas_BLT_initScreen(params)
% tapas_BLT_initScreen initilaizes the screen for the BLT experiment
% Here we call some default settings for setting up Psychtoolbox
PsychDefaultSetup(2);
% Psychtoolbox has some issues in Mac which only allows us to run this
% by skipping some default tests, we mig... |
78aef502b3aad8b7fbd9f1b7fc2117bbf90681bbd4338d1b42adfbf49e18f364 | MATLAB | 1,738 | 50 | function [new_pos] = applyDeformation(deffilename, pos)
%
% Input: deffilename <string> fullpath to the SPM deformation file
% pos <nx3 float> point coordinates to be transformed.
% Output: new_pos <nx3 float> transformed point coordinates.
%
% This function applies the nonlinear SPM voxelbas... |
bdef5e9eca90f907ddca726fdbba4850cc2130e0cfc83f0a7089d2dad661101a | MATLAB | 1,739 | 30 | function [] = path_statistics ()
%%path_statistics (tracks.xvalscm, tracks.yvalscm, tracks)
% This function calculates pathlength, max displacement, distance ratio,
% and (if applicable) displacement relative to user provided reference ROIs
global tracks
global vals
%% Calculate path and max displacement for gene... |
15e21453d90bb0b4e1531a1900ddd7cd5659552e15c17c62a205e788ce8fe72f | MATLAB | 1,740 | 58 | % generateSimulatedBOLD - Generate simulated BOLD time series with noise
%
% Generates clean BOLD responses from ground truth pSFT parameters and adds
% Gaussian noise at multiple SNR levels
%
% Inputs:
% gt_params - Ground truth parameters [mu; sigma; beta; beta_0] (4 x num_voxels)
% I - Stimul... |
3fe7ea9ae2be6df5c76d84892397815b57b6a61a3c9d4314c0f9d074edfd6e06 | MATLAB | 1,740 | 51 | function [ output_args ] = findAssemblyPatterns( activityPatterns )
%FINDASSEMBLYPATTERNS( activityPatterns )
%
% INPUT:
% activityPatterns [1x? cell]: cell array of binary activity patterns
%
% EXAMPLE:
% findAssemblyPatterns( num2cell( [ sort( randi( [0,1] , 20 , 40 ) , 2 , 'ascend' ) ; sort( randi( [0,1] , 2... |
6495e3a5291864933c9e3aad79268b08391d65a438f130e57c092f86d89f4eda | MATLAB | 1,740 | 54 | classdef BatchNorm < dagnn_bc.ElementWise
properties
numChannels
epsilon = 1e-5
opts = {'NoCuDNN'} % ours seems slightly faster
end
properties (Transient)
moments
end
methods
function outputs = forward(obj, inputs, params)
if strcmp(obj.net.mode, 'test')
outputs{1} = vl_nnb... |
05fe1b6c8e38e796b23248c082e6ac4eb1de532d177e1a0a15955225735ab1b2 | MATLAB | 1,741 | 48 | function plot(data,cfg,varargin)
% Function to plot the contents of a McsData object.
%
% function plot(data,cfg,varargin)
%
% Input:
%
% data - A McsData object
%
% cfg - Either empty (for default parameters) or a structure with
% (some of) the following fields:
% ... |
4bb03afc07b6a7221dadd2fad9930bde3b5d9732c8f6d51dc5f1a60c4b851c52 | MATLAB | 1,741 | 43 | function data = fixcoordsys(data)
% FIXCOORDSYS ensures that the coordinate system is consistently
% described. E.g. SPM and MNI are technically the same coordinate
% system, but the strings 'spm' and 'mni' are different.
%
% See also FT_DETERMINE_COORDSYS
% Copyright (C) 2017-2022, Robert Oostenveld
%
% This file is... |
d3e841fa991c4ed73a33d6ab3737ae0cfdb08e1847027a987778f9fa5a7d10de | MATLAB | 1,741 | 43 | % SPHER - return the sphering matrix for given input data
%
% Usage:
% >> sphere_matrix = spher(data);
%
% Reference: T. Bell (1996)
% Copyright (C) S. Makeig CNL / Salk Institute, La Jolla CA 7-17-97
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribut... |
ede19b151d9aae3a239e30d52988b6b74a603cbaaee61b52656150e163857fe7 | MATLAB | 1,741 | 58 | function tidy_ref_models()
% Update reference models to latest MatConvNet version
run(fullfile(fileparts(mfilename('fullpath')), '..', 'matlab', 'vl_setupnn.m')) ;
models = {...
'imagenet-resnet-152-dag', ...
'imagenet-resnet-101-dag', ...
'imagenet-resnet-50-dag', ...
'imagenet-matconvnet-alex', ...
'image... |
f87cd01e20e744d72318c131a77c0d4c717430b68582b2b11c834c155f573711 | MATLAB | 1,741 | 79 | %% S = Signal_mGRE(m0,x2s,te,varargin)
%
% Description: Multiple exponential decay model for multiecho GRE
%
% Input
% ----------
% m0 : T1weighted signal
% x2s : either T2* or R2*
% te : echo times
% ***flag***
% ----------
% 'r2s' : input R2* instead of T2*
% 'freq' : frequency shift of... |
cf7b2220013e1fc06d6944c2ec80751a8d15d1aeea7e4304abdcdfc80f30e2d9 | MATLAB | 1,742 | 63 | function [this, hasRegressors, hasConditions] = init_glm(this)
% This method initializes MrGlm, i.e. checks for consistency and saves
% neccessary files
%
% Y = MrGlm()
% Y.specify_Glm(inputs)
%
% This is a method of class MrGlm.
%
% IN
%
% OUT
%
% EXAMPLE
% init_glm
%
% See also MrGlm
% Author: Saskia Boll... |
5d653e73e4aebfae7da0e4fcaaabfdc0728c1da3777204c873cac2b340a6bc8a | MATLAB | 1,743 | 49 | function orthobasis = tangentorthobasis(M, x, n)
% Returns an orthonormal basis of tangent vectors in the Manopt framework.
%
% function orthobasis = tangentorthobasis(M, x)
% function orthobasis = tangentorthobasis(M, x, n)
%
% M is a Manopt manifold structure obtained from a factory.
% x is a point on the manifold M.... |
7794981c70083317f9959a1336dd3acc80829b01b47b775906a284ffb664091d | MATLAB | 1,743 | 51 | function waveforms = LoadSpikeWaveforms(filename,nChannels,nSamples,list)
%LoadSpikeWaveforms - Read spike waveforms from disk.
%
% USAGE
%
% waveforms = LoadSpikeWaveforms(filename,nChannels,nSamples,list)
%
% filename spike waveform file name
% nChannels number of channels in electrode... |
84944cb51ea0d776204352e6fd7c9bf3bad977c58425e0a7c0c2200ab461793e | MATLAB | 1,743 | 61 | function [p0,pa_h0] = p0_monte_carlo_FWE(DB,iterations)
% [p0,pa_h0] = p0_monte_carlo_FWE(DB,iterations)
%
% needs fields:
% DB.XYZmm % mm coords for each study
% DB.maskV % mask mapped volume
% DB.radius % in voxels
% ----------------------------------------------------
% * get list of all coordinates; selec... |
a6f8bc40eb52e78cb5718b253394408d083c6b9bc344b1a1bde3329588f6680a | MATLAB | 1,743 | 55 | function img = read_avw_img_slice(filename,slice);
% [img] = READ_AVW_IMG_SLICE(filename,slice)
%
% Read in one slice of Analyze (or nifti .img) file into either a 2D or 3D
% array (depending on the header information).
% The purpose is to allow reading big 4D volumes on slice at a time,
% thereby reducing the ris... |
df6c20c1645afc53971a293026052611b3859b7c45b40356aeea8dfad045a8ed | MATLAB | 1,743 | 54 | function fitUtilityFunction(decTab)
% from: https://www.mathworks.com/matlabcentral/answers/154879-using-fminsearch-to-estimate-utility-function-with-mle?s_tid=srchtitle
% I want to estimate the alpha (a) of a simple utility function of the form
%
% EU(P,V) = P*V^a
%
% where P is probability of outcome, and V is mag... |
6d833b7a171990bd5b4856dbc53debd218602fda03f1d810898187427310e3ac | MATLAB | 1,744 | 56 | function [groupNameBeginsWnumber, groupNameContainsSpecial, allDIVisValid, groupNameIllegal] = checkCSV(csv_data)
%CHECKCSV Summary of this function goes here
% Detailed explanation goes here
groupNames = csv_data(:, 3);
groupNames = groupNames.(1);
groupNameBeginsWnumber = 0;
groupNameContainsSpeci... |
3efdf8bbf30376da516d25190b0c28993ef180cec789b84c8bc8720e1e3f616b | MATLAB | 1,745 | 71 | function [s, s_stds, s_means] = norm_std_mean(s, s_stds, s_means)
% Usage: [s, s_stds, s_means] = norm_std_mean(s, s_stds, s_means)
%
% Compute std and mean of a sample, z-score using them, return z-scored
% data, stds, and means.
%
% Essentially the same as matlab's "zscore.m", but with optimization for
% very large... |
4aa66cdd54a8c71982e0a0cb75584358b28edd7035b0618526ee4e0372feb402 | MATLAB | 1,745 | 64 | function [DA, AUC, pval, rcorr, T, ITI_legend, bins]...
= ITI_effect(bstruct, pstruct, ITIbins_density,...
event, binnum, window)
bdata = bstruct.(event);
pdata = pstruct.(event);
% define bins
ITIs = bdata.ITI;
ITIs(ITIs>prctile(ITIs,99)) = NaN; %remove outliers
ITIs = [ITIs(2:end); NaN]; %shift initiation... |
58c4b80f6ea8ffe79e6653dced6df4316e7f3675732d5ec3df2940059b6a6fde | MATLAB | 1,745 | 57 | function c = tapas_softmax_mu3_wld_config
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Contains the configuration for the softmax observation model for multinomial responses with phasic
% volatility exp(mu3) as the decision temperature and parameters accountin... |
1b01bae0655f9b7a82a6da2c4ff88720de958aa758709aa14407b0319fa6170e | MATLAB | 1,746 | 65 | function plotEC_spectrum2axes(EC, freqAxis, timeAxis, cLims, clz, EC_info)
% plots effective connecivity (EC) data as imagesc to axes
% (c) Jiri, Nov22
%% defualt settings
if ~isfield(EC_info, 'plot_xlabel'), EC_info.plot_xlabel = true; end
if ~isfield(EC_info, 'plot_ylabel'), EC_info.plot_ylabel = true; end
%% >>> ... |
299f885e7ee3a24d6b8d2b15e09afcded7efbcfdd74a5a82bf4597bb6d07fd49 | MATLAB | 1,747 | 47 | function [ S_index_significant, sis_query ] = Search_significant(csi_num,tf_idf_Rasterbin,Rasterbin)
%LC En14 A partir del diccionario de vectores tf-idf
%calcula el indice de similitud basado en el angulo entre las celulas
%clave y cada vector. csi_num es una matriz [celulas edo] que contiene las celulas mas
%represe... |
9db570b6505a4c98fc9b925fe243cc2a6d9ba3d0cad5fb7197844cbe001ff72f | MATLAB | 1,747 | 48 | function ndef = notDefined( varString )
% Test whether a variable (usually a function argument) is defined
%
% ndef = notDefined( varString )
%
% This routine is used to determine if a variable is defined in the calling
% function's workspace. A variable is defined if (a) it exists and (b) it
% is not empty. This r... |
a2806572fe76462413ea78249b2a864dece37d8319513171fd6364399e99cc1d | MATLAB | 1,747 | 53 | function otherImage = permute(this, order)
% Permutes array dimensions (and corresponding)
%
% Y = MrImage()
% permutedImage = Y.permute(order)
%
% This is a method of class MrImage.
%
% IN
% order [1, nDims] vector or permutation of 1:nDims indicating order
% of dimensions after permutation.
% ... |
e3488cdea72142737e05f854d3163b870aa97604a5c2f0e2b71e2259713811fa | MATLAB | 1,747 | 65 | function [val, status] = ft_findcfg(cfg, var)
% FT_FINDCFG searches for an element in the cfg structure
% or in the nested previous cfgs
%
% Use as
% val = ft_findcfg(cfg, var)
% where the name of the variable should be specified as string.
%
% e.g.
% trl = ft_findcfg(cfg, 'trl')
% event = ft_findcfg(cfg, 'eve... |
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