sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
db17f87c133b231e1b1a98b6072b813c000364677c7613513c71a06f3470124d | MATLAB | 962 | 30 | function mustBeLogicalScalar(A)
%MUSTBELOGICALSCALAR Validate that value is a generalized logical scalar
% MUSTBELOGICALSCALAR(A) throws an error if A isn't one of: false, true, 0, 1, "off", "on".
% Copyright (C) 2025 by Pietro Bozzo
%
% This program is free software; you can redistribute it and/or modify
% it under... |
1d004fe9c29dac454797d3fb3711b1750bb978c2010428a544df2728c94a52c2 | MATLAB | 963 | 23 | function [pvec, pstruct] = tapas_kf_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2016 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Licenc... |
40b2fb0b2c6f9f86dc60d9e59bbcc72d53fe427183c85aaef2fd62abf651c2ef | MATLAB | 963 | 49 | function obj = update_model(obj, do_plot)
% ----
% mean
% ----
obj.update_mean();
obj.elbo_obs();
obj.elbo_mean();
if do_plot, obj.plot(); end
% ----------------
% latent precision
% ----------------
obj.update_latent_precision();
obj.elbo_latent();
obj.elb... |
e2ca12feb0287ee4c7ea775a12c3e78985c4ecf7c68bb1a3ef1f81de9fb4a0da | MATLAB | 963 | 32 | function iDim = get_non_singleton_dimensions(this)
% returns vector of indices of non-singleton dimensions (i.e. 2 or more elements)
%
%
% Y = MrDimInfo()
% Y.get_non_singleton_dimensions(inputs)
%
% This is a method of class MrDimInfo.
%
% IN
%
% OUT
%
% EXAMPLE
% get_non_singleton_dimensions
%
% See also MrDi... |
433da358df080db4eaf843dba8c3aa9ac3ee5a1dd820a64875bb9ab40f4d1300 | MATLAB | 964 | 18 | %{
vis.FlashingBar (manual) # flashing bar
-> vis.Condition
---
pre_blank : float # (s) blank period preceding trials
luminance : float # (cd/m^2) mid-value luminance
contrast : float # (0-1) M... |
8abcc7579c631de7b5723e466e72f68649fb1f5fad9fe7e434255b92cbc0f1cd | MATLAB | 964 | 27 | function pstruct = tapas_hgf_binary_pu_tbt_namep(pvec)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2016 Rebecca Lawson, Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU Genera... |
9fa70d257f68c3a47e3aba3ee6cec6b641426e1c435463a62f39e01e33c8c90a | MATLAB | 964 | 35 | function outputImage = mod(this, divisor, varargin)
% Computes modulus of division with divisor
%
% Y = MrImage();
% modY = Y.mod(divisor)
% modY = mod(Y);
%
%
% This is a method of class MrImage.
%
% IN
%
% OUT
% outputImage value modulo
%
% EXAMPLE
% modY = mod(Y, 2*pi)
%
% See also MrImage... |
f601f90d9eb02515e85d47dcc48f0102a2ab0dacadcb6831c82c8d9fb0684ca7 | MATLAB | 964 | 29 | function [subsequences, lengths] = findSubsequences(sequence)
% Finds sequences of 1 in binary vector of 1s and 0s
% Assign initial and allocate
subsequences = {};
subseqN = 0;
inSubsequence = false;
% Loop over idx
for idx = 1:length(sequence)
% Current value is 1 and idx is not in a subsequence of 1s
if sequ... |
fa6533876d0addda1642bab57cbbb7574b88cfe3038669b68fa7f0e6285adf2c | MATLAB | 964 | 36 | clc
close all
clear all
[angle_left,distance_left] = textread(['left_dod.txt'], '%f %f');
[angle_right,distance_right] = textread(['right_dod.txt'], '%f %f');
distance = (distance_left+distance_right)/2;
distance_list = [] ;
for i = 1:4:192
distance_list(end+1) = mean(distance(i:i+3));
end
% DoD = arctan (Pd/... |
6b11c4862de8d94397338cfb9256050085299b114809ce6afa9a22c8824c1f1e | MATLAB | 965 | 23 | function E = staticMiniEnergy(As,B,T,x0,xf)
% Calculate the minimum static control energy under unrestricted control path
%
% E(x_0, x_f) = \frac{1}{2} d^T W^{-1}d
%
% Inputs: As, N-by-N matrix, system matrix
% B, N-by-M matrix, control matrix with M control nodes
% T, ... |
b7772f217048bb490c6b96b2e85990bb252d0c157de730225e125c7ef389d91c | MATLAB | 965 | 58 | function [err, hndl] = addsquare(Pll, Pur, C)
%
% [err, hndl] = addsquare(Pll, Pur, C)
%
%
%Purpose:
% adds a rectangle on current plot
%
%
%
%Input Parameters:
% Pll : [x y] of lower left point
% Pur : [x y] of upper right point
% C : rgb triplet, between 0 and 1 rectangle color
%
%
%
%Output Parameters:
% err... |
088e79a6940560d5a58941e20055874411cc55d48539a4f4e3113a2e2ad7647e | MATLAB | 966 | 45 | % op_firstPointPhase.m
% Georg Oeltzschner, Johns Hopkins University 2019.
%
% USAGE:
% [out]=op_firstPointPhase(in);
%
% DESCRIPTION:
% Performs a zero-order phase correction by multiplying each point of the
% FID with the normalized complex conjugate of the first point.
%
% INPUTS:
% in = input data in mat... |
cf6ba011a98d9c53552dec39206cfbcda1002045b6ba8a225b4c60c89f584b7f | MATLAB | 966 | 34 | function set_filename(this, filename)
% Takes input filename and sets parameters.save.path/fileName accordingly
%
% Y = MrImage()
% Y.set_filename(filename)
%
% This is a method of class MrImage.
%
% IN
%
% OUT
%
% EXAMPLE
% Y.set_filename('newFolder/newFile.nii');
%
% See also MrImage
% Author: Saskia Bollm... |
ed7896490aaa3225dd9c9ada4160f6033e50677947ec8465db980977af825bb8 | MATLAB | 966 | 34 | function outputImage = fliplr(this)
% Flips all slices Right-Left; mimicks fliplr in matlab functionality
%
% Y = MrDataNd()
% Y.fliplr(K)
%
% This is a method of class MrDataNd.
%
% IN
%
% OUT
% this MrDataNd where data matrix is flipped and dimInfo is updated to
% reflect that change
%
% EXAMPLE
% ... |
f1c6c7a6115aab1219775200a20e2ac615670bc0c0b2af46ec4372c1c5d75fc0 | MATLAB | 967 | 42 | function [spikeRaster]=plotSpikeRaster(spikes,Fs,thres,varargin)
% assume row > timestamps and column > neuron ID
nTrace=size(spikes,2);
[b,a]=butter(6,100/(Fs/2),'high');
Time=0:1/Fs:(size(spikes,1)-1)/Fs;
spikeRaster=cell(nTrace);
negDFF=false;
if negDFF
spikes=-spikes;
end
spikeRaster=zeros(length(Time),nTr... |
fc3d3308973275bf095b41310c2d9fd060ba6daf30cd6a4f7a21b101053b2653 | MATLAB | 967 | 41 | function tapas_validate_state(state)
%% Checks that a state complies with the interface.
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
if ~ isstruct(state)
error('tapas:validate:state', 'state is not a structure');
end
if ~ isfield(state, 'graph')
error('tapas:validate:state', 'state lacks field graph');... |
79fd48463c52beca71c2bc9871132037f80f34d41afe74d7290cc360027b5974 | MATLAB | 968 | 26 | function vl_nnnotfound(fname)
%VL_NNNOTFOUND Prints a help error message to set up MatConvNet
% Warn users about common pitfalls in setting up MatConvNet.
% Copyright (C) 2017 Karel Lenc.
% All rights reserved.
%
% This file is part of the VLFeat library and is made available under
% the terms of the BSD license (see... |
7dd72ad546204907b377c8821225404fc81c18225209dee7cedfa6fd6857754e | MATLAB | 968 | 30 | function A = multiscale(scale, A)
% Multiplies the 2D slices in a 3D matrix by individual scalars.
%
% function A = multiscale(scale, A)
%
% Given a vector scale of length N and a 3-dimensional matrix A of size
% n-by-m-by-N, returns a matrix A of same size such that
% A(:, :, k) := scale(k) * A(:, :, k);
%
% See also:... |
d8515e0a6eda975c143abbfd74c3f63f2bdac3fcd4bf8fe31390fb612de19b36 | MATLAB | 969 | 38 | function [itiMdl, itiOpt, V, rpe, alpha, G] = generate_ph_mdl(...
R, alpha0, D)
% generate_ph_mdl - generates data for Pearce-Hall model
% INPUTS:
% R - reward vector. Must be 1:5
% alpha0 - Base learning rate
% D - Scale parameter
% OUTPUTS:
% itiMdl - trial intiation time with added noise
% itiOpt - opt... |
39ae17cfee44e25292faa19ebfd83f179ac95ff5013ab9a17d63f1ed04093672 | MATLAB | 971 | 26 |
% Function to calculate the passive forces of the muscle
% The passive force is a function of the sarcomere length
function PF = passiveForces(SL,time,tDrugApplication,fmyo)
SL_rest = 1.9; % (um)
PCon_titin = ((time<tDrugApplication)*1+(time >= tDrugApplication)*fmyo(9)) * 1.0*0.002; %(normalised for... |
d3dc637aa7a3d6e3cbc81de4c5e52f07b8bf0d896715b5c9ac2b995f92ac8408 | MATLAB | 971 | 41 | function [RHSdiv, RHSdivx, RHSdivy, RHSdivz] = divergenceTerm(F)
% This function calculates the divergence of a field using its face
% average value and the vector F, which is a face vector
%
% SYNOPSIS:
% [RHSdiv, RHSdivx, RHSdivy, RHSdivz] = divergenceTerm(F)
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE AL... |
fe0d031a7f5e11cb51d39dc7c0d54da20f6a8ce3e959e2b20b96aad0a6dfd61e | MATLAB | 972 | 43 | function [y] = randdv_sigmoid(dim,dvmu,fixdvmu)
% RANDDV_SIGMOID Random decision value generator using sigmoid PDF
% [y] = randdv_sigmoid(dim,dvmu,[fixdvmu])
if nargin < 3
fixdvmu = false;
end
if nargin < 2
error('Missing input argument(s).');
end
if size(dim) ~= 2
error('dim should be [n(tri... |
3e98dda59d533e1862fcab6820214b94d06b98e65f46c128d4058046032c89ec | MATLAB | 973 | 26 | function trialsData = plotTrials_trialsDataInfo(data_info)
% returns auxiliary info in trialsData.info
% (c) Jiri, Oct20
%% decoding: 'trialsData' auxiliary info
clear trialsData;
trialsData = struct;
trialsData.info.verLines = [-1, 0, 1];
trialsData.info.xlabel = 'time offset (s)';
trialsData.info.ylabel = 'DA (CC)... |
caf40beb2fd1d8b8e12022d0729f2e45d9d4e40cd6331ee65f91f146fe929f20 | MATLAB | 973 | 47 | function shortStr = shortenChannelName(longStr, maxLngth)
% shortens the anatomical assignemnt strings
% 'maxLngth' = maximum number of characters in 1 word
% (c) Jiri, Sep16
%% input
if nargin < 2
maxLngth = 4;
end
tmp = longStr;
%% exchange Left (=L)
str2ex = 'Left';
k = strfind(tmp, str2ex);
if ~isempty(k)
... |
1b19e5b51e36d031241f28d1bfad65cf7b6dae7e3aa276b76f0915179dfa56b9 | MATLAB | 974 | 30 | %% function [Ex,Ey,Ez,EtE] = GradientOperatorKspace(matrixSize)
%
% Input
% --------------
% matrixSize : matrix size of chi
%
% Output
% --------------
% Ex : gradient in x-direction
% Ey : gradient in y-direction
% Ez : gradient in z-direction
% EtE : ... |
d277c26b0cfb5b44fb19789ec3a2312f914fee1dd1c3ce90d9874cdf167eec57 | MATLAB | 974 | 30 | %% addon_config
%
% Description: Addon script to incorporate new method to the SEPIA framework
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 27 June 2020
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the SEPIA f... |
f66f02d6108ea01605d60162fab0ea4b6b2714d306e887e5e01f86a012977e78 | MATLAB | 974 | 61 | function [err, Qd, dfx, dmat2] = QRDecom(dmat, cmat)
%
% [err,] = QRDecom.m ()
%
%Purpose:
%
%
%
%Input Parameters:
%
%
%
%Output Parameters:
% err : 0 No Problem
% : 1 Problems
%
%
%
%Key Terms:
%
%More Info :
%
%
%
%
% Author : Gang Chen
% Date : Tue Mar 23 16:09:23 EST 2004
% SSCC/NIMH/ Nation... |
926411ede5b21459b9a68903aa684bced8cff3173924d2025152f515b4cc4cd9 | MATLAB | 975 | 29 | function [potentials,mask_index0] = computePotentials2D(D, meshstruct, M, RHSbc)
% Compute potentials 2D
% Define mask
Nx = D.domain.dims(1);
Ny = D.domain.dims(2);
G=reshape((1:(Nx+2)*(Ny+2)), Nx+2, Ny+2);
mnx = Nx*Ny;
rowx_index = reshape(G(2:Nx+1,2:Ny+1),mnx,1); % main diagonal x
% Compute conductance
aux = sum... |
4a7f8a6fd358ace1df7cefac8194e2914184c469e3aa4f6b323d352bae654c07 | MATLAB | 976 | 30 | %% addon_config
%
% Description: Addon script to incorporate new method to the SEPIA framework
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 27 June 2020
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the SEPIA f... |
825a3b75aa4727f31031f08217f2a54d4b329bc453d972b63926551bec2309cf | MATLAB | 976 | 37 | function renameParam(obj, oldName, newName, varargin)
%RENAMELAYER Rename a parameter
% RENAMEPARAM(OLDNAME, NEWNAME) changes the name of the parameter
% OLDNAME into NEWNAME. NEWNAME should not be the name of an
% existing parameter.
opts.quiet = false ;
opts = vl_argparse(opts, varargin) ;
% Find the param to... |
8a16b752d6de9dcabc9937baebbcbd5421053964d59ef9b05cf8842f1c5fa299 | MATLAB | 977 | 34 | function this = t_filter(this)
% high-pass filters temporally (4th dimension of the image) as SPM
%
% MrSeries = t_filter(MrSeries)
%
% This is a method of class MrSeries.
%
% IN
% parameters.TR_s
% parameters.t_filter.cutoffSeconds
%
% OUT
%
% EXAMPLE
% t_filter
%
% See also MrSeries
% Author: Saskia Klei... |
91a7aeb86d76612bd4b61526a9255f80a56e281f5eb485b33888dfd198d62bbb | MATLAB | 977 | 31 | function [RSS,rms_val,chi,AIC,BIC,R_sq_mean] = qualityFit(Nb,Np,observed_arr,predicted_arr)
numVoxels = size(observed_arr,2);
RSS = zeros(numVoxels,1);
rms_val = zeros(numVoxels,1);
chi = zeros(numVoxels,1);
AIC = zeros(numVoxels,1);
BIC = zeros(numVoxels,1);
for i = 1:numVoxels
observed_signal = observ... |
d06734b0e84fba36df6eaa158372475d37078e4d0a3c5c60f5e1b429c9291eeb | MATLAB | 977 | 38 | %Creado por Luisca Mayo09.
%A partir de Spikes, toma los picos con un umbral determinado y genera la
%matriz Rasterbin y el arreglo Pks_Frame que indica los frames
%correspondientes a cada pico diferente. Pks_Frame correspondería a
%Rasterbin_Ren
function [Rasterbin,Pks_Frame_Ren,Pks_Frame]=PksFrame(Spikes,pks)
%S... |
2914c2dafaea7fdd04049771a72f2472ae06186c623b35b5f6576925f3c74b5e | MATLAB | 978 | 45 | function tmppath = fsgettmppath(tmppathdefault)
% tmppath = fsgettmppath(<tmppathdefault>)
% Gets path to a temporary folder (does NOT generate a random file name)
% First looks in the following order:
% 1. $TMPDIR - env var must exist and folder must exist
% 2. $TEMPDIR - env var must exist and folder must exist
% ... |
8878f16c93b237d891a8fa6a35e800771fed79d0f8254004556763243e009b74 | MATLAB | 978 | 35 | function opts = mergeOptions(opts_sub, opts_master)
% Merges two options structures with one having precedence over the other.
%
% function opts = mergeOptions(opts1, opts2)
%
% input: opts1 and opts2 are two structures.
% output: opts is a structure containing all fields of opts1 and opts2.
% Whenever a field is prese... |
3e79bea6d023f462f040d66b74099893a6c0675fe3a06f58f57c740127eea902 | MATLAB | 979 | 32 | function bVals = binningVals(vals, binRangeLabels)
% given a column vector 'vals' and binRangeLabels with format:
% binRangeLabels =
%
% -1.0000 -0.7854 0.7854
% 1.0000 -3.1416 -2.3562
% 1.0000 2.3562 3.1416
% label loRange hiRange
% bins the vector into N unique bins and returns the... |
a2c11f99b1d5151cc5027a949e2b416045af1800e19ab6960fb86aadba1f7f91 | MATLAB | 979 | 62 | function out = getResiduals(input,coeff,proc12,dfactor)
out = cell(size(input));
for i = 1:numel(input)
d = [];
e = [];
dec = [];
proj = [];
res = [];
numtrials = [];
num_times = [];
num_channels =[];
e= input{i};
nan_mask = isnan(e);
rows_with_nan = any(any(nan_mask,... |
1cbe0e1f9cfa55854d8794553992b487fe4caabebac87411271adcd52ba3dd3b | MATLAB | 980 | 35 | function RHSbcM = computeCurrentsROI3D(im_sizes, RHSbc, atlas, mask)
% Compute potentials 3D
%
% Author: Aina Frau-Pascual
% Define mask
Nx = im_sizes(1);
Ny = im_sizes(2);
Nz = im_sizes(3);
G = reshape((1:(Nx+2)*(Ny+2)*(Nz+2)), Nx+2, Ny+2, Nz+2);
rowx_index = reshape(G(2:Nx+1,2:Ny+1,2:Nz+1), Nx*Ny*Nz, 1);
% Compute... |
36ed6f6d085bc683f45a20efd7447574aaddea45a736cbf1050de98ec99ff72c | MATLAB | 980 | 30 | %% addon_config
%
% Description: Addon script to incorporate new method to the SEPIA framework
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 27 June 2020
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the SEPIA f... |
2a14098300abde852838a44265aa8a80025a52ec2d8ab804f08a364e9f8fd399 | MATLAB | 981 | 37 | function [indEx, indRef, indSat] = sero_pulseq_getRFBlockInd(seq, blockInd)
% function [indEx, indRef, indSat] = sero_pulseq_getRFBlockInd(seq, blockInd)
if nargin < 2
blockInd = [];
end
indAll = sero_pulseq_getAllRFBlockInd(seq);
indEx = sero_pulseq_getExcitationBlockInd(seq);
nShot = numel(indEx);
indRef = z... |
0bd329cc34519a273c21b9adabad51ce89b59b846f8d0b4e9eaf7753620ee59a | MATLAB | 982 | 28 | function pstruct = tapas_hgf_binary_pu_namep(pvec)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2012-2015 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Lice... |
657dc83e94da2cd16c8fa495b8cac4fce5a1c24376abf51b316ec10ec5150e3a | MATLAB | 982 | 35 | function outputImage = angle(this, varargin)
% Computes phase value per complex-valued image pixel
%
% Y = MrImage();
% angleY = Y.angle()
% angleY = angle(Y);
%
%
% This is a method of class MrImage.
%
% IN
%
% OUT
% outputImage phase value image for complex-valued image
%
% EXAMPLE
% angleY =... |
9b6de97b8fcf80bf7299759cebdf272e479683955de88b94de9f9a4116f4cb42 | MATLAB | 982 | 36 | function [nstate] = tapas_mh_mc3_node_sample(data, model, ...
inference, state, node)
%% Samples for a particular node assuming there is a function for it.
%
%
% This works as the conditional independency of the level allows one to sample
% without worrying about the values in other nodes.
%
% aponteeduardo@gmail.... |
11e884e6ccdbbefedbf308b4796c33f44775bee7a57691afe6d2e978fd05ca7b | MATLAB | 983 | 27 | rng('shuffle');
rngState = rng;
deltaSeed = uint32(feature('getpid'));
seed = rngState.Seed + deltaSeed;
rng(seed);
in_dir = 'test_data/raw_warped_seg';
out_dir = 'test_data/raw_warped_seg';
in_suffix = '_seg_warped_single.mat';
out_suffix = '_skel_warped_single.mat';
files = dir(fullfile(in_dir,'*_seg_warped_single.... |
4323fb1dd43b8fe7235fbb4f4461c5c07a932690b38f69b43f7affb7266c209a | MATLAB | 983 | 34 | function [x,varargout] = ZeroToOne(x,varargin)
%ZeroToOne - Normalize values in [0,1].
%
% USAGE
%
% [y,b0,b1...] = ZeroToOne(x,a0,a1,...)
%
% x array to normalize
% a0... additional inputs to transform using the same
% scale as x
% Copyright (C) 2008-2011 by Michaël ... |
84b14dd71589b2f36ca3546bd3ac86387f69c62b7d2e0edcf3595edd0df0ceab | MATLAB | 983 | 28 | function pstruct = tapas_ehgf_binary_pu_namep(pvec)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2012-2015 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Lic... |
bbc4393772b68bd3e5c1fd217be2ec308183e17d327ebc28e32c8a0fa8eea8b5 | MATLAB | 983 | 35 | function val=jsonopt(key,default,varargin)
%
% val=jsonopt(key,default,optstruct)
%
% setting options based on a struct. The struct can be produced
% by varargin2struct from a list of 'param','value' pairs
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% $Id: loadjson.m 371 2012-06-20 12:43:06Z fangq $
%
% input:
% ... |
02628ce9478efebebc9800c34d201e909e8cb7ee4b1c8e21ed627b1ce8f03635 | MATLAB | 984 | 31 | classdef SprottE < Environment
% SprottE system.
properties
D = 3; % system dimension
Ranges = [2.5, -1;
1.5, 0;
8, -3]; % variable ranges
Params = struct(); ... |
1c8e0fedc2328dd6ebe9dba4ecb50337c07632c8f577022f131df31d94cd8b9c | MATLAB | 984 | 39 | function mask = generate_target_mask(hsi,filt,halo)
%function mask = generate_target_mask(hsi,filt,halo)
%
% generates a binary image mask with halo of pixels around each target
% that matches the filter
%
% 10/30/2012 - Taylor C. Glenn - tcg@cise.ufl.edu
% determine which alarms to score
gt = hsi.groundTruth;
n_ta... |
2887b7e15230e41ece715fead8ba9f26a818185545397ff2012e2b136f4167fd | MATLAB | 984 | 31 | classdef SprottH < Environment
% SprottH system.
properties
D = 3; % system dimension
Ranges = [8, -6;
8, -1;
5, -3]; % variable ranges
Params = struct(); ... |
425aa5dee7e1907ff5d3c0f6ddbf5b1a6810d0d798446ad8e16b1d3f1f9ed086 | MATLAB | 984 | 31 | classdef SprottG < Environment
% SprottG system.
properties
D = 3; % system dimension
Ranges = [5, -3;
4, -3;
6, -3]; % variable ranges
Params = struct(); ... |
67d613b7b11afde7443574d24c2f141975d4faf64d0c8b19104578d74655bdfe | MATLAB | 984 | 44 | %% markCropBox
% video annotation GUI built on top of movieAnalyser
classdef markCropBox < movieAnalyser
properties
folder_name
mask
end % end properties
methods
function a = createGUI(a)
createGUI@movieAnalyser(a);
p = a.ui_handles.pause_button.Position;
a.ui_handles.mark_roi_button = uicontrol... |
d50729df559bbf0497fb1c0633bcf16adcad4e237aab60487327e2c84e8f6d6b | MATLAB | 984 | 30 | %% addon_config
%
% Description: Addon script to incorporate new method to the SEPIA framework
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 27 June 2020
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the SEPIA f... |
ddc0f76ed6194a20ff0ef63e9b3e31a6bf50895ba2924dbf1eb9de9e8b9ecb28 | MATLAB | 984 | 45 | function nii = nii_load(niifile,untouchopt,img_idx)
%author EML
vartype = 16;
if nargin < 2 || isempty(untouchopt)
untouchopt = 1;
end
if nargin < 3 || isempty(img_idx)
img_idx = 0;
end
if ~untouchopt
try
if ~img_idx
niiraw = load_nii(niifile);
else
niiraw = load... |
fb941dacea5dbcd3f6f56d5886441cc7cce387021e2fdf66a28abf1675f28e2e | MATLAB | 984 | 28 | function disp_centre_and_origin(obj)
% Displays centre and origin of MrImage object. Helper for demo script.
%
% disp_centre_and_origin(input);
%
% IN MrImage object
%
% EXAMPLE
% disp_centre_and_origin(data)
%
% See also demo_set_geometry
% Author: Saskia Bollmann & Lars Kasper
% Created: 2018-11-06
% Cop... |
0e559a3b5a5dfdc704a3d46035afb6441522359319fea839a1df1162836d4271 | MATLAB | 985 | 36 | function plot_ens_seq(ax,tt,ens_labs,ens_cols,sellabs)
% Reference paper: Herzog et al. 2020 "Scalable and accurate automated method
% for neuronal ensemble detection in spiking neural networks"
% https://www.biorxiv.org/content/10.1101/2020.10.12.335901v1
% Rubén Herzog October 2020
nens = max(ens_labs);
cla(ax);
t... |
f8ebd0a060da29dabed958373d723072a67bc07ffe4cbb65575d0782c8aa9122 | MATLAB | 985 | 31 | classdef SprottB < Environment
% SprottA system.
properties
D = 3; % system dimension
Ranges = [10, -5;
10, -5;
10, -5]; % variable ranges
Params = struct(); ... |
060fed15010576f75a3aa84cbb5f9036c63a6d34e2d5249014865cc6ea184f42 | MATLAB | 986 | 27 | function y = vl_nnreshape(inputs, inSize, dzdy, varargin)
%VL_NNCONCAT CNN concatenate multiple inputs.
% Y = VL_NNCONCAT(INPUTS, DIM) concatenates the inputs in the cell
% array INPUTS along dimension DIM generating an output Y.
%
% DZDINPUTS = VL_NNCONCAT(INPUTS, DIM, DZDY) computes the derivatives
% of the block... |
0ca03efbae18d7b3c74b94d1641b5e1d64be77b72926ef0d04643537e1a49cf6 | MATLAB | 986 | 41 | function A = triangulation2adjacency(face,vertex)
% triangulation2adjacency - compute the adjacency matrix
% of a given triangulation.
%
% A = triangulation2adjacency(face);
% or for getting a weighted graph
% A = triangulation2adjacency(face,vertex);
%
% Copyright (c) 2005 Gabriel Peyré
[tmp,face] = check_f... |
26b977a18fdd78a99f27205862eef43094dc2a3878274c75c289876a22797da7 | MATLAB | 986 | 55 | function [branch, revhash] = tapas_get_revision_info(directory)
%%
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
if nargin < 1
directory = pwd();
end
if ~(exist(directory) == 7)
error('tapas:get_revision_info', 'no directory');
end
gitroot = fullfile(directory, '.git');
if ~(exist(gitroot) == 7)
... |
aec7b0f52bb17200470f0a97f04cb17fed322303509036de41660997c5730165 | MATLAB | 986 | 31 | function origin = get_origin(this)
% Computes the origin of this image geometry.
%
% Y = MrImageGeometry()
% Y.get_origin()
%
% This is a method of class MrImageGeometry.
%
% OUT Voxel indices x, y, z of the origin, i.e. those voxel who are
% at location [0 0 0].
%
% EXAMPLE
% origin = Y.get_origin()
%
% ... |
f6039737e7a1429d17acb861dbd32d5aa63f682726bcbb12ebf35c079564102e | MATLAB | 986 | 31 | classdef SprottA < Environment
% SprottA system.
properties
D = 3; % system dimension
Ranges = [10, -5;
10, -5;
10, -5]; % variable ranges
Params = struct(); ... |
1c5588cd15bc70908f64fd31cdbd8674bb6b167f6c23cc8ccd78b63694aecc70 | MATLAB | 987 | 28 | function window = extractWindowForBiomarkers(V_ode,i_tot, Istim ,t,Cai,Nai,Frc,Lsrc,svl, wspan)
flag = 0;
[pks_MDP, idx_MDP] = findpeaks(-V_ode);
idx = find(pks_MDP<0);
pks_MDP(idx)=[];
idx_MDP(idx) = [];
if length(pks_MDP)<=10
disp('Error')
flag =1;
window=[];
return
end
numAPsBiomarkers = 9;
N = leng... |
82237eafe64390b68ef56ef12853bab9f33050d4cb8b775b6ead4141cd36a377 | MATLAB | 987 | 15 | %-----------------------------------------------------------------------
% Job configuration created by cfg_util (rev $Rev: 4252 $)
%-----------------------------------------------------------------------
function TMSwrite(MATdir,ROIlist)
ROIlist;
matlabbatch{1}.spm.spatial.normalise.write.subj.matname = {MATdir}... |
9e168657fbd9ee5edd22d6ccf7be9ddb192a59543cbeb8a796789094609f536a | MATLAB | 987 | 31 | function [sigma,bnd] = bdsqr(alpha,beta)
% BDSQR: Compute the singular values and bottom element of
% the left singular vectors of a (k+1) x k lower bidiagonal
% matrix with diagonal alpha(1:k) and lower bidiagonal beta(1:k),
% where length(alpha) = length(beta) = k.
%
% [sigma,bnd] = bdsqr(alpha... |
de98ef3cdcc5e44b251ac0dc075d3b79024f9fcfdbc6c8684ba38c050a355732 | MATLAB | 987 | 20 | clear all
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% The following variates are needed to be loaded before performing each analysis step (step2-step6).
% set working paths
Pathnew=['D:\Documents\OneDrive - bnu.edu.cn\My_publications\0-8y... |
197559b6e0f487329a407d7769135f5397e0e04ffc3fc723d33f6b8d5fcfbb63 | MATLAB | 988 | 35 | function regressor=task_regressor(TR,T,taskfile)
%taskfile: If using the Custom 3 column format, prepare a plain text file (avoiding editors such as MS Word)
%containing one line for each stimulus associated with the condition to be modelled by this EV.
%Each line must contain three numbers: the onset time (in s... |
aaa708cde811ccff7617bf234701ae508101fcefc2a8061b97aed9962cd64982 | MATLAB | 988 | 31 | classdef SprottR < Environment
% SprottR system.
properties
D = 3; % system dimension
Ranges = [7, -5;
7.5, -2.5;
10, -9]; % variable ranges
Params = struct(); ... |
b8a82a8f2cd47f30f7b9ccc61cfd14dbea28e05f77628cd90172df44127b1dac | MATLAB | 988 | 31 | classdef SprottC < Environment
% SprottC system.
properties
D = 3; % system dimension
Ranges = [5, -2.5;
5, -2.5;
5, -2.5]; % variable ranges
Params = struct(); ... |
bd9b1ddb07bd08ccbdbe93e4e9861784cb4abaecb2b857083b78acf3a48e3a0f | MATLAB | 988 | 28 | function spikeTimes = findSpikeTimes(spikeTrain, method, samplingRate)
%findSpikeTimes calculate spike times given binary matrix
% assumes input matrix in the form numSampl x numChannel
% returns spikeTimes as an array of vectors
% if method is 'seconds', then spike times are returned in seconds
% otherwis... |
d23b1331fd93f685e20a8cbe586e0ea26096c164551f645ce948a8181484a13c | MATLAB | 988 | 46 | function [vertex,face] = read_off(filename)
% read_off - read data from OFF file.
%
% [vertex,face] = read_off(filename);
%
% 'vertex' is a 'nb.vert x 3' array specifying the position of the vertices.
% 'face' is a 'nb.face x 3' array specifying the connectivity of the mesh.
%
% Copyright (c) 2003 Gabriel Peyr... |
0b9a23915bddd371f8bad877f93d5d9dd3213c3d41d3acd8a8483af47cc757c1 | MATLAB | 989 | 30 | %% addon_config
%
% Description: Addon script to incorporate new method to the SEPIA framework
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 27 June 2020
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the SEPIA f... |
67261b5648ae783f9d4113457d31201ce02542ec6b84603c2cbdfeab83ddbc76 | MATLAB | 989 | 34 | function [loss, tstar] = computePerformance(o, utest)
% Computes loss and t*.
% Parameter
% ---------
% o (DxT, double) : reservoir output (forecast) of T time steps
% utest (DxT, double) : ground truth/ prediction target
%
% Returns
% -------
% loss (1x1, double) : prediction loss
% tstar (1x1, double) : pre... |
096d4317de480afce1c8f9dfb318cb6c06f62ed2d739d441c1e358dc510d189a | MATLAB | 990 | 35 | function [nstate] = tapas_mh_mc3_hier_node_sample(data, model, ...
inference, state, node)
%% Samples for a particular node assuming there is a function for it.
%
%
% This works as the conditional independency of the level allows one to sample
% without worrying about the values in other nodes.
%
% aponteeduardo@g... |
d2975e6039bb49e78957775c7a260f73779642eb4da52aa4005e956e67fe613f | MATLAB | 990 | 34 | %% fgColor = sepia_theme_fg_color()
%
% Output
% --------------
% fgColor : text (foreground) colour (RGB triplet) for interactive
% uicontrols (edit/popup/pushbutton fields)
%
% Description: Companion function to sepia_theme_bg_color.m - returns the
% text colour that keeps typed/selected text legible ag... |
011326259a118094f93183ee8d6b09ec6a2a63b06c3261a0f31b93b3a31e22ab | MATLAB | 991 | 31 | function [stop, reason] = stopinteractive(problem, x, info, last) %#ok<INUSL>
% This became a tool: see stopifclosedfigure
reason = 'Interactive stopping criterion: figure closed.';
% Fix a likely unique figure id.
figureid = 1465489213;
% If first iteration, create a figure to capture interactio... |
2071772331e3de8a2e6d75e10c29bfc2246187e489512114dd18cf33379db22a | MATLAB | 991 | 42 | function [posterior] = tapas_sem_hier_estimate(data, model, inference, pars)
%% Estimates the hgf using mcmc.
%
% Input
% data -- Data of the model. It should be a structure array with
% fields y, and u of dimensions n times 1, when n is the
% number of subjects.
% model ... |
3f3bcddcc5e6782ced473807e45a4f43caf7c3298cea830eddf2199d6155a279 | MATLAB | 991 | 30 | %% addon_config
%
% Description: Addon script to incorporate CLEAR-SWI to the SEPIA framework
%
% Korbinian Eckstein @ UQ
% korbinian90@gmail.com
% Date created: 26 September 2022
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the S... |
47e1c73254cef6751b4d897a8a7d15ff7beebed33d339a36c2269a079072048b | MATLAB | 991 | 41 | function clims(varargin)
%clims - Equalize the the color limits on all the axes of the current figure
% Copyright (C) 2017 by Ralitsa Todorova
%
% 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; ... |
b373d8cfb7671118a0486c2425e7491269d733d5042a185b91e2164d6b51a6e5 | MATLAB | 991 | 31 | classdef SprottN < Environment
% SprottN system.
properties
D = 3; % system dimension
Ranges = [100, -93;
61, -44;
22, -13]; % variable ranges
Params = struct(); ... |
32bf1caf2570ce2e2d0ce57884c9ff4ddd75e2f61cbb04c4a9d3ac50f5020e4f | MATLAB | 992 | 33 | classdef nnmnist < nntest
properties (TestParameter)
networkType = {'dagnn', 'simplenn'}
end
methods (TestClassSetup)
function init(test)
addpath(fullfile(vl_rootnn, 'examples', 'mnist'));
end
end
methods (Test)
function valErrorRate(test, networkType)
clear mex ; % will reset GP... |
7629fd26aa125b301ea6fe057d402ff7317388e714836bdbbf7f30257c05144e | MATLAB | 992 | 28 | function [N, S] = getUsedROIs(GRUP, minSubj)
% returns N = vector(freq), number of used ROIs in trialsData of each frequency band (FB)
% returns S = number of used ROIs in spectra (significance taken from the last FB)
% used = more than minSubj
% (c) Jiri, Jul22
%% number of used ROIs in trialsData of each frequency ... |
b24441ad5d6ce9a583ac425bb4e4536d134b4a6574ae7d62ec9c255ce2e7e0f5 | MATLAB | 992 | 31 | classdef SprottP < Environment
% SprottP system.
properties
D = 3; % system dimension
Ranges = [2.8, -0.8;
2, -1.5;
2, -0.4]; % variable ranges
Params = struct(); ... |
b270fb734dcbf5e5be79a56e933c2c885390499d3d2fb3ee0677d815f97a03e2 | MATLAB | 992 | 28 | function varargout = covMaternard(d,varargin)
% Wrapper for Matern covariance function covMatern.m.
%
% Matern covariance function with nu = d/2 and with Automatic Relevance
% Determination (ARD) distance measure. For d=1 the function is also known as
% the exponential covariance function or the Ornstein-Uhlenbeck cov... |
b28d02f9c39f293d229b699cebd4321e1f7d6bbf31c5f7144909c359a604dbc8 | MATLAB | 992 | 19 | % Evaluate the order R elementary symmetric polynomials using Newton's identity,
% the Newton-Girard formulae: http://en.wikipedia.org/wiki/Newton's_identities
%
% Copyright (c) by Carl Edward Rasmussen and Hannes Nickisch, 2010-01-10.
% speedup contributed by Truong X. Nghiem, 2016-01-20.
function ... |
df03ff7aa6bd5d3c4bcf8f302f924f2f223a238610dfbfe03c49496516e336f5 | MATLAB | 992 | 28 | function[] = ellipse (xycenter, hr, vr, facecolor, edgecolor, edgethickness)
%% Function Description
% circle (xycenter, hr, vr, facecolor, edgecolor, edgethickness)
%
% Draws an ellipse horizontal radius 'hr' and vertical radius 'vr' centered around a given x,y coordinate.
%
% Inputs:
% hr = horiztonal radius... |
f8e8e9fc4c2bbd1d95cbaab0744ea0cb9c7a66675fd70e7d5c5bfa2119641ba6 | MATLAB | 992 | 26 | function [pvec, pstruct] = tapas_logrt_linear_binary_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2016 Christoph Mathys, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Pub... |
03b28750398c103afc7bade45576410450b69436521d67cf925b5d2c7fec67f5 | MATLAB | 993 | 31 | classdef SprottK < Environment
% SprottK system.
properties
D = 3; % system dimension
Ranges = [6.6, -4.7;
4, -2.5;
6.7, -0.8]; % variable ranges
Params = struct(); ... |
3f4717e74e7ba03da98cbd4e29fd456617e0d1c1afc5dbaf6a4196a6d010db33 | MATLAB | 993 | 35 | %% [weights, fieldmapSD]= compute_optimum_weighting_combining_phase_difference(magn, TE)
%
% Input
% --------------
% magn : multi-echo magnitude images, 4D
% TE : echo times
%
% Output
% --------------
% weights : weighting factors, 4D
% fieldmapSD : theorectical noise derived from magnitu... |
451dab9d00b4d2de133a391f70cd4a46cfa0d881881276f51448ac489759f8d9 | MATLAB | 993 | 29 | function Y = vl_nnsoftmax(X,dzdY)
%VL_NNSOFTMAX CNN softmax.
% Y = VL_NNSOFTMAX(X) applies the softmax operator the data X. X
% has dimension H x W x D x N, packing N arrays of W x H
% D-dimensional vectors.
%
% D can be thought of as the number of possible classes and the
% function computes the softmax alon... |
11895f25937a3cb30ae5dc6cc5450d8fb3aecb492a29d9610f252e5faac68237 | MATLAB | 994 | 25 | % solve_chol - solve linear equations from the Cholesky factorization.
% Solve A*X = B for X, where A is square, symmetric, positive definite. The
% input to the function is R the Cholesky decomposition of A and the matrix B.
% Example: X = solve_chol(chol(A),B);
%
% NOTE: The program code is written in the C language ... |
18effc0dc2d0d81d2971b069b7178d0a6b40e578c1664c24fa7cd373b18c2b58 | MATLAB | 994 | 29 | %% Generate36data
% Script for making 36 attack data
basePath = 'D:\Data\Lobster\BehaviorData';
filelist = dir(basePath);
sessionPaths = regexp({filelist.name},'^#\S*','match');
sessionPaths = sessionPaths(~cellfun('isempty',sessionPaths));
fprintf('%d sessions detected.\n', numel(sessionPaths));
% Session
for sessi... |
c2d94e955411b167f9b0dc831bed2ef8b32f963d8725f315de52c7d3a2b383f9 | MATLAB | 994 | 23 | function [inputPath, outputsFolderPath] = configurePaths(dataRawLoc, dataOutLoc, cohort, timepoint, task, params)
% Configures the input and output file paths based on the cohort,
% timepoint, task, and pruning method. Creates output directories if they
% don't exist, ensuring proper file organization throughout the... |
5b9bc79c9ee9eb80b59d4c0d2014734ddec94f701cec99320b62b5ec4e253c6e | MATLAB | 995 | 41 | function [posterior] = tapas_sem_mixed_estimate(data, model, inference, pars)
%% Estimates the hgf using mcmc.
%
% Input
% data -- Data of the model. It should be a structure array with
% fields y, and u of dimensions n times 1, when n is the
% number of subjects.
% model ... |
9ee1dca0ce9a10753e2089d7be24bd1b079de29b0657995475f8aa0608f22ff3 | MATLAB | 995 | 30 | %% addon_config
%
% Description: Addon script to incorporate new method to the SEPIA framework
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 27 June 2020
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the SEPIA f... |
b34002c0721e73a320a2a7b6a9cb8e6e580719990aa0357511435e7dce88853d | MATLAB | 995 | 36 | function U = randunitary(n, N)
% Generates uniformly random unitary matrices.
%
% function U = randunitary(n, N)
%
% U is a n-by-n-by-N array such that each slice U(:, :, i) is a random
% unitary matrix of size n (i.e., a matrix in the unitary group U(n)),
% sampled from the Haar measure (uniform distribution).
%
% By... |
730439d72fcc249806210895da85ab0870d8964aedf0ef81a22cd842a10fde16 | MATLAB | 996 | 43 | function database = DBUse(database)
%DBUse - Set (or determine) current database.
%
% Set (or determine) current database to store/retrieve processed data.
%
% USAGE
%
% DBUse(database)
% database = DBUse()
%
% database database name
%
% SEE
%
% See also DBConnect.
%
% Copyright (C) 2007-2012 ... |
79ee3bba7f10528bba7f55dba06cb8885fcd8ef263a7a0efe1827fbb977cf378 | MATLAB | 996 | 43 | function [old_dirs,old_stps,Hdiag,Bcompact] = dampedUpdate(y,s,corrections,debug,old_dirs,old_stps,Hdiag)
%B0 = eye(length(y))/Hdiag;
S = old_dirs(:,2:end);
Y = old_stps(:,2:end);
k = size(Y,2);
L = zeros(k);
for j = 1:k
for i = j+1:k
L(i,j) = S(:,i)'*Y(:,j);
end
end
D = diag(diag(S'*Y));
... |
7c47d568f69c91c8d86cbeb1948fb1cdab28f0b257891f905b444aed8b2e43b6 | MATLAB | 996 | 30 | %% addon_config
%
% Description: Addon script to incorporate new method to the SEPIA framework
%
% Kwok-shing Chan @ MGH
% kchan2@mgh.harvard.edu
% Date created: 6 July 2025
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the SEPIA f... |
4726ce0aa397160a20e8c1bfdb3f66f589160c93652018ef0306d86fc69ab6f6 | MATLAB | 997 | 40 | function [lab, pos] = read_besa_sfp(filename, uniqueonly)
% READ_BESA_SFP reads a besa style electrode location file.
%
% Use as:
% [lab, pos] = read_besa_sfp(filename, uniqueonly)
%
% Input arguments:
% filename = the file name
% uniqueonly = flag to determine behavior, to return the positions of the
% ... |
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