sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
80f260fc1d248a7e1248afcf80dc225e25f0b0e70fe3e3b4653acb371f747894 | MATLAB | 1,652 | 55 | %% Plot test error vs C for differnet gammas in an SVM
% Same as Figure 12.6 in "The elements of statistical learning" 2e
% by Hastie, Tibshirani, Friedman
%%
% This file is from pmtk3.googlecode.com
if ~svmInstalled
fprintf('cannot run %s without svmfit; skipping\n', mfilename());
return;
end
data = loa... |
8394787ba9b8a28b72790c41a467465e0df438f37f9d9cf2364dd4417adf3d92 | MATLAB | 1,652 | 62 | function [style, colors] = meg_manuscriptStyle
% parameters for reproducing manuscript figures
style.widthTS = 470;
style.widthScatter = 300;
style.height = 300;
style.ebLineWidth = 0.2; % line width of shaded error bar edges
% scatterplots
style.xBuffer = 1;
style.xBufferSml = 0.2;
style.scatter.MarkerSize... |
c996b5c808a7a5b76f36a209bdfcdc49d149448852862e43f5ce5d52982a4b8b | MATLAB | 1,652 | 65 | function pin = GetOneInteriorNode(t,p)
% Asssuming a closed manifold surface is defined in 't' and 'p'
% this routine returns coordinates of a point within the surface.
% It assumes the surface is oriented and the normals of the triangles are
% pointing outward.
pin = [];
bbx1=max(p);
bbx2=min(p);
ld=min(bbx1-bbx2);
... |
28db03bc1d18ed30ed9e65cde75385ce5365a2cd7a785e5b6d4591285148f0a4 | MATLAB | 1,653 | 61 |
% model 4
load test_minentest4;
x = randn(2000000,2);
vXEdge = linspace(-5,5,70);
vYEdge = linspace(-5,5,70);
xHist2d = hist2d(x,vYEdge,vXEdge);
nXBins = length(vXEdge);
nYBins = length(vYEdge);
vXLabel = 0.5*(vXEdge(1:(nXBins-1))+vXEdge(2:nXBins));
vYLabel = 0.5*(vYEdge(1:(nYBins-1))+vYEdge(2:nYBins));
Sigma = [1... |
e80ba21842ac7f8c82e7906ffd910fed6b98f78a2bb1f2445104fb522e8360bc | MATLAB | 1,653 | 53 | % HIFDE_CHOLMV Multiply using generalized Cholesky factor from hierarchical
% interpolative factorization for differential equations.
%
% Typical complexity: about half that of HIFDE_MV.
%
% Y = HIFDE_CHOLMV(F,X) produces the matrix Y by applying the generalized
% Cholesky factor C of the factor... |
eb8630b3ace01d6507472989f67012885a54aa29b731a98d1fe05eb426814485 | MATLAB | 1,653 | 47 |
function output = cellfetch(cellinput, field, branchindex)
% searchresults = cellfetch(input, field)
%
% This function parces a nested cell variable 'input', and assumes nothing about
% the structure of the internal cell tree. It returns a structure with the value of the
% field variable in the field 'field' at the en... |
5aa56adf2d60564794f5d4926f915b6576c6b4da87f5419e94a6b6f78f0a66bf | MATLAB | 1,654 | 50 | function y = amgauss(N,t0,T);
%AMGAUSS Generate gaussian amplitude modulation.
% Y=AMGAUSS(N,T0,T) generates a gaussian amplitude modulation
% centered on a time T0, and with a spread proportional to T.
% This modulation is scaled such that Y(T0)=1
% and Y(T0+T/2) and Y(T0-T/2) are approximately equal to 0.5 .
%
% N... |
66cc45cbdc4dae765a00838da4737f21ff89643c8daf427c72c231387dd67f18 | MATLAB | 1,654 | 51 | function se = strel3D(shape, size)
% 3D version of matlabs 2d strel function
% Implements 'sphere' and 'cube'
%
% strel3d(shap,size)
%
% see also strel
%---------------------------------------------------------------------
% license
%--------------------------------------------... |
7fe28eeaf29e76379a8aa1424b90beb4bc7104b93d12363fb60dc7015c6893d8 | MATLAB | 1,654 | 54 | % Example using lsqnonlin optimizer and registration error image
% instead of value.
% clean
clear all; close all; clc;
% Add all function paths
addpaths
% Read two greyscale images of Lena
I1=im2double(imread('lenag1.png'));
I2=im2double(imread('lenag2.png'));
% b-spline grid spacing in x and y dire... |
a3896ce8c814c9fcbd5e2dd38530a8364804c5fcf471d796399993f43ac48d9d | MATLAB | 1,654 | 60 | % 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,... |
7bd057385b2bddda637c386a87927ba5f798026d7945f5d45cb55a78a8b962a3 | MATLAB | 1,655 | 72 | function hintonDiagram(w,max_m,min_m)
% Display a matrix W where the square's area represents W(i,j)
% and red = negative, green = positive
%
% Examples
%
% W = randn(4,5); hintonDiagram(W)
% This file is from pmtk3.googlecode.com
% Based on hintonw function from Mathworks neural net toolbox
if nargin < 1,error... |
f4f3a02501f939800c4c3d1ffb9efd1b39e891c177450e67c57fc1d0cc496daf | MATLAB | 1,655 | 91 | function EEG = lan2eeglab(LAN)
% v.0.2
% provisorio
% para guarda en .set y hacer ica
%
% 12.12.2022
EEG = lan_check(LAN);
%EEG = LAN;
ref_field = {
'trials',...
'srate',...
'xmin',...
'xmax',...
'data',...
'event',...... |
35505d1c9095dc06e060b93229219a3f7f5f0c106d295e234ce4b200fe3ee90a | MATLAB | 1,656 | 49 | %% Function for PRx analysis
function [PRx] = func_PRx(ICP, MAP)
% Input:
% ICP: Continuous intracranial pressure time series
% MAP: Continuous mean arterial pressure time series
% Time series should be synchronized and span the same timeperiod, and
% optionally filtered to remove noise from pulse ra... |
46220a9bdf8defec6010af75d152cf167a727268846ba63958bd914316bb7ba7 | MATLAB | 1,656 | 57 | %{
Copyright (c) 2025 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
classdef EntryRecordID < uint8
%ENTRYRECORDID Values for entry record types used in headers /
% subheaders
%
% Terminate: Used to indicate the end of the record entries in
% he... |
de3ac3670132c655b77509d405005879f42fa3109d4284f565df8c8c4c27149a | MATLAB | 1,658 | 64 | function meg_multiplot(vals, layout, cmap, highlightChannels)
%
% function meg_topoplot(vals, [layout], [cmap], [highlightChannels])
%
% INPUTS
% vals is an N x t matrix one value per channel, where N is number of channels
% layout is an ft layout (see ft_prepare_layout). will generate layout from
% custom file if not ... |
0d83ee9eea461358ed6f28c629d22795402495f68496c79ee51d5e1674d61af1 | MATLAB | 1,660 | 50 | function [list, badnodes]=GetListofConnectedTetsToNodes(t,p,verbose)
% list=GetListofConnectedTetsToNodes(t,p)
% This function assumes that the mesh in 't' is a valid mesh and has been
% checked by our diagnostic tool CheckMesh3D. It then returns a cell array
% whose members are list of elements attached to each node.
... |
1d44096d0de9bf22d301d49cb3f4fda837844958508fa1b237656bc0af0b7cf3 | MATLAB | 1,660 | 66 | function h_searchAndRemoveFromGroup3(handles)
global h_img3;
UData = get(handles.h_searchForGroupGUI3, 'UserData');
structName = ['I', num2str(UData.instanceInd)];
pathname = get(handles.pathName,'String');
basename = get(handles.fileBasename,'String');
fileExtension = get(handles.fileExtensionOpt,'String')... |
a82c467f305b0f28400da5403db59a8e9a4f4d8be93d9120824323052fb6ad0d | MATLAB | 1,660 | 47 | function model_fit = predict_venous_model(t_fit,covariates)
% Predict FDG venous radiotracer concentration from subject's covariates,
%
% Volpi T et al., Modeling venous plasma samples in [18F] FDG PET studies: a nonlinear mixed-effects approach.
% Annu Int Conf IEEE Eng Med Biol Soc. 2022 Jul;2022:4704-4707. doi: 10.... |
c8c1efd8b852a0a11dd3d79f20fc27366b0b3d6f410d1efe60136aaa85475562 | MATLAB | 1,660 | 44 | function si = import_simulation_files(fileNamePtrn,sort_by_par)
if (nargin < 2) || isempty(sort_by_par)
sort_by_par = '';
end
f = dir(fileNamePtrn);
assert(numel(f)>0,'No file found that matched the pattern');
fn = fullfile(f(1).folder,f(1).name);
si(1) = import_single_file(fn);
for ... |
751d72c63d6da9250c733dce7e4934a1f1a4ace7a244b51f0dd5253c80d62485 | MATLAB | 1,661 | 51 | function [st badtets badfaces] = check_tetrahedron_faces(e)
% check faces to make sure every face is only used by 1 or 2 tetrahedrons
% Returns:
% 0: OK
% 2: invalid mesh with more than 2 tetrahedron per face
%
% Written by:
% Hamid Ghadyani, 2009
st = 0;
fprintf('\nChecking tetrahedral faces..... ')
faces=[e(:,[... |
77a65a7800a0d13e4df0a760bb7468a7d15d7df11437bc0e173b3256cadd704d | MATLAB | 1,661 | 67 | function varargout=savebnm(fname,varargin);
% a compact binary format for saving a matrix. (using float)
%
%
% savebnm(fname,M1[,M2,M3,...]);
%
% Can save multidimensional matrices containing: Nans,Imaginary numbers and Inf
%
% see loadbnm
%
% Aslak Grinsted 2004 april
%
% --------------------------------------------... |
8f81856626bb4e6c6402589f103f3b706dc7ff209735c72bfb3c22878a062a16 | MATLAB | 1,661 | 88 | %% Demo of error correcting code
% -----
% | |
% | v
% x1 x2->x3
% | | |
% y1 y2 y3
%
% x3 = even parity bit
% yi = noisy copy
% This file is from pmtk3.googlecode.com
%% Build model
xs = 1:3;
ys = 4:6;
G = zeros(6,6);
G(xs(1:2), xs(3)) = 1;
for i=1:3, G(xs(i), ys(i)) = 1; end
ns = 2*ones(1,6... |
aec5aa7046770eb58b01b2e4fa383b84a31f37f61b88e150ac8613abf679d38b | MATLAB | 1,661 | 91 | function [events, mappings] = fiff_read_events(source, tree)
%
% [events, mappings] = fiff_read_events(source, tree)
%
% Read the events
%
% If tree is specified, source is assumed to be an open file id,
% otherwise a the name of the file to read. If tree is missing, the
% meas output argument should not be specified.
... |
c5ffdb0070f325250b65df4b0823e49dd0905bc3eb31333ef466d411964ca43f | MATLAB | 1,661 | 53 | function [cRow, cCol, ra, rb, phi] = gauss2ellipse( mu, C, rad )
% Creates an ellipse representing the 2D Gaussian distribution.
%
% Creates an ellipse representing the 2D Gaussian distribution with mean mu
% and covariance matrix C. Returns 5 parameters that specify the ellipse.
%
% USAGE
% [cRow, cCol, ra, rb, phi]... |
6b387f2e4b4ae36041904ee186bdf735f98a506b6833cfae7ca2649c8d29123f | MATLAB | 1,662 | 57 | function tests = test_VBA_sqrtm
% Unit Tests for VBA_sqrtm
tests = functiontests (localfunctions);
% -------------------------------------------------------------------------
function test_empty (testCase)
actual = VBA_sqrtm ([]);
testCase.verifyEmpty (actual);
function test_scalar (testCase)
C = ... |
a9d857dca21e8943b46ef23432953578fa1c1de1182655bf3decff28c07aefdd | MATLAB | 1,662 | 50 | function logstack = LOG(stack, sigma)
% Laplacian of Gaussian in 2 or 3 dimensions
%
% LOG(stack,sigma)
%---------------------------------------------------------------------
% license
%---------------------------------------------------------------------
% Copyright 2015 Idse Heemsker... |
90533e95849628785eeb231d34baff0aab0ba95ec32a9d8115dae40ebf41d46d | MATLAB | 1,663 | 74 | function [video,n_frames] = mat_to_video(array,filename,frame_rate)
%
% >>> OPERATION >>>
% Converts series of TIFF files into an AVI video. Uses MPEG-4 compression by default.
%%
% >>> USE >>>
%Select first TIFF file in the folder. The remaining files will be
%automatically found and concatenated
%If not provided, f... |
6ee4923e43462cc022464c6bea870b2640b22e7af8e9f7cfd7c8a4302c95d0b8 | MATLAB | 1,665 | 51 | function hdrols = deconvTseries(scm,dat,err)
% hdrols = deconvTseries(scm,dat,err)
%
% computes a ordinary least squares estimate
% of hemodynamic response function from
% from ER-fMRI time series (dat) and stimulus convolution
% matrix (scm)
%
% dat = scm * hdr + noise
% hdr_ols = inv(scm' * scm) * scm' * dat
%... |
70351ad7d8898bf83602d24d08c670c56dd6e1b0bedfd0c3035a1704fdb2e892 | MATLAB | 1,665 | 60 | function [error, devs, s, STEP, DELAY] = fiterror (param, model, startpar, g, typestat, d, iter, statweight, parange)
% This function calculates the cost function.
penalty = 0;
if nargin >= 9 & ~isempty (parange)
difmin = param .* startpar - parange(:,1)';
penalty = sum (abs(difmin)-difmin);
difmax = parange(:,2)'... |
e18ce83b83b2701ea2e24f2282bbcd1398e22a8b85ad36b8831cf6c5078cd35e | MATLAB | 1,665 | 53 | % HIFDE_CHOLSV Solve using generalized Cholesky factor from hierarchical
% interpolative factorization for differential equations.
%
% Typical complexity: about half that of HIFDE_SV.
%
% Y = HIFDE_CHOLSV(F,X) produces the matrix Y by applying the inverse of the
% generalized Cholesky factor C o... |
9d9831d633ea15d689e816a26b009ec61af9af3b1ce56b889e24936be6c1b599 | MATLAB | 1,666 | 58 | function address = getaddress(hostname)
% GETADDRESS returns the IP address
%
% Use as
% address = getaddress();
% or
% address = getaddress(hostname);
%
% See also GETUSERNAME, GETHOSTNAME
% Copyright (C) 2015, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the do... |
10b12d92301f44577062e03db5035340c2ab4be31745a56b1a75959d923cf3d1 | MATLAB | 1,667 | 52 | function [OutputArray]=String2Array3(InputString)
%Handles Negatives and Decimals
NumChar=length(InputString);
OutputArray=[];
Count=0;
position=2;
NegVal=0;
DecimalCount=0;
DecimalOn=0;
while position<=NumChar
isvalue=1;
CurrentNum=[];
while isvalue
... |
6709da8d71886f8fde5436097ed8a1d4066c6b09c9356436811ff4982ee59e07 | MATLAB | 1,667 | 66 | function [Y,dYdom,dYdT] = rigid_motion(X,om,T);
%rigid_motion.m
%
%[Y,dYdom,dYdT] = rigid_motion(X,om,T)
%
%Computes the rigid motion transformation Y = R*X+T, where R = rodrigues(om).
%
%INPUT: X: 3D structure in the world coordinate frame (3xN matrix for N points)
% (om,T): Rigid motion parameters between worl... |
7211651ebc6df1cd66b492f15e44082f11aa0eca1d1cef47fbea353e7f3d73ca | MATLAB | 1,668 | 44 | function I3=movepixels(I1,T,mode)
% This function movepixels, will (backwards) translate the pixels
% of an 2D/3D image according to x, y (and z) translation images
% (bilinear interpolated).
% The function is a wrapper around mex files movepixels_2d_double.c and
% movepixels_3d_double.c and movepixels_3d_single... |
f9d8487bba59749c51748e3f4556be46b3cb4893bb3f3959f3a1fb1d0e79fc28 | MATLAB | 1,668 | 58 | function ts_shift = AlignWave(wave, peakLoc, varargin)
% REQUIRED ARGUMENTS
% wave - clip of data containing a single spike waveform, # samples
% peakLoc - target location of waveform peak
% OUTPUT
% ts_shift - timing shift, in sample numbers, required to align the spike
% waveform to peakLoc
[... |
0883be360b93485048c1f58683616adce9143657b31617882aa25d9a53829146 | MATLAB | 1,669 | 53 | function [] = VBA_pause(options)
% used to pause the VB inversion from the GUI interactively
% NB: when paused, the inversion allows interactive diagnosis...
if ~ options.DisplayWin
return;
end
try
dt = toc(options.tStart);
timeString = sprintf('Elapsed time: %d min and %d sec', floor(dt/60), round(rem(dt,... |
1012ea9e52e409b192d03b05ea977e34fc75641b86be62de6653b0b43090e855 | MATLAB | 1,669 | 80 | %% sample from a DP mixture of 2D gaussians
%PMTKauthor Yee Whye Teh
%PMTKurl http://www.gatsby.ucl.ac.uk/~ywteh/teaching/npbayes/mlss2007.zip
%PMTKmodified Kevin Murphy
% Originally called DPmixgenerate
clear all
seeds = [2 3];
for trial=1:numel(seeds)
seed=seeds(trial);
setSeed(seed);
aa = 2; % alpha
nn = 1000; %... |
097ba45038c50b969550e3c6fd683204aae038f50b4633382611acf5acc32294 | MATLAB | 1,670 | 51 | function [rho,pval]=MySpearman(x,y)
% This function is to be a dedicated super-fast Spearman correlation
% calculation for the input data X(col vector) and Y(matrix). Inputs are
% assumed to have the same number of rows and have no NaNs or Infs. Y is
% also assumed to have no duplicates within a column.
% Steps:... |
92f0795d4036f6bf7af8a20047a1da8f2a8805d56075d24dcaa0ee5a46604823 | MATLAB | 1,671 | 44 | % FHN evolution function:
%
% [fx] = f_CaBBI_FHN(Xt,Theta,Isyn,inF)
%
% this function contains the equations and parameters of the FHN neuron
% model, and the over-time integration scheme
function [fx] = f_CaBBI_FHN(Xt,Theta,Isyn,inF)
dt = inF.dt;
Tau_Ca0 = inF.Tau_Ca0;
% Hidden variables
V = Xt... |
a7b6a578d4b38055dd7b23380514c2b5a815af3a29e7917dd5e6eb37799fc3a4 | MATLAB | 1,671 | 53 | % function coreg_check( ...
% bkgnd_file, ...
% out_path ...
% )
function coreg_check(bkgnd_file,out_path,tpm)
% Make a nice at-a-glance image to check registration between structural
% and functional. Works great with the mean functional as the background
% and the gray matter segmented image as the overlay.... |
114290cef83cdb330f4d7201b498373d22a65dda173ce2060e3326c4153ccf2f | MATLAB | 1,672 | 66 | %% Demonstrate inference in a small 2d grid of a noisy image of an X
% Based on
% http://www.cs.ubc.ca/~schmidtm/Software/UGM/linprog.html
%%
%PMTKrequireOptimToolbox linprog is called by UGM_Decode_LinProg
%PMTKrequireOptimToolbox bintprog is called by UGM_Decode_IntProg
% This file is from pmtk3.googlecode.com
%... |
2e5ea4acddd1003a58a9d710b08510edd037e39f20164cab44e699ddb23c8b26 | MATLAB | 1,672 | 70 | function motion_filt = CBIG_preproc_motion_filtering(motion, TR, f_min, f_max)
% MR_filt = CBIG_preproc_motion_filtering(motion, TR, f_min, f_max)
%
% This function filters out respiratory pseudomotion from motion estimates
%
% Inputs:
%
% - motion:
% N by 6 matrix of the motion estimates. N is the number of fra... |
33f425aa348d09222c361bca0eb1103c8c567402e118792e1ce3ec04a2a136c8 | MATLAB | 1,672 | 33 | function y_ZStandardization_Bilateral_Surf(InFile_LH, InFile_RH, OutputName_LH, OutputName_RH, AMaskFilename_LH, AMaskFilename_RH)
% y_ZStandardization_Bilateral_Surf(InFile_LH, InFile_RH, OutputName_LH, OutputName_RH, AMaskFilename_LH, AMaskFilename_RH)
% Calculate z-standardized data for bilateral hemispheres
% Input... |
441940630b2256b80f83d86d8690710532bf801c6667e82c5c3b7711c04ad3ca | MATLAB | 1,672 | 64 | function fp_linsys = analysis_fixed_points(model,fixed_points)
unpackStruct(model);
unpackStruct(fixed_points);
n_units=length(wO);
%%% output at fixed points
fp_linsys.o1=f1*wO'+bO;
fp_linsys.o2=f2*wO'+bO;
% fp_linsys.sat1=nan(n_units,size(f1,1));
% fp_linsys.jacs1=nan(n_units,n_units,size(f1,1));
fp_linsys.in11=... |
62f6e92f1a6dd85c50ec887e7a2e82bd11d42927247dcb2a1f57c48df3724540 | MATLAB | 1,672 | 52 | function [myhist precomp_grads] = buildOriHists(x,y,z,radius,pix,fv,sift_params, precomp_grads)
if (sift_params.Display_flag ==1)
figure;
hold on;
axis equal;
for i=1:sift_params.nFaces
tmp(1,:) = fv.vertices(fv.faces(i,1),:);
tmp(2,:) = fv.vertices(fv.faces(i,2),:);
tm... |
d0c6ec8a438cc63e9e1280e196c8bf2952a59d76c7bfda72642d01653b20b74b | MATLAB | 1,673 | 53 | function G = mkRndDag(nnodes, maxFanIn, maxFanOut, sparsityFactor)
%% Make a random, directed, weakly connected, topologically ordered, acyclic graph
%
% A directed graph is called weakly connected if replacing all of its
% directed edges with undirected edges produces a connected (undirected)
% graph. From http://en.... |
795d3435cd8a0382d0e21da83ecbbc5c7ba3ef82bcc849ca67585b625f9bad27 | MATLAB | 1,674 | 53 | % % This code will calculate the MSD from relative displacement value for the 2d glass. call this function after loading your data in run_relativeDisp_2d.
function [wmsd_eps,wmsd_aveps] = caculate_window_dmin(small_x,big_x,small_y,big_y)
af = '70';
ns = length(small_x(:,1));
nb = length(big_x(:,1));
Np=ns+nb;
savepat... |
ee8b2cab7acac6c0be5723aad30f92939ffaf3b5f2ac1e3572c15cf198f5c9bd | MATLAB | 1,674 | 51 | function jtree = mcsCliques2Jtree(clqs)
% input: clqs, a 1 x t cell array of nonempty cliques
% of a chordal graph in the order produced by maxCardinalitySearch
% This is algo 4.8 of Cowell 1999 except
% we exploit the fact that the clqs were generated by mcs
% This file is from pmtk3.googlecode.com
% This is... |
78eb4bef90459c4a826062ea0b6e2fdd455b8d4054575e1abe60fe6d49c6c65e | MATLAB | 1,675 | 65 | function [f, cxy, scxy95] = lan_coherence_shuffle(LAN, cfg, samples)
%***************DEPENDENCIES***************
% - hann (Signal Processing Toolbox)
% - hamming (Signal Processing Toolbox)
% - lan_cspd (LAN toolbox)
% - lan_cspd_mt (LAN toolbox) # See Dependencies (Chronux)
if ~isfield(cfg, 'twin')
disp('Setting ... |
95030d8f9939fc988306619f34380480e40345670d2e41c1ecc6285198589665 | MATLAB | 1,676 | 51 | %% force_delete
%
% force_delete(filename)
%
% does what it says on the tin. No 'permission denied' nonsense.
%
function force_delete(filename)
fID = find_fID_for(filename); % find all file IDs for meta file, might be open for reading and writing so may have more than one file ID
if ... |
10dac7cfdb9a843c22413e3d7e3ac133769624dc0a81214858e460287e3caea5 | MATLAB | 1,677 | 53 | function [assignment, cost] = assignmentsuboptimal2(distMatrix)
%ASSIGNMENTSUBOPTIMAL2 Compute suboptimal assignment
% ASSIGNMENTSUBOPTIMAL2(DISTMATRIX) computes a suboptimal assignment for the
% given rectangular distance (or weight) matrix, for example the assignment
% of tracks (in rows) to observations (in ... |
ed53fe7ea8de90fe0345c6058b0e62d80a9779e3a3ce0a91aec23e175d984c4c | MATLAB | 1,677 | 38 | function nc_spm_group_newsegment(SPMFilePath, newseg_jobmatfile, subj_t1files)
% SPMFilePath='G:\guobin\spm12\';
nsubj=length(subj_t1files);
parfor i=1:nsubj
[fpath, ~, ~]=fileparts(subj_t1files{i});
yfile=nc_get_specific_file_path(fpath, 'y_', '');
if exist(yfile, 'file') == 2
continue
... |
a2ff41b7ef427bd96578c0f841781be8c310242b774d0d0a85200983403b61ff | MATLAB | 1,678 | 62 | %% init
clear all
addpath(genpath('src'));
parameters;
%%
files = dir(fullfile('input', '*.tif'));
% Display the names
names = {files.name};
n_files = max(size(names));
disp(['number of files: ' num2str(n_files)]);
results = {'Name', 'Sholl, k', 'Determination R^2', 'Volume, um^3', 'Edge Lengths, um'};
%% Run loop
... |
22feb54a59a3a46cac08f4b600839fae9060e1283653e0267162e2570379a6a3 | MATLAB | 1,679 | 36 | % SOFA API - demo script
% Load HRTF in ARI format and save as SOFA format
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences
% Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the European Commission - subsequent versions of the EUPL (the "License")
% You m... |
335803e7916c2025a569161c9a4694ee42ff1bc512f40edcd12778468c7d7b43 | MATLAB | 1,679 | 73 | function sz = figsize(h, width, height)
%FIGSIZE Resizes the specified figure while keeping it on screen.
% Usage:
% figsize([width, height])
% figsize(width, height)
% figsize % returns figure [width, height]
% figsize(h, ...)
%
% Args:
% h: handle of figure to resize (default: gcf)
% width: new width ([]... |
91db44d765f340756db5d74b418e0ba7c6311e0211bd2a3708c5c46f90db15ce | MATLAB | 1,679 | 58 | % 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,... |
026a95368a238dde73b729fd7b0e066fb8f740600894828c47b63a5b99e4f90b | MATLAB | 1,680 | 52 | function [grid] = sel50p(cfg, grid, sens)
% This function will add the field "subspace" to the grid definition.
%
% The subspace projection corresponds to selecting 50% of the
% channels that are the closest to the dipole.
% set the defaults
if ~isfield(cfg, 'feedback'), cfg.feedback = 'text'; end
Ninside = ... |
959ab70ef768f40073e0034b5d366256aa9cf2fa7b9a92cc9400843fbc24d379 | MATLAB | 1,680 | 52 | %% Plot performance of linear regression vs sample size
%
%%
% This file is from pmtk3.googlecode.com
setSeed(0);
degrees = [1, 2, 10, 25];
for d=1:numel(degrees)
deg = degrees(d);
lambda = 0; %1e-3;
ns = linspace(10, 200, 10);
Nns = length(ns);
testMse = zeros(1, Nns);
trainMse = zeros(1, Nn... |
4790da3e20f4e568b48a14cf45eeec922eded9081dc8cdbc34532b9b5457a408 | MATLAB | 1,681 | 53 | function [S] = FreedDWSSFPOscillating(TR,alpha,D,T1,T2,b)
%
% calculates steady-state magnetization with diffusion weighting
% for oscillating diffusion gradient based on the Freed model. (Appendix 2)
%
% input:
% G = strength of diffusion gradient (mT/m)
% TR = repetition time (ms)
% alpha = flip angle (degrees)
% ... |
5ce277b0e8953a62c8b06231dfb8a715410151dd12fbe8c13bbceaa3d8a801a1 | MATLAB | 1,681 | 61 | function [idx1 idx2] = CorrespondingSpikes(spk1, spk2, maxDiff)
% 8/30/2016 M. Farries
% This function tries to find a one-to-one correspondence between elements
% of two arrays, "spk1" and "spk2." Elements of one array are "matched" to
% the closest elements of the other array, but no element in one array is
% a... |
73aa764205eb4b2a7c62893dd610513841498a3edfdb88e4bad685cad4c7901b | MATLAB | 1,681 | 56 | function [ newftdata cropdefs ] = wlFT_trimTrials(oldftdata, limitsfunc)
% function [ newftdata cropdefs ] = wlFT_trimTrials(oldftdata, limitsfunc)
%
% This function truncates trial records to limits computed by "limitsfunc",
% adjusting "sampleinfo" appropriately.
%
% "oldftdata" points to a Field Trip data structure... |
05ee7ceea71e6666d92a764284ca52dbbbd2a952301df0fc18ebd7e6b1428795 | MATLAB | 1,682 | 63 | function [fx] = f_Kalman4bandits (x, P, u, in)
% // VBA toolbox //////////////////////////////////////////////////////////
%
% [fx] = f_Kalman4bandits (x, P, u, in)
%
% Kalman filter learning rule for the N-armed bandit task as in
% Daw et al. 2006
%
% ////////////////////////////////////////////////////////////////... |
57ce7be65621c24515cc2049a2eaadca09360d461ed1b254f3b96ee8571fe16e | MATLAB | 1,682 | 58 | %% warn_supp
%
% Suppress printing of Matlab warning message
%
% <matlab:open('warn_supp.m') code>
%
%% Syntax
%
% oldstate = warn_supp(warnid)
%
%% Arguments
%
% _input_
%
% warnid Matlab warning identifier (default: 'all', for all warnings)
%
% _output_
%
% oldstate previous state of warning corresp... |
6938220581c0640b889ecb841abb6f547ac84d1b91dee32e9219ca7f6ac6f88e | MATLAB | 1,682 | 54 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% To remove the frequency components of the signal above a threshold
% (median of the frequency power + 5 standard deviations.
% Input:
% signal: row-wise signal
% fsamp: sampling frequency
% Output:
% filteredsignal: row-wise filte... |
6add182ddc3a7d7318d6db72daecb629f1d74661a1e64bcf2f88c9f90622b26a | MATLAB | 1,682 | 63 | Q = load('~/temp/stephen_fly325/Dropbox__fly325__0020_front.mat');
P = load('~/Dropbox/talks/labMeetingSep21_extra/basepredfly325.mat');
readfcn = get_readframe_fcn(Q.expname);
%%
fnum = 406;
im = readfcn(fnum);
llocs = [394 358; 332 336; 407 321; 351 294; 357 374];
f = figure('position',[675 171 1000 400]);
axis('ti... |
0fa78bc3a13c96dbf728be88deee0976ee4456847cf4e61a59167788af8f3ca1 | MATLAB | 1,684 | 43 |
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*']);
data_anat = dir([data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/nifti/anat']);
fprint... |
ce2cf1616346b6064dceee0a3435d975380696cee8a00141407f5f0ca8717908 | MATLAB | 1,684 | 56 | function m = medianw( x, w, dim )
% Fast weighted median.
%
% Computes the weighted median of a set of samples.
% http://en.wikipedia.org/wiki/Weighted_median
% "A weighted median of a sample is the 50% weighted percentile."
% For matrices computes median along each column (or dimension dim).
% If all weights are equa... |
fee86d88918fd669b355ab7b545b02f3c81155e3d4967df64af9098a05432895 | MATLAB | 1,684 | 43 | function [wfunc_file,wmeanfunc]=normalise_4d(cfunc_file,deformation,cmeanfunc_file)
cfunc_vols=[];
for i=1:length(cfunc_file)
[other_p,other_n,other_e] = fileparts(char(cfunc_file{i}));
cfunc_vols= [cfunc_vols; cellstr(spm_select('ExtFPList',other_p,['^' other_n other_e '$'],inf))];
end
%normalise all the fun... |
6e1152521c4898a60d77a4be0ae6f4f0cac4beae9cafb9f4e658518637cd7cdf | MATLAB | 1,685 | 62 | %% Demo of mlcomp
% This file is from pmtk3.googlecode.com
addtosystempath('C:\Octave\3.2.3_gcc-4.4.0\bin');
%localdir = tempdir(); %'C:\users\matt\desktop';
localdir = fullfile(pmtk3Root(), 'data');
%% regression
% This is pure matlab code and works fine
if 1
setSeed(0);
N = 10; D = 3;
X = randn(N,D);
w ... |
57799b51dafaff3711b2531103fa9f0edccbd48be379a25c2c6477aeab497594 | MATLAB | 1,687 | 83 | function A = convn_custom(A, B, power2flag)
% CONVN_CUSTOM FFT-BASED N-dimensional convolution.
% C = CONVN_CUSTOM(A, B) performs the N-dimensional convolution of
% matrices A and B. If nak = size(A,k) and nbk = size(B,k), then
% size(C,k) = max([nak+nbk-1,nak,nbk]);
%
% METHOD: CONVN_CUSTOM uses Fourier transfo... |
bbf3696944f690bfc3c9d4332b642079a6752db482709f7dbb05855c16377ea2 | MATLAB | 1,687 | 46 | function score = circleloss_score(mapper_path, tr_names)
% This score computes the length for each node to the low and up
% states. The loss is the subtraction of the distances to the two
% low and up states. The loss is computed and added for transition_plus
% and transition_minus.
datapath = fullf... |
d162e0e183317c1badd85b3884ae222eab6f399440958183d1e0ec2e994a0185 | MATLAB | 1,687 | 44 | % Preprocess neuropixel data
% Extract and reformat behavioral data and spikes for each session
% Output structures:
% beh, behMap, behView: behavioral indicators by trial in RDM, mapping
% and motion viewing tasks
% spk, spkMap, spkView: neural data by trial in RDM, mapping
% and motion viewing tasks
%% Loa... |
152e6501e94fc3acd15e1828249b6b92d090d5a6be70ff2fb96e061e9668f4cb | MATLAB | 1,688 | 62 | function [order, chordal, cliques, numpa] = perfectElimOrder(G, initNode)
%% Compute the perfect elimination order of a chordal graph
% Uses the Maximum Cardinality Search algorithm
% chordal = false if graph is not chordal
% Also returns maximal cliques of the graph, in an order
% that satisfies running intersection ... |
ce86636d04d213bf5ecb3d0691f0b938ff8de316af0c9c450ccb90305c3d8e3b | MATLAB | 1,688 | 41 | function mscmd_remove_noise_subclusters(timeseries_path,firings_in_path,firings_out_path,opts)
%MSCMD_REMOVE_NOISE_SUBCLUSTERS - Remove noise subclusters by splitting clusters
%into shells and comparing the subcluster template waveforms with the
%expected waveform shape in the situation of pure noise detected via
%ampl... |
930d24c82aeeddd30b22c30ac3a5ba918499cf4f7f6726917576dbd3c4539338 | MATLAB | 1,690 | 47 | function [Iall,Icombo] = load_and_combine_and_mask_multiplexed_channels(parentfolder,fov,fnames,refch,threshpct,medfilt)
%Loads multiple channels of the same image, e.g. from multiplexed data.
%Assumes all are the same width, height, and z-stack length
%fnames = list of filenames to load
%Iref = name of reference c... |
a2bf43b1e50da22dc0722ef37826e22d3e173c9cc7228afb9b0258de0cf8ab27 | MATLAB | 1,691 | 39 | function flag=istfr2(method);
% flag=istfr2(method) returns true is method is a
% time frequency representation of type 2 (only positive frequencies).
% See also istfr1, istfraff.
% F. Auger, may 98
% Copyright (c) CNRS - France 1998.
%
% This program is free software; you can redistribute it and/or modify
% it und... |
c895643e7dd03c084912200fddc78bb4c438e7eb85de9612598e48dc122a3055 | MATLAB | 1,691 | 48 | function [a, b] = VBA_guessHyperpriors (y, rangeEV)
% // VBA toolbox //////////////////////////////////////////////////////////
%
% [a, b] = VBA_guessHyperpriors (y, rangeEV)
% propose shape and scale parameters to use as hyperpriors for the
% measurement noise precision, based on the part of the variance one can
% exp... |
e4a6cb17c4ad4e0f861da878be0c9983afd2cad842ca0bb1ac2f0eb2329d9ae1 | MATLAB | 1,691 | 66 | function V = sphere_project(v,r,c)
% sphere_project - project point X,Y,Z to the surface of sphere radius r
%
% V = sphere_project(v,r,c)
%
% Cartesian inputs:
% v is the vertex matrix, Nx3 (XYZ)
% r is the sphere radius, 1x1 (default 1)
% c is the sphere centroid, 1x3 (default 0,0,0)
%
% XYZ are converted ... |
4ab2a050cc7ae82abaffc8459fad7dd33f6503a91f3e0ba2b2ea7a4e475b1098 | MATLAB | 1,692 | 77 | function data = ReadChoreSpineFile(filename)
nspinepts = 11;
nparams = 2*nspinepts + 2;
data = [];
fid = fopen(filename,'r');
if fid < 1,
error('Could not open file %s for reading',filename);
end
ids = [];
expname = '';
while true,
l = fgetl(fid);
if ~ischar(l),
break;
end
if isempty(l),
continue;... |
cb60eb715a36112ad8df0d466fd29bbfa0c142622fedf82c88edb19c398c377f | MATLAB | 1,692 | 54 | classdef FileLogger < handle
properties
filename_ % name of log file, or 1 for stdout, or 2 for stderr
tag_ % string added to start of each log message
is_fid_valid_ % if true, fid_ is valid. If not, fid_ is empty, and obj is a "null logger".
fid_ % a file_object of the log file
end
methods
... |
da71d51f6547415311f7126be221f347fa5685cd0fbcd39258675c311fd21a40 | MATLAB | 1,692 | 52 | function [ret,messages] = check_files_in_calculateDescriptors()
loadParameters;
if params.DO_DOWNSAMPLE
filename_root = sprintf('%s-downsample_',params.FILE_BASENAME);
else
filename_root = sprintf('%s_',params.FILE_BASENAME);
end
ret = true;
messages = {};
for r_i = 1:para... |
df11878ab99e197b114a52e425db040920f00c679da95ea64c3515d02c5693be | MATLAB | 1,692 | 65 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
%% EEG preprocessing wrapper script
clear; clc
delete(gcp('nocreate')) % clear parallel pool
%% variables that need to be changed
% loop
loop_number = 2
% subject, condition, and block info
subject_idx = [];
condition_idx = [];
%% define variables and paths
% experim... |
3d708d65a1dd490edd241816501297ff8a612ded2055c9e4213fde7937e02c0c | MATLAB | 1,694 | 48 | function mappedX = diffusion_maps(X, no_dims, alpha, sigma)
%DIFFUSION_MAPS Runs the diffusion map algorithm
%
% mappedX = diffusion_maps(X, no_dims, alpha, sigma)
%
% The functions runs the diffusion map algorithm on dataset X to reduce it
% to dimensionality no_dims. The variable sigma is the variance of the Gauss... |
e103ed0d97fee8d13f4a90c31b9516e594419cfe044eb658d45b8dbf949849cf | MATLAB | 1,694 | 54 | clear;
basefolder = fileparts(fileparts(fileparts(mfilename('fullpath'))));
codefolder = [basefolder,'/code'];
toolsfolder = [basefolder,'/tests/tools'];
addpath(genpath(codefolder));
addpath(genpath(toolsfolder));
res = load([basefolder, '/tests/fixtures/cme/mapper/res.mat']).res;
task_path = [basefolder, '/tests/f... |
5b56df34b03604282e429513a58f36fb8d64f982b533771a493f4dac05281a11 | MATLAB | 1,695 | 55 | function FC_cov = make_staticFCcov(datadir, n_sess)
% FC_cov = make_staticFCcov(datadir, n_sess)
%
% make subject-wise static FC (covariance) matrices for HCP rsFMRI
% This script uses groupICA50 parcellation
% Requires that both the behavioural data and the timecourses in groupICA50
% parcellation can be found in the ... |
061615cc73a42c1569a5c692e8f2d686c7eff2e74a0e3ff7cfe95c7a50692cd0 | MATLAB | 1,696 | 78 | % Demo for stable heteroclinic channel (SHC).
% This demo inverst a model of hierarchical SHC partly observable. The
% model has no observation/evolution parameters (except initial
% conditions).
clear variables
close all
% Choose basic settings for simulations
n_t = 5e2;
f_fname = @f_SHC;
g_fname = @g_Id;
u = ... |
89f2f7e4049f6588341dcf3a43b16bdc81e1747ec6dd6ec364fbc8ee32908121 | MATLAB | 1,696 | 45 | function [ind, int_func] = mytsearchn_fast(mesh, coord)
% MYTSEARCHN_FAST carries out a spatial point location search. It uses
% triangulation search algorithm that locates the triange/tetrahedron
% enclosing a query point. This is an interface for NIRFAST mesh format.
% This function also compensates for numeric... |
988cf408db8f2bacaf97947be2cc0cfdd6612d0ae2d700c64b47f33c65cad7d0 | MATLAB | 1,696 | 58 | function b = renamefields(a, old, new)
% RENAMEFIELDS renames a selection of the fields in a structure
%
% Use as
% b = renamefields(a, old, new)
% which renames the fields with the old name to the new name. Fields that
% are specified but not present will be silently ignored.
%
% See also COPYFIELDS, KEEPFIELDS, RE... |
e01b5f8b78b30c22420d700cdafddffab3e169e4c3d3f77592ffe9ec327d9826 | MATLAB | 1,696 | 61 | %% Plot the full L2 regularization path for the prostate data set
%
%%
% This file is from pmtk3.googlecode.com
loadData('prostateStnd');
setSeed(0);
%[X, y] = shuffleRows(X, y);
%X = centerCols(X);
NL = 20;
lambdas = [logspace(4, 0, NL) 0];
[n, d] = size(X);
nlambdas = numel(lambdas);
w = zeros(nlambdas, d);
... |
e43a73f43366009665d2cac7f8a67e25cb2db20bc6264c6589ff1b6dc4605172 | MATLAB | 1,696 | 70 | function [Tte,W,Va]=flinreg_l2(lambda,X1X1,Xtr_1,Ttr,Xte)
% linreg_ml -- perform linear regression by maximum likelihood estimate
% [Tte,W,Va]=linreg_ml(Xtr,Ttr,Xte)
%
% [Input]
% -Xtr: training data [N x M]
% -Ttr: target vector [N x 1]
% -Xte: test data [N2 x M]
%
%
% [Output]
% -Tte: prediction from the Xte... |
195e0da762daef47dc8249d418ffaae681a377ee95f973aec4257182349350de | MATLAB | 1,697 | 56 | %% Linear Regression Demo
%
%% Make data
% This file is from pmtk3.googlecode.com
[xtrain, ytrain, xtest, ytestNoisefree, ytest] = polyDataMake('sampling','thibaux');
Xtrain = xtrain; Xtest = xtest;
%% Fit using Matlab's functions
Xtrain1 = [ones(size(Xtrain,1),1) Xtrain];
w = Xtrain1 \ ytrain
Xtest1 = [ones(size(Xt... |
198e100ee1b741b257cc87d61213b6747bd94695809d18770f07d312b3466d26 | MATLAB | 1,697 | 65 | function javaTable(data,columnNames,tableName)
% Display a cell array of strings in a java JTable
% PMTKneedsMatlab
%%
% This file is from pmtk3.googlecode.com
if(isempty(data))
fprintf('\ndata cannot be empty\n');
return;
end
if(nargin < 2)
columnNames = cell(1,size(data,2));
columnNames(:) = {''};
... |
cdbdf794ac7d6f982bcfc195143f1284482fd5fe72c338965d75689a3293daba | MATLAB | 1,697 | 57 | % AverageCircularData.m
% Sarah West
% 7/20/23
function [parameters] = AverageCircularData(parameters)
% Display progress message to user.
MessageToUser('Averaging ', parameters);
% Pull out data.
data = parameters.data;
% Pull out weights
if isfield(parameters, 'weights')
weights =... |
e2d5941a1da89d7da09f9dce780fefab1f789aa21485662171487e46f56055de | MATLAB | 1,697 | 67 | function A = lan_smooth(A, span, fact, times)
% span = 0 : no change
if nargin<2
span=4;
end
if nargin<3
fact=0.5;
end
A = squeeze(A);
if nargin == 4
if size(A,3)>1
for i3=1: size(A,3)
for i = 1:(times)
A = lan_smooth(A, span, fact);
end
end
return
end
end
if size(A,3)>1
for i3=1: siz... |
2a3cb9d33f2a9472a267341af9d934e631f0d4f4d37698d9bcc9a287da3440ad | MATLAB | 1,698 | 46 | function [] = averageVelocitiesAcrossMice(parameters)
% Give parameters their original names
dir_exper = parameters.dir_exper;
periods_long = parameters.periods_long;
periods_transition = parameters.periods_transition;
full_transition_flag = parameters.full_transition_flag;
periods_ful... |
2dc9e521ffd7e9677ce076187d1adb1e2fb7db8d687be492eed6760ea5bcaef0 | MATLAB | 1,698 | 38 | % This script loads and processes model parameters for a single cell from
% a specified experiment. It reads the parameters from a text file in the repository,
% extracts relevant information (grid centers, model parameters, pixel size),
% and then converts the parameters into a structured format using either
% 'pa... |
4bed4e6f71cc1f7880fd353de915ab8337cde10db9d13ad63a41c5e628c8916f | MATLAB | 1,698 | 46 | % Example 2
%
%
% Citation: Cannavo' F., Sensitivity analysis for volcanic source modeling quality assessment and model selection, Computers & Geosciences, Vol. 44, July 2012, Pages 52-59, ISSN 0098-3004, http://dx.doi.org/10.1016/j.cageo.2012.03.008.
clear
clc
% create a new project
pro = pro_Create();
% add 3 i... |
c4ef625e11f0b5ee5cedbea45faa32d054e08dfe38d20616e850235a95f1300d | MATLAB | 1,698 | 51 | %% sdoAnalysis_testPxParams
% Utility to test the state mapping and filtering parameters on the
% background distribution of state. Useful for testing different parameters
% to optimize the state transitions
%
% NOT RECOMMENDED: Use 'xtDataCell' class w/ 'plot' method to test
% different state defintions
%____________... |
59898d380c4dfc9d8eded3edf2d03ad3a732bcd19aa01f69c2c5543a4117c0de | MATLAB | 1,699 | 80 | %% Visualize the effect of change the hyper-params for a 2d GP regression
% Reproduces fig 5.1 from Rasmussen and Williams
%PMTKauthor Carl Rasmussen
%PMTKslow
%%
% This file is from pmtk3.googlecode.com
n = 61^2; D=2;
[x1,x2]=meshgrid(-3:0.1:3,-3:0.1:3);
x=[x1(:),x2(:)];
h = figure(1);
clf
set(gca,'FontSize',24);
... |
b2e33e18098fc79827c03221550936b4574de5fe0e74925e3f0df7236e161dc6 | MATLAB | 1,699 | 54 | % PadMissingMouse.m
% Sarah West
% 1/20/23
% A quick and dirty function to concatenate data across conditions for the
% correlation fluor vs corr pipeline
function [parameters] = PadMissingMouse(parameters)
% Inputs :
% parameters.correlations -- 7 x 16 (mice x unique nodes)
% parameters.fluorescence --... |
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