sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d39519cd5d63b14a9e9f66f711efc38ba47d1e5572dd822a608d23effb250ee5 | MATLAB | 695 | 30 | function ok_to_run = plugin_check_required_fields(DAT, required_fields)
% Plugin helper function for Second_level_analysis_template_scripts
% See those scripts for usage.
%
% Example:
% ok_to_run = plugin_check_required_fields(DAT, {'EMO_CAT_SIG_conditions'});
nfields = length(required_fields);
isok = false(nfields, 1... |
01518709658490353cdc4bb22ac5d33cf3c3e9686f574309757336b7438a2b22 | MATLAB | 696 | 20 | function [outstruct, unknowns] = myargparse(myvarargs, allowed, allow_unknown)
unknowns = {};
if nargin < 3
allow_unknown = false;
end
for i = 1:length(allowed)
outstruct.(allowed{i}) = '';
end
for i = 1:2:(length(myvarargs) - 1) %need to allow for a solitary 'recursed' on the en... |
12042ef97aef9c7983159b4dce6a1416bcf8a433f5982c883011edee8de8dc43 | MATLAB | 696 | 28 | function [smp1_gauss,idxi_1]=fib_gauss(smp1,sig,trgt_coor,vcnty_thr,dim)
% Min Jae Kim (mkim@bwh.harvard.edu)
%% Step 1: Imposing Vicinity Threshold
% Running Fibertract 1
rmv_1=[];
for hh=1:length(smp1)
vc_euc=sqrt(sum((smp1(hh,:) - trgt_coor) .^ 2));
if vc_euc>vcnty_thr
rmv_1=[rmv_1;hh];
end
e... |
123b3d68d74d6bee25faea6a342332d00ad69de4f7f0d02b124e321a88a9b252 | MATLAB | 696 | 18 | if exist('paramBC','var') %for unit match
param = paramBC;
end
spikeFile=dir(param.rawFile);
fname = spikeFile.name;
dataTypeNBytes = numel(typecast(cast(0, 'uint16'), 'uint8'));
try %hacky way of figuring out if sync channel present or not
n_samples = spikeFile.bytes / (param.nChannels * dataTypeNBytes);
... |
5a73497b2d48b454c3e5fa5894e8e959914d2d0b0e6481a6477e19133cfcafa5 | MATLAB | 696 | 21 | function y = inv_pos( x )
%INV_POS Reciprocal of a positive quantity.
% INV_POS(X) returns 1./X if X is positive, and +Inf otherwise.
% X must be real.
%
% For matrices and N-D arrays, the function is applied to each element.
%
% Disciplined convex programming information:
% INV_POS is convex an... |
06f5a162d38bda4cd1359e0a89f96c85867331f75e3bbafa4512e27d7e72bfdb | MATLAB | 697 | 30 | function [OnOffs] = findOnsetsAndOffsets(boolVec)
% Returns list of aligned start and stops of chunks of 1's in a vector of
% 1's and 0's.
%
% INPUTS
% boolVec - vector of 1's and 0's
%
% OUTPUTS
% startEnds - Nx2 list of indices of the first and last 1's for the N
% contiguous blocks of 1's.
%
% % func... |
b5ddf0ac53f0de50fa1af1706978111ba75f59f2df5cda60b7efe433e6557065 | MATLAB | 697 | 25 | function [out, segmentLength] = suprathresh(V, thresh)
% This subroutine determines suprathreshold values
%%% INPUTS %%%
% V: a Nx1 (checked) vector of values
% thres: a scalar threshold
%
%%% OUTPUTS %%%
% out: a Nx2 array with the 1st column indicating first suprathreshold
% values and the 2n... |
3903d9e525ed5497cb6a270cdde0071564ee8a82d28b129ca37bb4bc045c9f76 | MATLAB | 698 | 25 | function g=lcvplot(alpha,varargin)
%
% Computes and plots the Likelihood Cross-Validation score (LCV)
% for local fits with different smoothing parameters.
%
% The first argument to lcvplot(), alpha, should be a matrix with one
% or two columns (first column = nearest neighbor component, second
% column = constant comp... |
9adbcd2d0c54ff39fb8ee30acd7361f43f3e3f81551ab91e506147391985e0cc | MATLAB | 698 | 27 | function p = circ_iqr(alpha)
% CIRC_IQR - estimates the interquartile range of circular data
%
% INPUT & OUTPUT
% -------------
% alpha - input data (in radians, not binned)
% p - estimated iqr
%
% METHOD
% -------------
% For normal distributions IQR can be estimated from the
% standard deviation of th... |
5446676187eeb5492fff3086ad01cad26c20b92614a9f7aabfdab628e133d625 | MATLAB | 699 | 25 | function g=gcvplot(alpha,varargin)
%
% Computes and plots the Generalized Cross-Validation score (GCV)
% for local fits with different smoothing parameters.
%
% The first argument to gcvplot(), alpha, should be a matrix with one
% or two columns (first column = nearest neighbor component, second
% column = constant com... |
f187e02106b17ecad6b1b9486f2e349e391445f9fcf5ca8ffde13cbc8340a557 | MATLAB | 699 | 18 | function ncoords_mm=ea_extrapol_coords(coords_mm,options)
% simple iterative extrapolation for more than 4 contacts
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
ncoords_mm=zeros(opt... |
1d61de6b1a9ae09308034df099813aee0412772af689f73e2c9f0f911a7253ee | MATLAB | 700 | 23 | function data=extractdatac(data,Fs,t)
% Extract segements of continuous data between t(1) and t(2)
% Usage: data=extractdatac(data,Fs,t)
%
% Input:
% data: continous data in the form samples x channels or a single vector
% Fs: sampling frequency
% t : time as a 2d vector [t(1) t(2)]
% Note that sampling frequ... |
42c984aec0a3900753f176fe09e2bf25c3b23fb9f65a96222392287b3be10e03 | MATLAB | 700 | 19 | %% Figure 7 analysis
YOURDATAPATH = '';
% Load ROIs and border classifier data
fileList = searchFilesRecursive(YOURDATAPATH, 'allROIs.mat');
load(fullfile(fileList.folder, fileList.name))
% Using only cue-modulated
allROIs = allROIs([allROIs.modCue] == 1);
% Using only cells within the 5 main areas
areas = {'M2', 'M1'... |
50b4cdc71af3c6ca15145f243c9102fda5b50ce71ff6c2940d8f24b9da4bd241 | MATLAB | 700 | 24 | function S = ea_activecontacts(S)
for pt=1:length(S)
for side=1:2
switch side
case 1
sidec='R';
case 2
sidec='L';
end
S(pt).activecontacts{side} = zeros(1,S(pt).numContacts);
for source=1:4
for c=1:S(pt).numContac... |
5adbc22465ff9087ee73a325609f1bf33754247400de72100f174ce97c25e5f0 | MATLAB | 700 | 13 | % CVX: Keywords for declaring variables and objectives
% dual - Declares one or more dual variables.
% epigraph - Declares an epigraph variable.
% hypograph - Declares a hypograph variable.
% maximize - Specifies a concave (or affine) objective to be maximized.
% minimize - Specifies a convex (or affi... |
969878cec8e0888362e6d0e119c5bcf19580b139a4ac5af2aece379d1ec2b39a | MATLAB | 700 | 17 | function ea_apply_normalization(options)
% Wrapper to apply normalization to the unnormalized files.
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
json = loadjson(options.subj.norm.log... |
d1ec9e01622929a487a3fd6e98cf25ab7adeca958df227a68b308bce4f604278 | MATLAB | 700 | 21 | function res = PFNd_integ(params,inputs,initconds)
% params = array where first row is AF, second row is OF
% inputs = array where:
% [ AF directions;
% AF speeds;
% OF directions;
% OF speeds;
% time ]
AF = D_response_de(params(1,:),inputs([1:2,5],:),initconds(1));
OF = D_response_de(params(2,... |
17aa4ff1df0ff25b2d9f865acd64d1c9e81f76faa789b66cfae3468466f81510 | MATLAB | 701 | 13 | % CVX: Keywords for declaring variables and objectives
% dual - Declares one or more dual variables.
% epigraph - Declares an epigraph variable.
% hypograph - Declares a hypograph variable.
% maximize - Specifies a concave (or affine) objective to be maximized.
% minimize - Specifies a convex (or affi... |
b53a05dc890fb4f821e3361551f85fe05d42095cab185952ce154d9397a1540e | MATLAB | 701 | 22 | function root = AlignSpike2Session(root, force)
% Aligns Spike times to the Session frames. Populates root.Spike(n,m).i
if ~exist('force','var')
force = 1;
end
%
% For every spike object in root.spike, realigns spike times to root.b_ts,
% and deletes the rest of the cells information other than label
for j = 1:nu... |
e1cacc97a2b5c71b01532852da99da38993575f6269f2fe920530990a7bc9fcb | MATLAB | 701 | 29 | function [n,filters] = plx_chan_filters(filename)
% plx_chan_filters(filename): read channel filter settings for each spike channel from a .plx or .pl2 file
%
% [n,filters] = plx_chan_filters(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
%
% OUTPUT:
% filter - array of filter... |
48ca9d6a14d94b5045c3d5960ddfbf40fdac4fffd221e09154632e028872ef7a | MATLAB | 702 | 16 | function Energy = GCO_Swap(Handle,MaxIter)
% GCO_Swap Run alpha-beta-swap algorithm.
% GCO_Swap(Handle) runs alpha-beta-swap until convergence.
% GCO_Swap(Handle,MaxIter) runs at most MaxIter swap cycles.
% Returns the energy of the computed labeling.
% The labeling itself can be retrieved via GCO_Ge... |
9e45ab462843d09d958f03e55841e6413c161df8e2d3cdcc64fd21d2604b6937 | MATLAB | 702 | 22 | % Returns the total number of edges given the adjacency matrix
% Valid for both directed and undirected, simple or general graph
% INPUTs: adjacency matrix
% OUTPUTs: m - total number of edges/links
% Other routines used: selfloops.m, issymmetric.m
% GB, Last Updated: October 1, 2009
function m = numedges(adj)
sl=sel... |
ad5adf330f2059d3b1b3a2c09a4d340612c6fc16f85e3b0220a9e856c2d6c74e | MATLAB | 703 | 25 | function display(this)
% Display method for GIfTI objects
% FORMAT display(this)
% this - GIfTI object
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: display.m 4182 2011-02-01 12:29:09Z guilla... |
bc75e398146c71898449da928f07f40111972e23056add456cc9191ac9341587 | MATLAB | 703 | 19 | function scoresOUT = updatestages(scoresIN, srate, epochLength)
%%
% Authors: Dan Denis
% Date: 2021-07-14
epochSampleIdx = indexepochs(epochLength * srate, (length(scoresIN.stages) * epochLength) * srate);
epochSecIdx = indexepochs(epochLength, (length(scoresIN.stages) * epochLength));
epochSecIdx = epochSecIdx(... |
c80f534f59d446dd249dc6b012ab2d3f39d82f6f4a24a77ffa90ab698c9c2b4b | MATLAB | 703 | 27 | function extras = read_extras(fname)
% Read extra bits of information
%__________________________________________________________________________
% Copyright (C) 2005-2011 Wellcome Trust Centre for Neuroimaging
%
% $Id: read_extras.m 4492 2011-09-16 12:11:09Z guillaume $
extras = struct;
[pth,nam,ext] = fileparts(fn... |
5ab96537494000c051622af194c27e3255885f321caa7f7a33c3d78c13bba27c | MATLAB | 704 | 21 | function cfs = makeErbCFs(mincf,maxcf,numchans)
%MAKEERBCFS Make a series of center frequencies equally spaced in ERB-rate.
%
% This function makes a vector of center frequenies equally spaced on the
% ERB-rate scale.
%
% CFS = IOSR.AUDITORY.MAKEERBCFS(MINCF,MAXCF,NUMCHANS) creates NUMCHANS
% centre frequen... |
76daaa6ef68aea8b3b22ac476cb76a59f38a1fc8ba0dd279f1e58a400071cb0f | MATLAB | 704 | 29 | % setdiff_bc - setdiff backward compatible with Matlab versions prior to 2013a
function [C,IA] = setdiff_bc(A,B,varargin);
errorFlag = error_bc;
v = version;
indp = find(v == '.');
v = str2num(v(1:indp(2)-1));
if v > 7.19, v = floor(v) + rem(v,1)/10; end;
if nargin > 2
ind = strmatch('legacy', varargin);
if... |
2905244fb2ba4d67797f2bd3f37941c07e60645134c08d8f85ac280bf63b4e61 | MATLAB | 705 | 33 | function cvx_optval = trace_sqrtm( X ) %#ok
%TRACE_SQRTM Internal cvx version.
narginchk(1,1);
if ndims( X ) > 2, %#ok
error( 'trace_inv is not defined for N-D arrays.' );
elseif ~cvx_isaffine( X ),
error( 'Input must be affine.' );
end
n = size(X,1);
if n ~= size( X, 2 ),
error( 'Matrix must be square.... |
4b86754ce8ca9b827ad59c629cc1591122bebc52f82242fc17447c1b8a75332d | MATLAB | 705 | 18 | % HTMLREPORTDEMO
% Generates a demo report in the Output directory of this module
%
%
clear
r = report_generator('Test Report', 'Output');
r.open();
r.section('A Demo Report');
r.add_text('This is an example HTML report generated from Matlab. Discuss what you did here, maybe give a few example calculations:');
... |
7ae4b058d142b38afc1b16421bfca1d63a6b0c8c0048d25d55a38d24e1fb6ca2 | MATLAB | 705 | 30 | function [n,gains] = plx_adchan_gains(filename)
% plx_adchan_gains(filename): read analog channel gains from .plx or .pl2 file
%
% [n,gains] = plx_adchan_gains(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
%
% OUTPUT:
% gains - array of total gains
% n - number of channels
... |
7ced24f3663cc1f66dd960791b19779636f66c5e439efe6f5fd86e915a44a42c | MATLAB | 706 | 24 | function data=extractdatapb(data,Fs,t)
% Extract segements of binned point process data between t(1) and t(2)
% Usage: data=extractdatapb(data,Fs,t)
%
% Input:
% data: binned point process data in the form samples x channels or single
% vector
% Fs: sampling frequency
% t : time as a 2d vector [t(1) t(2)]
% Note that... |
f808b3529a8fb4c08ae2d55cc0735daed9db08eec71068d3cf82cbfbbcc775f2 | MATLAB | 706 | 18 | function out = M_motion( param, img , img_prev, prev_img_shift , ti )
if ( nargin == 1 )
out.weight = param.motionWeight;
out.numtypes = length( param.motionAngles );
for i = 1 : length( param.motionAngles ),
out.descriptions{i} = sprintf('Motion Direction %g',param.motionAngles(i));
end
el... |
0655c6346dfcdcf336e7f35526b77060a5e80e4e224f10a64237c9b79e493c2d | MATLAB | 707 | 23 | function maxChannels = getWaveformMaxChannelEP(templateWaveforms)
% JF, Get the max channel for all templates (channel with largest amplitude)
% ------
% Inputs
% ------
% templateWaveforms: nTemplates × nTimePoints × nChannels single matrix of
% template waveforms for each template and channel
% ------
% Outputs
% -... |
61b8638430f89b7aded7f5385cf682cb5c444fbe8c83b15293fe8791b4e06d2a | MATLAB | 707 | 28 | function r = circ_dist(x,y)
%
% r = circ_dist(alpha, beta)
% Pairwise difference x_i-y_i around the circle computed efficiently.
%
% Input:
% alpha sample of linear random variable
% beta sample of linear random variable or one single angle
%
% Output:
% r matrix with differences
%
%... |
bfdc419393040445b44ce05040459847d2483dd0bfae734836aa05638d51050e | MATLAB | 707 | 22 | function Output = A_applyfilter_decimate(Data,Lowcut,Highcut,fs,dsfs);
% Apply filter between Lowcut and Highcut (Hz) for Data sampled in given
% frequency (fs).
% "Data": data source ready to be filtered
% "fs": sampling frequency (Hz) of Data
% "Lowcut": lowcut frequency (Hz) of filtering
% "Highcut" Hig... |
f88c285549b06b779ae537c7e709924d4391f16b79ea6a85221ba38d96842d44 | MATLAB | 707 | 27 | function data_r = reorder_sctx(data)
%
% Usage:
% data_r = reorder_sctx(data)
%
% Description:
% Re-order subcortical volume data alphabetically and by hemisphere (left then right; author: @saratheriver)
%
% Inputs:
% data (table) - Data matrix
%
% Outputs:
% data_r (table) - Re-ordered data
%
% Sara Lariviere ... |
4dc0b15490cea647fcf75a9fd5ed0ff24e8ccfd2b0d639a25880466757291770 | MATLAB | 708 | 27 | function ea_init_coregmrpopup(handles, defaultmethod)
% Initialize MR coregistration methods popupmenu.
% Set methods
names = {'ANTs (Avants 2008)'
'BRAINSFit (Johnson 2007)'
'FLIRT (Jenkinson 2001 & 2002)'
'FLIRT BBR (Greve and Fischl 2009)'
'Hybrid SPM & ANTs'
'Hybrid SPM & BRAINSFIT'
'Hybrid... |
7b3e2fcbf55ddb9813cf8dc546cb3894c9a5755f600b9600b7893a002307c8af | MATLAB | 708 | 26 | function pvalue_text = extract_pvalue_text(pval, is_corrected, correction_subscript)
if nargin<3
correction_subscript = 'FWER';
end
if nargin<2
is_corrected = 0;
end
if ~is_corrected
if pval>=0.01
pvalue_text = sprintf('p = %.3f', pval);
elseif pval<0.01 && pval>=0.001
pvalue_text ... |
d0db5164cb747abd20084d4b18ff9fc407f6e4cfc49451ef7f82b0aa2b10daac | MATLAB | 708 | 29 | function models = fitAreaGMMsPCA(allROIs, options, metricField, areas)
% Fits Gaussian mixture model distributions to the PC coefficients of
% neurons specific to a given anatomical area
% Get metrics
switch metricField
case 'PCs'
metrics = cat(1, allROIs.PCs);
case 'rotPCs'
metrics = cat(1, al... |
443050d4ec6865812f6a0e98a81c3e6868542948443bb99a0b0e0daccb5dd712 | MATLAB | 709 | 23 | function move_inside=CheckMoveInside3D(V,Fnew,Vertex_id)
% Orignal vertex position
P=V(Vertex_id,:);
move_inside=false(1,size(Fnew,1));
for i=1:size(Fnew,1)
A=V(Fnew(i,1),:); B=V(Fnew(i,2),:); C=V(Fnew(i,3),:);
normal = -cross(A-C,B-C);
normal=normal./sqrt(sum(normal.^2));
% Calculate... |
5c6d3cdc737bf40f3b5a97f04f3935fbfe6d0b3b0a024110b0ed3b7c1542be95 | MATLAB | 709 | 25 | function S = struct_mfile_reference(mfile,struct_name,strs)
% S = struct_mfile_reference(mfile,struct_name,strs)
% AF 11/1/01
pattern = [struct_name '.'];
if (~isempty(mfile))
strs = grep(mfile,pattern);
end
S = [];
for i = 1:length(strs)
inds = strfind(strs{i},pattern);
for j = inds(:)'
... |
6674441bdda6e03adbfb5beddd2bec3b24fe3500520632c82b7c3f44c91dd672 | MATLAB | 709 | 36 | function [newL2] = bestMap(L1,L2)
%bestmap: permute labels of L2 to match L1 as good as possible
% [newL2] = bestMap(L1,L2);
%
% version 2.0 --May/2007
% version 1.0 --November/2003
%
% Written by Deng Cai (dengcai AT gmail.com)
%===========
L1 = L1(:);
L2 = L2(:);
if size(L1) ~= size(L2)
error('size... |
acaa4236015b272eb85e7807e705b0374ec6243477c9b43f84ed76f022f4d298 | MATLAB | 709 | 29 | % helper function for CrossCorrelationsOnCombinedData.m
function corrVals = crosscorr_nan_safe_prachi(x, y, maxLag)
nLags = 2*maxLag + 1;
corrVals = nan(nLags, 1);
lagOffsets = -maxLag:maxLag;
for i = 1:nLags
lag = lagOffsets(i);
if lag < 0
xLag = x(1:end+lag);
... |
7362b9842d19348f4f1fd309e36490c7a8d53d80583e2625cf2aef7af097e2b8 | MATLAB | 710 | 19 | function zx = cvx_expand_dim( z, dim, nx )
%CVX_EXPAND_DIM Expands an N-D array along a specified dimension.
% CVX_EXPAND_DIM( X, DIM, NX ) stacks NX copies of the matrix X along the
% dimension NX. It is equivalent to CAT( DIM, X, X, ..., X ), where X is
% repeated NX times.
%
% This is an internal C... |
df157bfdb517622f49f459b97a68bf525edf0091565a3ce30c52bbed83396da6 | MATLAB | 710 | 33 | function cvx_optval = trace_inv( X ) %#ok
%TRACE_INV Internal cvx version.
narginchk(1,1);
if ndims( X ) > 2, %#ok
error( 'trace_inv is not defined for N-D arrays.' );
elseif ~cvx_isaffine( X ),
error( 'Input must be affine.' );
end
n = size(X,1);
if n ~= size( X, 2 ),
error( 'Matrix must be square.' );... |
261f64dc32fd606e7d9d79742cf2d474b3682c71f2cda208319bd33ddad8936e | MATLAB | 711 | 27 | function [inface, outface]=innersurf(node,face,outface)
%
% outface=innersurf(node,face,outface)
%
% extract the interior triangles (shared by two enclosed compartments) of a complex surface
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% node: node coordinates
% face: surface triangle list
% out... |
67baa23a676c7e1be7d3e4319e3db0c8918d081032c1edca4240da0a49d70ee5 | MATLAB | 711 | 26 | function h5_2_bin(path_to_file,output_name,precision,batch_size)
info = hdf5info(path_to_file);
dims = info.GroupHierarchy.Datasets.Dims;
T = dims(end);
if nargin < 4 || isempty(batch_size);
batch_size = T;
else
batch_size = min(batch_size,T);
end
if nargin < 3 || isempty(precision)
precision = ... |
cbec3415aa5bdf85cb464f0c2773c8a5227f6d958840f6cff2307280ec9ec2dd | MATLAB | 711 | 29 | % ismember_bc - ismember backward compatible with Matlab versions prior to 2013a
function [C,IA] = ismember_bc(A,B,varargin);
errorFlag = error_bc;
v = version;
indp = find(v == '.');
v = str2num(v(1:indp(2)-1));
if v > 7.19, v = floor(v) + rem(v,1)/10; end;
if nargin > 2
ind = strmatch('legacy', varargin);
... |
5d711cc0f308123ee5f290edfb5f29a57bd6d9dab921b3e27d66ab45ce4fdf9a | MATLAB | 712 | 26 | function v = getOr(s, field, default)
%getOr Returns the structure field or a default if either don't exist
% v = getOr(s, field, [default]) returns the 'field' of the structure 's'
% or 'default' if the structure is empty of the field does not exist. If
% default is not specified it defaults to []. 'field' can a... |
bff639f07a77e3ca858dbf91934bb61aff3b41d47fbd7aef12b172bbaa0df779 | MATLAB | 712 | 22 | function outStr = LeG_dialogCellstrHelper (inputStr)
% Copyright 2010-2011 The MathWorks, Inc.
% Helper used by MSGBOX, ERRORDLG, WARNDLG, QUESTDLG to parse the input
% string vector, matrix or cell array or strings.
% This works similar to the CELLSTR function but does not use deblank, like
% cellstr, to eliminate ... |
149c6750e4b9461f3a87e8b758acec0736ea94cc9a3c6b036b39245c4498728f | MATLAB | 713 | 35 | function [ WS , DS , n ] = convertimstocounts( ims )
% count the total number of pixels activated
n = sum( sum( ims > 0 ));
w = zeros( n , 1 );
d = zeros( n , 1 );
c = zeros( n , 1 );
nims = size( ims , 1 );
ii = 0;
for di=1:nims
imnow = ims( di , : );
% find activated pixels
wh = fi... |
3548dec97de2de560a8f15adbd581dd36531bc9a0b8dd306008a79e3597d952b | MATLAB | 713 | 23 | % datasets = Doric.getDatasets(filename)
% List datasets within Doric's h5 datafile.
% 2023-02-03. Leonardo Molina.
% 2024-01-22. Last modified.
function datasets = getDatasets(filename)
root = h5info(filename, '/');
datasets = get(filename, root);
datasets = datasets.cellstr();
end
function lo... |
4232f242bfe46f97eb622f1eaa09b247d776ba2e4cec807392d7682aff3ebe6d | MATLAB | 713 | 22 | function frame = getframe(vr)
%FRAME=GETFRAME(VR)
% Returns the current frame that has been read in from video VR. Calling
% GETFRAME does not automatically advance the current frame so the user
% must first call NEXT, STEP, or SEEK before calling GETFRAME the
% first time. This makes it easy to write loops ... |
9d7294aeadb7d81a03c8e3d39d40a99dfa8aa9490b9f706c3846324d0e0f2c26 | MATLAB | 713 | 17 | function [colors,contrastID] = getContrastDRCvars()
% Initialize variables for operations on contrast DRC data
contrastID = {'LowContrast','HighContrast'};
%COLORS for sound level contrast plots
colors.lohiPre = [0 0.4510 0.7412; ... %light blue: 0 0.4510 0.7412
0.8510 0.3294 0.1020]; %light red/orange... |
f6197bc1bf69e88d8a683dd4d09ca1233dd0f19bddd7cd692c7479c8dc74b576 | MATLAB | 713 | 24 | function [pth,nam,ext,num] = spm_fileparts(fname)
% Like fileparts, but separates off a comma separated list at the end
% FORMAT [pth,nam,ext,num] = spm_fileparts(fname)
% fname - original filename
%
% pth - path
% nam - filename
% ext - extension
% num - comma separated list of values
%___________________... |
0fd29171b6c126602e2b73554a36247314e191944aba59831c3ddff09784c47b | MATLAB | 714 | 19 | [fname,pname]=uigetfile('*');
eval(['load ' pname '\' fname]);
params.tapers=[5 9]; params.pad=2; params.Fs=1000; params.fpass=[0 100]; params.trialave=1;
movingwin=[0.5 0.1]; % duration of moving window used to evaluate spectrograms
win=[2 2]; % window around events
fignum=[2 3 6 9 8 7 4 1]; % figure numbers for parti... |
96c8cdc861dd5f0dd20cbb020efcef0c42c02e18f6085e844089ffc96a88060c | MATLAB | 715 | 26 | function p = SquareSubplot(n,i)
%SquareSubplot - Layout subplots in a square arrangement.
%
%
% USAGE
%
% p = SquareSubplot(n,i)
%
% n total number of subplots
% i current subplot
% Copyright (C) 2008-2011 by Michaël Zugaro
%
% This program is free software; you can redistribute it... |
9d44bb65596c708d1add36b0b84235327187f7056e01ff0dc14b5191d82298cc | MATLAB | 715 | 27 | function plotOnsetPDFSubpops(allROIs)
% Wrapper to plotMetricPDFSubpops, for onset data
% Offset Y axis slightly in post, no need to do so here
% Plot
plotMetricPDFSubpops(allROIs, 'onset', [-200 400])
% Format figure
panelwidth = 2.25;
panelheight = 1.35;
leftoffset = 0.5;
bottomoffset = 0.5;
formatFigure(gcf, panel... |
8b6c5727e721db4a823958d1f0b456e638b53543695b0020e27e25c51ab48280 | MATLAB | 716 | 23 | % Run this after example.m in order to write the detected event times to disk
ts_data = [];
num_subj = numel(timeseries);
num_trials = 200;
event_times = cell(num_subj * num_trials, 1);
for subj_idx = 1:num_subj
ts_data = [ts_data, timeseries{subj_idx}];
trial_idxs = specEvents(subj_idx).Events.Events.trial... |
f12f57f937f2d4dcb426ab88e9b8e58dc260ab2af06b9c5959958c65a011d736 | MATLAB | 716 | 18 | function showregresult(RegPara, imagefilename)
scrsz = get(groot,'ScreenSize');
meanImg_PreReg = RegPara.meanImg_PreReg;
meanImg_PostReg = RegPara.meanImg_PostReg;
if isempty(findobj('type','figure','number',10))
pos = round([10 20 scrsz(3)/3*1 scrsz(4)/2*1]);
else
h1_handles = get(figure(10));
pos = h1_han... |
4e348c873d222b062991c6a7d6702c3c23ce96a9f3c1399306d8c5a58c36c090 | MATLAB | 717 | 35 | %%
%syms k t
%/ ((3.1416^(1/2)*erfi((k)^(1/2)))/(2*(k)^(1/2))))
%int(exp(k*t^2)*orthpoly::legendre(12,1.0*t),t,0,1)
for l = 2:2:14,
x = evalin(symengine,sprintf('simplify(int(exp(k*t^2)*orthpoly::legendre(%i,1.0*t),t=0..1) / ((PI^(1/2)*erfi((k)^(1/2)))/(2*(k)^(1/2))));',l))
y = strrep(char(x),'erfi','tm... |
a49e61f4ce89138f8f966b06225382d0874e4f660a6b046d830f5beecb91a615 | MATLAB | 717 | 29 | % unique_bc - unique backward compatible with Matlab versions prior to 2013a
function [C,IA,IB] = unique_bc(A,varargin);
errorFlag = error_bc;
v = version;
indp = find(v == '.');
v = str2num(v(1:indp(2)-1));
if v > 7.19, v = floor(v) + rem(v,1)/10; end;
if nargin > 2
ind = strmatch('legacy', varargin);
if ~... |
0c24eee388b3a94e27ecb032948b773bafc3c642aa50c81c4048ec721da6c51b | MATLAB | 718 | 20 | function ea_hyperlink_label(label, url, position)
% Creates a clickable hyperlink label
%
% USAGE:
%
% ea_hyperlink_label(label, url, position)
%
% INPUTS:
% label: label text
% url: linked URL
% position: position of the label
labelStr = ['<html><a href="">' label '</a></html>'];
jL... |
9e8a2edcf255aef78ec8a782ab27c3f33065a02e74c838bd7fd5623599d0d2e8 | MATLAB | 718 | 18 | function y = square_abs( x )
%SQUARE_ABS Square of absolute value.
% For real X, SQUARE_ABS(X) produces the same result as SQUARE(X); that
% is, it squares the elements of X. For complex X, SQUARE_ABS(X) returns
% a real array whose elements are the squares of the magnitudes of the
% elements of X; that is, ... |
d09670c1c2da22ed8bfca9315641107a396ce26c133438b7c9669e9909e25439 | MATLAB | 718 | 18 | function [power_log, freq, time] = analysis_lfp(data, bin, window, noverlap, nfft, fs, pre)
% data: K x Nsamp（每行一个trial）
% 输出 power_log: (power - baseline_mean) ./ baseline_mean，逐 trial 做基线
% 基线定义：time-pre <= 0（把 spectrogram 的时间轴左移 pre 秒）
% ---- 计算每个 trial 的时频功率 ----
K = size(data,1);
[~, freq, time... |
15a62fdca6e179068ab956e9c526201f7a8a7bd88b500f2aec35a5dd66ebd7bd | MATLAB | 719 | 29 | function cm=ea_export_CM_png(varargin)
X=varargin{1};
name=varargin{2};
options=varargin{3};
cm=figure('color','w','NumberTitle','off','Name',name);
if nargin==4
% BIDS FIX: Ensure valid color limits
clim = varargin{4};
if length(clim) == 2 && clim(2) > clim(1)
imagesc(X, clim);
else
%... |
bd7f015d1f39baeac7714b376a1b5189075c38614b2cdfe74ffff2c5d5651283 | MATLAB | 720 | 25 | % % Input data
% data = [201:240]; % Sample data
% indices = [3 4 5 6 10 11 12]; % Vector of indices
micsampsperframe = 23.6;
data = flydata(1).gaussianfluor;
indices = bouts{13}{1};
imginds = floor( bouts{13}{1} / micsampsperframe );
% Chunk data based on consecutive sequences of indices
chunks = {};
curr... |
ca55693d8598e4c09e3c383578f2b8047e80d2d88782932093d269dceeb9ffb5 | MATLAB | 720 | 18 | function [Theta_global] = doMLRRInference(cfg, data_counts_filtered, ...
total_biomass, perturbations, T)
params = cfg.ridgeRegression;
mesh = logspace(params.min, params.max, params.N);
[F,time,ID,U,taxa_data,time_data,ID_data,U_data,F_prime,X, magnitude]=...
import_data_and_construct_matrices(data_counts_filter... |
6a4142862ae148d3a5df2c1891750f594115bc999cc61ad39338a315eec5f1b8 | MATLAB | 721 | 35 | % V = idwt3(W)
%
% Implements the inverse discrete 3D wavelet transform, using Matlab 2D
% functions.
%
% See also: dwt3
% Code written by Iman Aganj.
function V = idwt3(W)
sC = size3(W.dec{1,1,1});
for i=1:3
s(i) = length(idwt(zeros(sC(i),1), zeros(sC(i),1), W.wl));
end
V = zeros(s);
F = cell(... |
7dd64059e0c0cf5ee15eab1670a9950b7f98cd01581849a3dac5aeb8e49728eb | MATLAB | 721 | 36 | function r = circ_dist2(x,y)
%
% r = circ_dist(alpha, beta)
% All pairwise difference x_i-y_j around the circle computed efficiently.
%
% Input:
% alpha sample of linear random variable
% beta sample of linear random variable
%
% Output:
% r matrix with pairwise differences
%
% Refe... |
b5417f9380b879d541e2648c8c6dacfc2a4d950cb502675bc8352650016ef290 | MATLAB | 721 | 20 | function subject( to )
%SUBJECT Implements the "subject to" keyword.
% The keyword
% SUBJECT TO
% is a "no-op"---that is, it has no functional value. It is provided
% solely to allow CVX models to read more closely to their mathematical
% counterparts; e.g.
% MINIMIZE( <objective> )
% SUBJECT TO... |
eea5d319ed25954ffea24b09139745e26838bfaf80fe0985012e07c2b149d70c | MATLAB | 721 | 33 | function vol_res = reslice(vol,hdr,hdrref,oversamp)
T1 = getMat(hdr);
T2 = getMat(hdrref);
SC = diag([[1 1 1]/oversamp 1]);
T2 = T2*SC;
if isfield(hdrref,'dataAy');
destdim = size(hdrref.dataAy)*oversamp;
else
destdim = hdrref.dime.dim(2:4)*oversamp;
end;
[X Y Z] = ndgrid(1:destdim(1),1:destdim(2),1:dest... |
0ec5190faf04513b875e1d19afca942848d6df6bbfc879084fb35663375182b6 | MATLAB | 723 | 21 | function cvx_clearspath
%CVX_CLEARSPATH Clears the cvx solver path.
% CVX_CLEARSPATH removes the internal solver directories to the Matlab
% path. CVX automatically clears the solver path after completion of a
% model computation, so calling this function should not be necessary.
% Nevertheless, we provide i... |
34e7b71be2282e8ef7b6e18c8d93017d9d5bd3a425d43bce04ca69fa571848ff | MATLAB | 723 | 39 | % rmsave() - return the RMS in each channel, epoch
%
% Usage:
% >> ave = rmsave(data,frames);
% Scott Makeig, CNL/Salk Institute, La Jolla, 9/98
function ave = rmsave(data,frames)
if nargin<1
help rmsave
return
end
if nargin<2
frames = size(data,2);
data = reshape(data, size(data,1), size(data,2)*size... |
8b9463744bb01283d638b7503ca1cf7d41e88a3460d416414a360bb9f175e527 | MATLAB | 723 | 28 | function extras = write_extras(fname,extras)
% Write extra bits of information
%__________________________________________________________________________
% Copyright (C) 2005-2013 Wellcome Trust Centre for Neuroimaging
%
% $Id: write_extras.m 5451 2013-04-26 14:03:05Z guillaume $
if ~isstruct(extras) || isempty(fie... |
eb7749e2ac86b1bd3e237a4b2639e86896ebe797da7fa4fdc5cfd90f22ce669f | MATLAB | 723 | 17 | function cellByTRFlinIDX = repFreqMask2linTRFidx(freqMaskByCell,nAmplInTRF)
% compileAnimalDataTable compiles data table of all ROI for all animals
% respective to stimulus parameters and TRF
%
% INPUT:
% freqMaskByCell --> logical mask of frequencies of interest
% ... |
ef48ddb21ebaffa52cedf09b093a7d327447e5470b5028fa2bedcdfa4b4e6adc | MATLAB | 723 | 22 | function rms = rms(x,dim)
%RMS Calculate the rms of a vector or matrix
%
% RMS = IOSR.DSP.RMS(X) calculates the Root Mean Square of X along the
% first non-singleton dimension of vector or matrix X. For vectors,
% IOSR.DSP.RMS(X) is the RMS value of the elements in x. For matrices,
% IOSR.DSP.RMS(X) is a row v... |
344cdbbf30cd774b3dc17c03d83a75ca593fe98112c8b30d21e749aa173bc657 | MATLAB | 724 | 29 | % union_bc - union backward compatible with Matlab versions prior to 2013a
function [C,IA,IB] = union_bc(A,B,varargin);
errorFlag = error_bc;
v = version;
indp = find(v == '.');
v = str2num(v(1:indp(2)-1));
if v > 7.19, v = floor(v) + rem(v,1)/10; end;
if nargin > 2
ind = strmatch('legacy', varargin);
if ~i... |
ab70f2ba957a724f5281185cf4bec174bb6b78fa09d83e0af18a62eb1f2ebedf | MATLAB | 724 | 32 | function [P bins] = JointDist(x,y,nbins)
%JOINTDIST
% Usage: [P bins] = JointDist(x,y,nbins)
%
%This function calculates the joint distribution of the variables x and y.
%It is simply a normalized histogram using hist3. nbins can take any form
%of bins that hist3 can take, but no other hist3 options.
%Writ... |
e8a54a757f7ead6ae145ec7ce152b2cb3f785404ef352d3a2b753fca21b165c0 | MATLAB | 724 | 35 | function varargout = scl_slope(varargin)
% Format
% For getting the value
% dat = scl_slope(obj)
%
% For setting the value
% obj = scl_slope(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: scl_slope.m 1143 2008-02-0... |
10581f5e7dc5b976dc1fa1a58201980cacd8e30523a8e137e08c5a22eb22f3f5 | MATLAB | 725 | 36 | function varargout = scl_inter(varargin)
% Format
% For getting the value
% dat = scl_inter(obj)
%
% For setting the value
% obj = scl_inter(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: scl_inter.m 1143 2008-02-0... |
6f20f2c0fde15ea211efe78bbc95cdf4649c061e1a9c3ad990967b8bc02726ac | MATLAB | 725 | 32 | function y = ipermute( x, order )
% Disciplined convex/geometric programming information for IPERMUTE:
% IPERMUTE(A,ORDER) imposes no convexity restrictions on A. ORDER
% must be constant.
%
% Determine the permutation
%
s = x.size_;
ndxs = 1 : prod( s );
ndx2 = ipermute( reshape( ndxs, s ), order );
%
... |
ad0b25a80ada2d66c6b29faeebcf43898f52e58585a3c7c7296c4a2a84ff95c2 | MATLAB | 725 | 21 | % ttl = Inscopix.loadTTL(filename, ttlTarget)
% Returns timestamps where tllTarget changes from low to high and high to low in Inscopix DAQ.
% 2019-02-01. Leonardo Molina.
% 2023-11-09. Last modified.
function [rise, fall] = loadTTL(filename, ttlTarget)
% Get time of transitions from low to high.
fid = ... |
debedf315073b2b3791a1b43ca1e9cc48034a93a5c33c1f291c58c624166daf9 | MATLAB | 725 | 29 | function error = sem(x,varargin)
% error = sem(x,varargin): Compute the standard error of the mean(SEM)
%
% Syntax
% error = sem(x,varargin)
% e.g. sem(magic(3)); sem(magic(3),1); sem(magic(3),2);
%
% Input
% x: vector or matrix
% varargin: none or 1 or 2
%
% Output
% SEM
if isempty(varar... |
14cc834bd4b7153afb9401eb67e05277526afe75a7718991365439914e2cd100 | MATLAB | 726 | 30 | function handles = dan_prepare_specData(handles)
% Function to plot spindle detections etc. specDataIn is a struct
% containing detections from fun_sleep_spindles and fun_slow_oscillations
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
% Now for each channel, find the start & end IDX of the event, look
% up the ch... |
ff57f339f848ba97ca2b9cc818b9260f7341941d7e57a76a96b03ca86043bf11 | MATLAB | 726 | 13 | [fname,pname]=uigetfile('*');
eval(['load ' pname '\' fname]);
params.tapers=[5 9]; params.pad=2; params.Fs=1000; params.fpass=[0 100]; params.trialave=1;params.err=[1 0.05];
movingwin=[0.5 0.1]; % duration of moving window used to evaluate spectrograms
win=[2 2]; % window around events
fignum=[2 3 6 9 8 7 4 1]; % figu... |
1e392959c98458d4fb7c74b98f766d19dfb29cd54afb40c4c0bfa8ccd190ca1d | MATLAB | 727 | 32 | function [n,gains] = plx_chan_gains(filename)
% plx_chan_gains(filename): read channel gains from .plx or .pl2 file
%
% [gains] = plx_chan_gains(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
%
% OUTPUT:
% gains - array of total gains
% n - number of channels
if nargin ~=... |
936c10b023635c69c4a5709babd9102679f3664e3851417e66b31bf80519fca5 | MATLAB | 727 | 25 | % Copyright 2009-2013 The MathWorks Ltd.
f = figure();
% Box Panel
p = uix.BoxPanel( 'Parent', f, 'Title', 'A BoxPanel', 'Padding', 5 );
% HBox
b = uix.HBox( 'Parent', p, 'Spacing', 5, 'Padding', 5 );
% uicontrol
uicontrol( 'Style', 'listbox', 'Parent', b, 'String', {'Item 1','Item 2'} );
% Grid Flex
g = u... |
966bb744286d3a3a9053a83f43ac1591ada34ce08ed0ebf58a1d9e958e0171ab | MATLAB | 728 | 31 | function [A xy] = star_graph(n)
% STAR_GRAPH Generate the star graph of order n
%
% The star graph is a simple star with n vertices. Vertex n is the center
% vertex.
%
% [A xy] = star_graph(n) generates a star graph with n vertices and
% returns the adjacency matrix in A. The matrix xy stores two-dimensional
... |
e384359cbe3c24d80ed94d93f074319c4563b655dc16ed226350fec367b74d31 | MATLAB | 729 | 17 | function z = lambda_sum_smallest( Y, k )
% LAMBDA_SUM_SMALLEST Sum of the k smallest eigenvalues of a symmetric matrix.
% For square matrix X, LAMBDA_SUM_SMALLEST(X,K) is SUM_SMALLEST(EIG(X),k)
% if X is Hermitian or symmetric and real; and +Inf otherwise.
%
% An error results if X is not a square matri... |
0f24fd807f95ca7de60b63acdc53975fa5dda81f4273f2253bd5861b8062de10 | MATLAB | 730 | 24 | function data=extractdatapb(data,Fs,t)
% Extract segements of binned point process data between t(1) and t(2)
% Usage: data=extractdatapb(data,Fs,t)
%
% Input:
% data: binned point process data in the form samples x channels or single
% vector
% Fs: sampling frequency
% t : time as a 2d vector [t(1) t(2)]
% ... |
d88cd69e5cae9889e9cdcea9e31937cfd949c5a3f3d1718afca131bcb856d899 | MATLAB | 730 | 34 | function DBListFigures(query)
%DBListFigures - List figures matching certain criteria.
%
% USAGE
%
% DBListFigures(query)
%
% query optional database query (WHERE clause)
%
% EXAMPLE
%
% DBListFigures('name="Spectrogram"');
%
% SEE
%
% See also DBGetVariables, DBGetFigures.
%
% Copyright (C) 2... |
da9a2a66c17a6b6b60ccb4c915483f41ee99e7e40aa8bebd82569cd724365e8d | MATLAB | 730 | 34 | function islands=bwislands(img)
%
% islands=bwislands(img)
%
% return the indices of non-zero elements in a 2D or 3D image
% grouped by connected regions in a cell array
%
% author: Qianqian Fang (fangq <at> nmr.mgh.harvard.edu)
%
% input:
% img: a 2D or 3D array
% output:
% islands: a cell array, each cell records t... |
e4141f1fab870335a6ac32aa6469a2afd1dee8e983a5029de9ddaa8c38244403 | MATLAB | 730 | 25 | %%********************************************************************
%% checkdense : identify the dense columns of a matrix
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%********************************************************************
funct... |
427811ee003c3bc6ca825c53c5bbe17d4b73268dc455124a38dd9a40157bf608 | MATLAB | 731 | 19 | function ea_run_Martinos_Launchpad(options)
% This is a function that runs code for each subject on a cluster. It needs
% to be adapted to suit your needs. Then, you can "Export code" using
% Lead-DBS and simply change the command ea_run to ea_run_cluster.
jobFile = [options.root, options.patientname, filesep, 'job_'... |
5042b8c66b152c972ef7fddf7b39a5f7c39d7904108078813e032044378884cc | MATLAB | 731 | 26 | function [nch, npoints, freq, d] = ddt_v(filename)
% ddt_v(filename) Read data from a .ddt file returning samples in mV
%
% [nch, npoints, freq, d] = ddt_v(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
%
% OUTPUT:
% nch - number of channels
% npoints - number of data point... |
524862188f31c0ad40f5070fbcef2c4752790dac93bcb9c61966ab07bf1cb48e | MATLAB | 731 | 27 | function newelem=meshreorient(node,elem)
%
% newelem=meshreorient(node,elem)
%
% reorder nodes in a surface or tetrahedral mesh to ensure all
% elements are oriented consistently
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2010/05/05
%
% input:
% node: list of nodes
% elem: list of elements (each row a... |
a4323f100bf02a220d477c6f9d9c5fa0040df04cbb789e6591a1459abc9e46f4 | MATLAB | 731 | 18 | function score=ea_exportscore()
% for now static sample export:
score.studyOrigin='Earlystim'; % Tag label study name
score.studyDoi='10.1056/NEJMoa1205158'; % Tag label study name
score.metric='UPDRS-III'; % clinical score label
score.dbsOff.vals=[1,2,0,0,0,0,0,0,0,0,0,0,0,0,2,3,2,2,3,3,1,1,1,2,2,2,2];
score.dbsOff.... |
144aabd5060284e8df40ee1114d257562d4b2361ee49ddef13ef31de29e68a53 | MATLAB | 732 | 28 | function ringRemoval(niinames)
for k = 1:length(niinames),
[pa na ext] = fileparts(niinames{k});
if strcmp(ext,'.nii'),
im = nifti(niinames{k});
for i = 1:size(im.dat,4),
v = double(im.dat(:,:,:,i));
v = ringRm(v,[1 3 10]);
im.dat(:,:,:,i) = v;
f... |
279f862d7508ff80d12b839d22169f06dd1c0a776687cf34a3541a4afb87eec5 | MATLAB | 733 | 19 | [fname,pname]=uigetfile('*');
eval(['load ' pname '\' fname]);
params.tapers=[5 9]; params.pad=2; params.Fs=1000; params.fpass=[0 100]; params.trialave=1;
movingwin=[0.5 0.1]; % duration of moving window used to evaluate spectrograms
win=[2 2]; % window around events
fignum=[2 3 6 9 8 7 4 1]; % figure numbers for ... |
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