sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a787ccba8860525b75823c96c7b9ae9788c3d7c0f597702dcb071f5726422860 | MATLAB | 1,039 | 28 | function [sta_traces] = make_raw_sta_traces(input_traces, stim_frames, pre_frames, post_frames,varargin)
% grab episodes from input traces only
baseline_frames_offset = [];
for v = 1:numel(varargin)
if strcmpi(varargin(v),'baseline_frames_offset') % back trace to the baseline of eventonsets
baseline_fr... |
d1f4dbaa5c6bbf92fce786fb7976b95a0a20569005e9145382d8b25e72610483 | MATLAB | 1,042 | 30 | function pstruct = tapas_hgf_jget_namep(pvec)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2017 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Licence (GPL),... |
7c2a6241052f0dfa74687d1846400363f311719d65d516c51ec0750ccaa120ee | MATLAB | 1,043 | 19 | function [event_frames] = reindex_subsession_event_frames(event_frames,sub_session_frame_range)
num_offset_frames = cumsum(cellfun(@(x)numel(x),sub_session_frame_range));
num_offset_frames = [0 num_offset_frames(1:end-1)];
for s = 1:numel(event_frames)
event_fds = fields(event_frames{s});
this_event_frames... |
8ff736112ba245d79155fbaab429a81d7179cad2e831d621b4ec8b168f17dc88 | MATLAB | 1,043 | 46 | function [model] = tapas_sem_multiv_model(data, ptheta, pars)
%% Set up the model.
%
% Input
% hgf -- Hgf model.
% pars -- pars structure.
% Output
% model -- Model structre.
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
%% Define the model.
%
% aponteeduardo@gmail.co... |
905728e69d642eb7617754d3a55c53c2a35ff5565ee5168c601075933413a346 | MATLAB | 1,043 | 34 | function data = importfileXLS(workbookFile, sheetName, range)
%IMPORTFILE Import data from a spreadsheet
% DATA = IMPORTFILE(FILE) reads all numeric data from the first worksheet
% in the Microsoft Excel spreadsheet file named FILE and returns the
% numeric data.
%
% DATA = IMPORTFILE(FILE,SHEET) reads fr... |
25f16e340c9f7c8a51c7119d731895ee3498849ee3a843152db70d2c29ed96a0 | MATLAB | 1,044 | 26 | function [cnm_struct] = make_cnm_struct(results)
% make cnm_struct out of cnmfe results
cnm_struct = struct();
cnm_dims = [results.options.d1 results.options.d2];
cnm_A = full(results.A);
num_frames = size(results.C,2);
num_comp = size(results.A,2);
cm = com(sparse(double(cnm_A)),cnm_dims(1),cnm_dims(2)); % cent... |
48e4dd178dc4ff51fda22735b8b7bc2222bef6f281638cf33ba54a23fc66b0ff | MATLAB | 1,044 | 30 | function pstruct = tapas_ehgf_jget_namep(pvec)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2017-2020 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Licence ... |
f07623026c1dc4295e2c6a017ebd85a5b70fb57215657cd0fccbb1f3be96d112 | MATLAB | 1,044 | 44 | function cell2csv(filename,cellArray,delimiter)
% Writes cell array content into a *.csv file.
%
% CELL2CSV(filename,cellArray,delimiter)
%
% filename = Name of the file to save. [ i.e. 'text.csv' ]
% cellarray = Name of the Cell Array where the data is in
% delimiter = seperating sign, normally:',' (it's defa... |
10e8b5dedadcea4b98f31f8b3637d68091acbd8e92637b959e4db64abd83e629 | MATLAB | 1,045 | 45 | %% h = sepia_handle_panel_bkgRemoval_BFRnet(hParent,h,position)
%
% Input
% --------------
% hParent : parent handle of this panel
% h : global structure contains all handles
% position : position of this panel
%
% Output
% --------------
% h : global structure contains all new and ot... |
27a60c9c75246e9b9b27d23acd44c0137edee54b64f4f86ba63bd80cd4295b34 | MATLAB | 1,045 | 37 | function [this, saveFileName] = save(this, varargin)
% Saves 4D MrImage in single file.
%
% Y = MrImageSpm4D()
% Y.save('fileName', fileName)
%
% This is a method of class MrImageSpm4D.
%
% IN
% fileName string: default via get_filename
% OUT
%
% EXAMPLE
% save
%
% See also MrImageSpm4D MrDataNd.save MrDat... |
f20089ca98754cb531dcbb7c751bfa2311649d46adff87bbb804129533123324 | MATLAB | 1,045 | 26 | function EEG = threshContinous(EEG, V_tsh)
%% mark segments w/ extreme values (exceeding threschold V_tsh)
% will be stored in EEG.etc.valid_eeg
EEG.etc.valid_eeg = true(EEG.pnts,1); % edit these indices later to keep samples out of analysis
bad_seg = find(any(abs(EEG.data) > V_tsh));
bad_EEG = false(EEG.pnt... |
34f2210d3972fbdf460f6033062564693cf7917d93f353a3abcd68b7b92cb914 | MATLAB | 1,046 | 48 | function [C,volLR,probLR,condlist] = getallContingencies(file_idx,A,ops)
%gets contingencies for all files from A struct
condlist = {'prevWin'...,
'prevLoss',...
'prevOptOut',...
'left',...
'right',...
'win',...
'loss',..... |
903a1b73346a5a4faa4723286e0c1dd23688f1ed552693f000764e9bc5615e12 | MATLAB | 1,047 | 54 | %% Colormaps that are pretty awesome: DEMO2
% In this demo we will show how to supereasily use the new colormaps
%
%
% this is an exampe of 4 colormaps that are being considered as the default
% colormap in python's matplotlib lybrary.
%
% All of them look quite good and they dont have any official name, so at
% the m... |
725b7d783d6395af933f46c2c187547ad3fcc79e0b38c574ade4e8ae794158e3 | MATLAB | 1,048 | 46 | function xcorr = crosscorr(x,y)
%% xcorr = crosscorr(x,y)
% This function calculates the cross-correlation between two vectors x and y.
%
% USAGE:
% xcorr = crosscorr(x,y)
%
% INPUTS:
% x = a vector
% y = another vector
%
% OUTPUTS:
% xcorr = cross correlation between vector x an... |
9bac0e2b193bbe850f7a8e329945708d7c5a076d190e22ef37d5236f1aa15cbb | MATLAB | 1,048 | 25 | function [mouse_position,mouse_bodyparts,mouse_heatmap] = get_mouse_position(data, dlc_vars,mouse_vars,frame_size, varargin)
mouse_vars_savenames = mouse_vars;
for v = 1:numel(varargin)
if strcmpi(varargin{v},'mouse_vars_names')
mouse_vars_savenames = varargin{v+1};
end
end
[~,var_idx]=intersect... |
b8110b3b991cd4ac8e856921e588d29dc07d5dc480ba7a37cc0b3d9cc7d621cb | MATLAB | 1,048 | 40 | %%%make PSTH
function [h,p,spk_row,ind_row] = psth_ST(unitdata,unitSR, stampdata,stampSR,binlength,sttime,endtime)
if unitSR == stampSR
else
stampdata = round(stampdata.*unitSR./stampSR);
end
spk_row=[]; ind_row = [];
for trial = 1:max(size(stampdata))
st=stampdata(trial)+sttime*unitSR;
et=stampdata(tri... |
ecb766945a09b5c999c52d6e45c0bfa8f405af4a489b6baa2d6748745573ba50 | MATLAB | 1,049 | 19 | %{
# table that stores the paths for the params for pupil_tracker
pupil_tracker_param_id : int # id for param collection
---
convex_weight_high=null : float # parameter for tracking
convex_weight_low=null : float # parameter for tra... |
d6d0877ba7355af3f6b829e80b49c96fac190d52eb43b3fcc02f3e7dcb984c19 | MATLAB | 1,050 | 38 | function c = redblue(m)
%REDBLUE Shades of red and blue color map
% REDBLUE(M), is an M-by-3 matrix that defines a colormap.
% The colors begin with bright blue, range through shades of
% blue to white, and then through shades of red to bright red.
% REDBLUE, by itself, is the same length as the current figu... |
e97868356e66d6986cf0fb591f7c159bd0821f8eca84c9d0f9f47d896c252588 | MATLAB | 1,050 | 36 | function figHandle = plotStimHeatmap(stimInfo, figHandle)
%PLOTSTIMHEATMAP Summary of this function goes here
% Detailed explanation goes here
if ~exist('figHandle', 'var')
figHandle = figure();
elseif ~isgraphics(figHandle)
figHandle = figure();
end
p = [100 100 600 600];
set(figHandle, 'Position', p);
... |
4155b734bb7c2852939fd56e1c2566e7673231ba7db2bcd7c5c3dd3a9c304d98 | MATLAB | 1,051 | 51 | function [npp, ipp, nt] = tapas_genpath(t, llh, minv, type)
%% Create a new path for thermodynamic integration using a Hermite
% polynomial.
%
% Input
% t -- Temperature schedule. Nx1 double array
% llh -- llh. Samples of the temperature. N x M array, where M is the
% number of samples.
% ... |
3f14f62a43dd30d4da519bd5ab994b7a8bb2c9cea84c7321766949d61d10c932 | MATLAB | 1,052 | 31 | function param_diff_w = sero_srr_f_params(param_diff, num_edge, lower_val, rampType)
%param_diff_w = sero_srr_f_params(param_diff, num_edge, lower_val, rampType)
if nargin < 3 || isempty(lower_val)
lower_val = 1e-3;
end
if nargin < 4 || isempty(rampType)
rampType = 'linear';
end
N ... |
deceb1981d64782e894f8839debef98b111cbeb3939115b8656de1bf68a5217d | MATLAB | 1,052 | 31 | classdef Roessler < Environment
% Roessler attractor.
properties
D = 3; % system dimension
Ranges = [50, -20; 50, -25; 100, 0]; % variable ranges
Params = struct('a', 0.2, ... % ODE parameters
'b'... |
4f0ae6419ed1070b1811e0fb1ceadb77635de3dbcd2b8015a05480f1fbf4493a | MATLAB | 1,053 | 39 | function [DA, T, tzero, delay_legend, bins] =...
delay_effect_cg(bstruct, pstruct, event,...
block, delaybins)
%%Plot dF/F as a function of reward delay. Exclude first 2s following side
%%LED to avoid cue response (see SideLED_resp.m for reference) cmc 8/6/20.
%currently, it's using screened behavioral data 9/... |
c3be9db67d376ca76b090aed532cc6bf8baf53aaa8eb75d365db3d8f9cabd4c8 | MATLAB | 1,053 | 41 | function pfx = tapas_uniqc_get_common_prefix(fileArray)
% determines tapas_uniqc_common prefix in list of strings
%
% pfx = tapas_uniqc_get_common_prefix(fileArray)
%
% IN
%
% OUT
%
% EXAMPLE
% tapas_uniqc_get_common_prefix
%
% See also
% Author: Saskia Bollmann & Lars Kasper
% Created: 2016-11-08
% Copyright... |
2424c03cf511682c347a61ec3b8cec5e4e2f89dbb4652f74eab20897624fbeb5 | MATLAB | 1,054 | 30 | % (C) Copyright 2020 CPP visual motion localizer developpers
function varargout = preSaveSetup(varargin)
% varargout = postInitializatinSetup(varargin)
% generic function to prepare structures before saving
[thisEvent, thisFixation, iBlock, iEvent, duration, onset, cfg, logFile] = ...
deal(vararg... |
bfcc3b69d2f733d5225872d3a23574523a3ef832089d57d3e0357f6f646de327 | MATLAB | 1,054 | 47 | function [state] = tapas_linear_init_state(data, model, inference)
%%
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
nc = numel(model.graph{1}.htheta.T);
np = size(data.u, 1);
nb = size(data.u{1}, 2);
state = struct('graph', [], 'llh', [], 'kernel', []);
state.graph = cell(4, 1);
state.llh = cell(4, 1);
state.k... |
b2d817b3cfffc9b58e5ccdc0a225c5b33dafde317d3ddc86894281a4728cf326 | MATLAB | 1,055 | 28 | function [spatial] = Tidy_To_Plot(spatial)
% TIDY_TO_PLOT
%
% Fills empty cells in spatial data structures with Inf for plotting purposes.
%
% INPUT:
% spatial - structure containing cell arrays for C1, C2, C3, and myelin states
%
% OUTPUT:
% spatial - updated structure with no empty cells
%% Replace empty fields... |
e2c91d3d9a6e2989c47c9f5f424aae7e163c352265a1a16ba10529f3155d7285 | MATLAB | 1,055 | 39 | function bw_img = getLargestCC(bw_img, number_cc)
%GETLARGESTCC Select largest connected components in a binary image.
%
% DESCRIPTION:
% getLargestCC selects the largest connected components in a binary
% image. The number of connected to components can be specified using
% number_cc.
%
% USAGE:
% bw_i... |
e57061e7f9c3fbcb645fa8148ecc67b0f325e3d6308ea7e8beabc3e6dd23037a | MATLAB | 1,055 | 58 | function [pp, pa, ap, aa] = tapas_sem_prosa_gen_lh(x, theta, ptheta)
%% Generate the likelihood function.
%
% Input
% x Time interval to plot the likelihood function.
% theta Parameters to use
% ptheta Priors
%
% Output
% pp Prosaccade trials, prosaccade action
% pa Prosaccade trial, antis... |
0412d6a9d7d43a6ba054bea8861206b7a47232ad3203c118a72367e279f64222 | MATLAB | 1,056 | 35 | function test_permuanova2
%TEST_PERMUANOVA2 Unit tests for permuanova2.m.
% © 2018-2026 Mick Crosse <crossemj@tcd.ie>
% CNL, Albert Einstein College of Medicine, NY.
% TCBE, Trinity College Dublin, Ireland.
% Generate test data
rng(42);
x = randn(30,5);
group = 1:5;
% Perform one-way ANOVA
[p1,tbl1,stats1] = ... |
2515b75f334cbbe25ebdb4ae05009c9209cdac2bdfe803e3ceb3b781ac3b0d3b | MATLAB | 1,056 | 35 | function test_permuanova1
%TEST_PERMUANOVA1 Unit tests for permuanova1.m.
% © 2018-2023 Mick Crosse <crossemj@tcd.ie>
% CNL, Albert Einstein College of Medicine, NY.
% TCBE, Trinity College Dublin, Ireland.
% Generate test data
rng(42);
x = randn(30,5);
group = 1:5;
% Perform one-way ANOVA
[p1,tbl1,stats1] = ... |
317e79d8d1b5e1b7e16f48ea002b9d0bbe0aeded7aa70b5f34cbe3ca0a0e677a | MATLAB | 1,056 | 34 | classdef nnmnist < nntest
properties (TestParameter)
networkType = {'simplenn', 'dagnn'}
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... |
78dde944260aa7b272c821891a1835b73264b2ea2dab23e76df08cb4af30ba0d | MATLAB | 1,056 | 35 | function test_permuanova1
%TEST_PERMUANOVA1 Unit tests for permuanova1.m.
% © 2018-2026 Mick Crosse <crossemj@tcd.ie>
% CNL, Albert Einstein College of Medicine, NY.
% TCBE, Trinity College Dublin, Ireland.
% Generate test data
rng(42);
x = randn(30,5);
group = 1:5;
% Perform one-way ANOVA
[p1,tbl1,stats1] = ... |
a9ec325e1d667ae7417eef7c7b113f8411322c4d6604f2c1aea19228bca3e7f9 | MATLAB | 1,057 | 50 | function [y_img,dice]=svm_test(img_dil,Out,s_test,ind)
% INPUT
% img_dil:3-D image (matrix) comprises region of interest and its uncertainty zone
% Out: classifier computed from svm_train.m
% s_test: similarity matrix of new subject in testing samples
% ind: index of all subcortical voxels in the 3-D atlas image... |
10875bc753d3492d2d9f4b024e1cdb8c1c5b33e5b10984635c8544a69aa24884 | MATLAB | 1,058 | 32 | function subj_data = update_latent_one(obj,subj_data)
% -----------------------------------
% Update latent [posterior precision]
% -----------------------------------
% Common to all subjects so we just copy the pre-computed value
% > Az = A + lam * (U'*L*U + Au)
subj_data.Az = obj.Az;
% ... |
70a64475126ca4d2183480c1792875e751579d0392e4fc2463052733673c3eeb | MATLAB | 1,058 | 26 | function volumeName = getChSpecBrainVolName(channelStruct, volume2plot, groupInfo)
% TBD !!! (now = Nov22)
% returns volumeName (e.g. wDefault, wDorsal Attention, ...)
% based on channel information in channelStruct and specification in volume2plot
% (c) Jiri, Nov21
brainAtlas_name = strrep(volume2plot, 'ch-spec_', '... |
f20b099e4b0fd4f219f05739194d23d49b46302785ad0fbce96e562dfae8cf51 | MATLAB | 1,058 | 31 | % (C) Copyright 2020 CPP visual motion localizer developpers
function varargout = preSaveSetup(varargin)
% varargout = postInitializatinSetup(varargin)
% generic function to prepare structures before saving
[thisEvent, thisFixation, iBlock, iEvent, duration, onset, cfg, logFile] = ...
deal(vararg... |
61a38adcb02cdbc49000fb7bbb288bcd9ac83bfffe8a2a1b24d3264c4d458c60 | MATLAB | 1,059 | 28 | function [meshstruct, D, M, RHSbc] = computeDiffusionMatrix3D(im, voxel_size)
% Compute Diffusion Matrix M from mesh 3D of tensors
%
% Author: Aina Frau-Pascual
% Construct mesh structure
Nx = size(im, 1); % number of cells
Lx = Nx * voxel_size(1); % domain length
Ny = size(im, 2); % number of cells
Ly ... |
de14ac5358c6afa6dc5c57c2d4cd0c0d05680da042870b3c68cde76ec0c37e38 | MATLAB | 1,059 | 31 | %{
aodpre.Scan (imported) # synchronized AOD scans
-> vis2p.Scans
---
hdf5_file : varchar(255) # raw data file
%}
classdef Scan < dj.Relvar & dj.AutoPopulate
properties
popRel = (vis2p.Scans & 'aim="Cajal"') - aodpre.Ignore
end
methods(Access=protected)... |
f25754fdbdd0f2972da085bb93e12665d3f43fea80583ff46664e08048ab0871 | MATLAB | 1,059 | 45 | function glm_nsdimagery2(ppdir,ppdirname,designfile,hrfbasisfile,tr,glmdirname,hrfmanifoldfile)
% notes:
% - essentially unchanged wrt glm_nsd...
% - 3-s events for vis, imag, and att.
% - att does have two adjacent 3-s trials. it's going to be noisy.
glmdir = regexprep(ppdir,'ppdata',glmdirname);
mkdirquiet(glmdir... |
cf6236f8affa77a9ec14870c84d3199bef62bbd9b73d221b1b58616df42834a2 | MATLAB | 1,060 | 34 | function [data, missingFields] = bc_addMissingFieldsWithDefault(data, defaultValues)
% JF, Check input structure has all necessary fields + add them with
% defualt values if not.
% ------
% Inputs
% ------
if ~isstruct(data) && ~istable(data)
error('Input must be a structure or table');
end
if... |
dfac2f9b8a0ba7424e294835c1b265d82be89b7a48bde9de48a81eed2a8ff96e | MATLAB | 1,060 | 41 | % Calculate the value of lambda so that if lambda >= lambdamax, the TVD
% functional solved by l1pwc is minimized by the trivial constant
% solution x = mean(y). This can then be used to determine a useful range
% of values of lambda, for example.
%
% Usage:
% lambdamax = l1pwclmax(y)
%
% Input arguments:
% - y ... |
4f66a3bfcac7d11fdd1c3c96bf5902188b4a9b8f0c5c4fa43cd8f170a4300525 | MATLAB | 1,061 | 31 | classdef Lorenz < Environment
% Lorenz system.
properties
D = 3; % system dimension
Ranges = [40, -20; 50, -25; 50, 0]; % variable ranges
Params = struct('sigma', 10, ... % ODE parameters
'rho', 28, ... |
77404557a3299fff660f617dbe5b05a5106d6a232090fa8641c8b1f73f990183 | MATLAB | 1,061 | 35 | function [color,MOLEC] = colorcodefunction (model, molec)
% Set legend color based on molecule and model
colorMatrix = [1, 0.4, 0.4; 1, 0.4, 0.4; 1, 0.4, 0;...
0, 0.8, 0.6; 0.2, 0.6, 0.6; 0, 0.4, 0.6; ...
0.6, 0.8, 0.8; 0.2, 0.6, 0.6; 0, 0.4, 0.6; ...
0, 0.8, 1; 0.2, 0.6, 0.6; 0, 0.... |
bdf3cb479ba50e41fa7e17b5e5604d2230745cb04b0c4c4a1cf0c4257b13f1f3 | MATLAB | 1,061 | 44 | function [img,msk]=vector2tensor(gx,gy,gz)
% This function convert vector file to tensor image (Model 1) for streamline
% visulization Diffusion Toolkit using the DTI model. Only show one direction
% with respect to each of the 3 eigenvectors
N=size(gx);
%Constrained tensor model parameters
d_parallel=0.001... |
5abbb5b7b33ee43ee2e9c79eb888c5d55ed34daea751592feeb9885615c09ede | MATLAB | 1,062 | 26 | %-----------------------------------------------------------------------
% Job saved on 29-Aug-2017 13:31:07 by cfg_util (rev $Rev: 6460 $)
% spm SPM - SPM12 (6906)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
function TMSwriteDTL(MATdir,ImgDir,vsize)
s... |
037ddf02ec3df388e8792a41539cbb558ef5c052fe301681bab8420760a5e81c | MATLAB | 1,063 | 20 | %{
twop_setup : varchar(256) # two photon setup name, e.g. 2P1
setup : varchar(256) # Setup name of behavior/stim computer, e.g. at-stim01
---
ip : varchar(16) # setup IP address, e.g. at-stim01.ad.bcm.edu
state="ready" : enum('systemReady... |
1419940508556faf86ffe8aa0b92ccb2fbec6116b44a6a52b6a010159c7c302c | MATLAB | 1,063 | 40 | function [lpp] = tapas_sem_prosa_lpp(theta, ptheta)
%% Log prior probability of the parameters of the prosa model.
%
% Input
% pv -- Parameters in numerical form.
% theta -- Parameters of the model
% ptheta -- Priors of parameters
%
% Output
% lpp -- Log prior probability
%
% aponteeduardo@gmail.com
% copyrig... |
3e505c540867e555c047bfe430493e27e08fdb6e9bb9cc8a6f2a68f6faa692b0 | MATLAB | 1,063 | 28 | function i_base = stftBaselineIndices(params, nSamples_sess)
% returns session indices used for STFT baseline
% nSamples_sess = number of samples of the processed session
% (c) Jiri, Aug16
% indices of game state "search"
if strfind(params.paradigm.usedParadigm, 'uboat')
gameState = 'search';
% load "raw"... |
0e43b78cd353738266ad5a7a28fc0352534cb895b439a60cc132ec38908a7d49 | MATLAB | 1,064 | 45 | % clear
% clc
Pdata = fullfile(Pbase, [filesep 'models' filesep 'DMN' filesep 'GCM_fitted']);
Psave = fullfile(Pbase, [filesep 'models' filesep 'DMN' filesep 'fitted_adjusted']);
if ~exist(Psave, 'dir')
mkdir(Psave);
end
files = dir([Pdata filesep 'GCM*.mat']);
use_parfor = 1;
%%
if use_parfor
... |
190bbb243ba61ca4277b096ef9be976e5d0c049b89519dcf0de61698823dfd28 | MATLAB | 1,064 | 46 | % clear
% clc
Pdata = fullfile(Pbase, [filesep 'models' filesep 'SN' filesep 'GCM_fitted']);
Psave = fullfile(Pbase, [filesep 'models' filesep 'SN' filesep 'fitted_adjusted']);
if ~exist(Psave, 'dir')
mkdir(Psave);
end
files = dir([Pdata filesep 'GCM*.mat']);
use_parfor = 1;
%%
if use_parfor
... |
4370b8a10f55537ac9e040a9c5504ae831d33a878eb78b1a3fbd5f2b9e7ebea8 | MATLAB | 1,064 | 37 | function faceGrad = gradientTermRadial2D(phi)
% this function calculates the gradient of a variable in x and y direction
% it checks for the availability of the ghost variables and use them, otherwise
% estimate them, assuming a zero gradient on the boundaries
%
% SYNOPSIS:
% faceGrad = gradientTermRadial2D(phi)
%
% ... |
6fe92d9f3361a3c74746db3334ef065eee77053e0cfa0e097f64063d6fc3650e | MATLAB | 1,064 | 28 | function pleaseComputeMetric = checkIfRecomputeMetric(Params, prevNetMet, lagValFieldName, netMetName)
%CHECKIFRECOMPUTEMETRIC Check whether to recompute metric
% Detailed explanation goes here
% TODO: write function to also check the Parameters related to metric
% calculation matches
% Check if user ask to recomput... |
d99aad41e45ded8e2b8c4cc89c16dfd908466548bd678487d2a4956b4f00ba88 | MATLAB | 1,064 | 26 | %{
# align a 2-d scan field to a stack
-> stack.RegistrationTask
---
reg_x : float # (px) center of scan in stack coordinates
reg_y : float # (px) center of scan in stack coordinates
reg_z : float ... |
6e230e1086ce99420bea070c31c1a58fac2526c2471e5cd32367d7ea8ef490f2 | MATLAB | 1,065 | 46 | %% output = zeropad_odd_dimension(input,mode,matrixSize_o)
%
% Usage:
%
% Input
% --------------
% input : input image
% mode : 'pre' - preprocessing (zero padding); 'post' -
% postprocessing (remove zero padding)
% matrixSize_o : original matrix size beofre zero padding
%
% Output
% -... |
8a69818c42569cb7d5c141a58f0f749814b5061ba8e301c85d1cd4db0363c3ad | MATLAB | 1,065 | 44 | function h = imshow_categorical(f, vs, z, slice, pal)
if nargin < 5
pal = [];
end
if nargin < 4
slice = 3;
end
dim = [size(f) 1 1];
if nargin < 3 || ~isfinite(z)
switch slice
case {2,3}
z = ceil(dim(slice)/2);
case 1
... |
e33fed253fa2545597c62aea2cee34c7f2c579528a022df4b9e04d486702efe7 | MATLAB | 1,065 | 35 | function [ptheta] = tapas_sem_prosa_ptheta()
%% Returns the standard priors of the model.
%
% Input
%
% Output
% ptheta -- Structure containing the priors. The prior distribution is assumed
% to be log Gaussian, so that the prior are the means and covariance
% matrix. It is assumed that the covaria... |
f15a958896b401530e5b6aea332633077b788938c3b77a7cfda5f1cbdf5aa829 | MATLAB | 1,065 | 61 | % function tau = MS_firstzero(y);
%
% Find the first zero of the autocorrelation function of y.
%
% Michael Small
% michael.small@uwa.edu.au, http://school.maths.uwa.edu.au/~small/
% 3/3/2005
% For further details, please see M. Small. Applied Nonlinear Time Series
% Analysis: Applications in Physics, Physiology and Fi... |
fcd840613362e7a07dcf5de591c65858a4fc71beaf5f8561981a66fc32945dd8 | MATLAB | 1,066 | 17 | %% Standard script to display input sepia header information
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 22 Jan 2021
% Date modified: 12 August 2021 (v1.0)
%
%
disp('----------------------');
disp('Basic data information');
disp('----------------------');
fprintf('Voxel size(x,y,z) = %s mm x %s ... |
237b8af69b3eae9f5d5fd8f50805a6683f084c0f44f6d786258f83d824281dac | MATLAB | 1,067 | 36 | function d_struct = load_fromCacheFile(dataStruct)
% loads results stored in cache file
% (c) Jiri, Oct20
d_struct = struct;
%% cache file
outName = [dataStruct.outName_prefix '_' dataStruct.this_neur '_' dataStruct.this_traj];
cacheFile = [dataStruct.pathBeg filesep outName filesep dataStruct.this_subj filesep 'cac... |
f25d094365e9b765c7d9d6bc47b28e44cc77370a6a52dc27af0a6136bcd81325 | MATLAB | 1,067 | 35 | function [times_resample, sorted_data] = heatmat_byblock(pstruct, bstruct)
resample_freq = 0.1;
T = linspace(-5, 10, size(pstruct.('CPIn'), 2)-1);
bdata = bstruct.('CPIn');
rewards = convertreward(bdata.Reward);
blocks = bdata.Block;
%reorder blocks into low=1, mixed=2, high=3
blocks(blocks==1) = 0;
blocks(blocks==3)... |
4033abe8ce6776b7dfabee0a8de3c645bb55791515aac1dfde0ee4508a7ec652 | MATLAB | 1,068 | 25 | function [new_traces, new_times, traceKeys] = getAdjustedSpikes(key)
% function [new_traces, new_times,traceKeys] = getAdjustedSpikes(key)
%
% Adjusts traces for time difference between slices in a scan
[traces, slice, traceKey] = fetchn( ...
preprocess.SpikesRateTrace * preprocess.Slice & preprocess.ExtractRawG... |
6da647082ea1c322f70a56142978b21163bd5514925b00c4a0f0cc2d2748e9ea | MATLAB | 1,068 | 39 | function basicexample()
% Verify that Manopt was indeed added to the Matlab path.
if isempty(which('spherefactory'))
error(['You should first add Manopt to the Matlab path.\n' ...
'Please run importmanopt.']);
end
% Generate the problem data.
n = 1000;
A = randn(n);
... |
0d01f2ebbc446006cde6d7f44a89ce785b80736c720886aa2595b032f4c2b821 | MATLAB | 1,069 | 26 | %{
# motion correction for galvo scans
-> meso.RasterCorrection
---
template : longblob # image used as alignment template
y_shifts : longblob # (pixels) y motion correction shifts
x_shifts : longblob ... |
1c06468c01f4e2e5d38dd0b97897cde8d43d1aec9989bec0002b902ce01acb61 | MATLAB | 1,069 | 26 | %{
# motion correction for galvo scans
-> reso.RasterCorrection
---
template : longblob # image used as alignment template
y_shifts : longblob # (pixels) y motion correction shifts
x_shifts : longblob ... |
4c03108b7073d87f6a1f4092df417720135b6bee5cb31d0be0a4851d2de86f7f | MATLAB | 1,069 | 56 | function [llh] = tapas_mixedlinear_llh(data, theta, ptheta)
%% Likelihood of the nodes of a linear multivariate model with diagonal
% precisions on each parameter.
%
% It is the likelihood of
%
% p(y|x, beta, pi) = N(y - x*b, 1/pi)
%
% Note that this is a multivariate regression problem, so beta is a matrix
% in whi... |
ad00c92d8a8927a9df245dbcacba532c386a838e17abf490fd01155e45520f56 | MATLAB | 1,069 | 36 | function tapas_add_tapas_prefix()
% directory where the renaming is to be done
dir1 = 'C:\Sudhir\Tapas\admin\testfolder\testtest\';
% prefix to be added
prefix = 'tapas_toolbox_';
% collect all filenames from current directory
filelist= dir(strcat(dir1,'*.m'));
% go through each file and replace filena... |
2576614fdda862c445e034f1a0072aedc981bf7c8d2b2785b8bf5b3d0d8d304f | MATLAB | 1,070 | 31 | function colors = getColorScheme(datatype)
% get color scheme for visualization
% INPUT
% datatype (string): 'volume', 'side', 'delay'
% 'volume': light purple (smallest reward offer) to dark purple (largest
% reward offer)
% 'side': orange (reward port contralateral to recording hemisphere) and
% light blue (reward p... |
3f5fb3b62f0b5471850299647584c52c93d6c2134c934be372e9d4dc9e13dd55 | MATLAB | 1,070 | 31 | %% filterSpec = sepia_get_nifti_uigetfile_filter()
%
% Output
% --------------
% filterSpec : filter spec to be passed as the 2nd input of uigetfile
% for selecting a NIfTI (*.nii or *.nii.gz) file
%
% Description: macOS's native uigetfile file-type selector does not
% reliably honour a ... |
4c5c1b6f04402a0feb8694751df0154d77803347d2b5db3e72869dc2fe27df0f | MATLAB | 1,070 | 37 | function medianValue = median(this, varargin)
% Returns median value of data matrix of MrImage by applying prctile(50)
%
% Y = MrImage()
% medianValue = ...
% Y.median('ParameterName1', 'ParameterValue1', ...)
%
% This is a method of class MrImage.
%
% IN
% varargin parameterName/Value pairs for selectio... |
35d563ccbc50912fa3fc334dd64be1c6cd52b6c5bccee0d85ab5f870489997b1 | MATLAB | 1,071 | 26 | function[column1_index, column2_index, number_of_columns] = FindColumnsNeeded(source, column1, column2)
% In the context of batchforce, use FindColumnsNeeded(headerinfo, 'vDeflection', 'measuredHeight')
% Find line in headerinfo which specifies the column names
indexc = strfind(source{1,1}, '# columns: ');
if ise... |
f2aa729c969caa1d90e64cb537d57e1b254d1973fc0528605347f6c239b27766 | MATLAB | 1,071 | 41 | function clusters = smooth_dens_and_mask(P,varargin)
% function clusters = smooth_dens_and_mask(P,[P2: extract img])
%
% tor wager
%
% P is an input file, usually a density results mask
% this function smoothes the image with a 3 mm kernel
% and thresholds the results at i1 > 0, so that
% you end up with a mask. Th... |
5a841bb5c54171d270edcbec38d38da2548cda59478f2127b63468c64c6ce4b5 | MATLAB | 1,072 | 34 | % [num, wh, weighted_num, conindx] = meta_count_contrasts(DB, testfield, fieldvalue)
%
% e.g., testfield = 'Stimuli'
% fieldvalue = 'faces';
% [num, wh] = meta_count_contrasts(DB, testfield, fieldvalue)
function [num, wh, weighted_num, conindx] = meta_count_contrasts(DB, testfield, fieldvalue)
wh = strcmp(DB.(tes... |
85435c9329ad74ba8711493f8ddc3cb08317bbd6ad6fe72d4f6bb2b8a809145e | MATLAB | 1,072 | 26 | function lims = sero_pulseq_sysLims_prisma()
% function lims = sero_pulseq_sysLims_prisma()
%
% Here, I hope that we can use three sets of limits so that we can optimize
% imaging, diffusion, and spoiling gradients separately.
B0 = 2.89;
deadTime = 10e-6;
% Set system limits for imaging
lims.img = mr.opts('MaxGrad',4... |
ebc2caab368264c731925008e4c3447509168c8fd498bbaf9a6a0df2a3f7afc7 | MATLAB | 1,072 | 35 | function [ordering,groupbreaks] = sortAmplitudeByCluster(X,grouping)
%does time 2 peak by subgroups of data
%
%Inputs:
%X: (nn x nt) data of interest, nn neurons, nt time points
%ops: structure with following
% useZScore: do normal sorting on X, or z score it first
% grouping: (nn x 1) vector of integers, assignign... |
f5acb4c922d979d369ea1859a6bfe917fd88b7563c616350e82a57434b2ba328 | MATLAB | 1,072 | 34 | function ellipse_parameter = read_csv(path,user_num,session,pattern,whicheye)
% path_folder_label= ['E:\label_ellipse\Data_Dvs_Unlabelled_',num2str(session),'_0_',num2str(pattern),'\user',num2str(user_num),'\',whicheye,'\','session_',num2str(session),'_0_',num2str(pattern),'\events\','user_',num2str(user_num),'.csv']... |
fea1d6a0d1deff82280295682f7ff61c84fe6adfe6ed64c12ed8dc99932f4409 | MATLAB | 1,072 | 33 | function t_trig = getTimeOfTrigger(params, trialStruct)
% returns trigger time of specific trial in trialStruct
% (c) Jiri, Jun20
t_trig = [];
switch params.triggering.cutPoint
case 'onGetReady'
if isfield(trialStruct, 't_prep')
t_trig = trialStruct.t_prep;
end
case 'on... |
0b74f2a82fdba6126fb0d37054153e0ee187c02205e80d6cfd6d6670a71da035 | MATLAB | 1,073 | 37 | function b = ShowBatch(bfile)
%ShowBatch - Show data sets in a batch job.
%
% USAGE
%
% b = ShowBatch(bfile)
%
% bfile batch file listing the parameters for each iteration
%
% See also StartBatch, GetBatch, BatchInfo, CancelBatch, CleanBatches, Store, Recall.
%
% Copyright (C) 2007-2013 by Michaël ... |
53b23363cb04a8c1517c1520bb7523aef5c1b9597985d02846ff30a10c5ba0b7 | MATLAB | 1,073 | 34 | % 2016/11/11 by T. Ezaki
% This function infers h and J by pseudo-likelihood maximization.
% binarizedData: nodeNumber x tmax
function [h,J] = pfunc_02_Inferrer_PL(binarizedData)
[nodeNumber,dataLength] = size(binarizedData);
iterationMax = 5000000;
permissibleErr = 0.00000001;
dt = 0.2;
dataMean = mean(... |
2d7d3e54f80084c58fbf01b7ce3b5b55d26190a60dbaf730d08f41251c09005a | MATLAB | 1,074 | 25 | function [pressure, flow] = ExtractData(nv,ntp,file_id)
% NOTE: Results are stored such that the first 1:N entries are the PROXIMAL
% large artery (1-15) and large vein (16-27) predictions, N+1:2N are the
% MIDPOINT predictions in the same vessels, and 2N+1:3N are the DISTAL
% predictions.
data = load(sprintf(... |
4d04343701222022ca42e9864a8f13fc812acf70f1f249efaf23be658f9e62fc | MATLAB | 1,074 | 36 | %{
pre.Spikes (computed) # traces of infered firing rates
-> pre.ExtractSpikes
-> pre.Trace
-----
spike_trace :longblob
%}
classdef Spikes < dj.Relvar
methods
function plot(self)
for key = fetch(pre.Segment & self)'
X = fetchn(self & key, 'spike_trace');
X =... |
93877171c6aa205a658f019b80ba1b10186eace8c3094075de40fdc3e8aba535 | MATLAB | 1,074 | 44 | %% function [tolerance,stepSize,iteration,weight,b0dir] = parse_varargin_NDI(arg)
%
% Description: parser for NDI.m
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 5 June 2019
% Date last modified: 27 Feb 2020 (v0.8.0)
%
function [tolerance,stepSize,iteration,weight,b0dir,isGPU] = parse_varargin_NDI(a... |
e0d361d037b177f77f846a1862a0fe009d61ed43e2eb73fd00a9f00af83da44d | MATLAB | 1,074 | 44 | function parcels_random_all=random_parcels(mskfile,MM)
[~,parcels]=read(mskfile);
parcels_random=zeros(size(parcels));
parcels_random_all=zeros([size(parcels),MM]);
for m=1:MM
ind=find(parcels);
J=length(ind); %total number of voxels in subcortex
M=length(unique(parcels))-1; %number of sub... |
455606e5340a8f60f43085b7610080c4814c49bab6fc1eb969e03eda9ed41c15 | MATLAB | 1,075 | 42 | function [slop, ampVec, kdVec, rSquare] = EnsembleMiniSearch(dataX, dataY, hillEq, slop0, ampVec0, kdVec0)
% dataX, size: trialNum-by-xPoint, same as dataY.
[trialNum, ~] = size(dataX);
p0 = [slop0; ampVec0; kdVec0];
eSSR = @(p) EnsembleSSR(p, dataX, dataY, hillEq);
% options = optimset('PlotFcns',@optimplotfval);
... |
a11daaccaf67aadbe01fe4c8170b01a0fdc7f47bdabce32b0eacd894cf5b1f6e | MATLAB | 1,075 | 19 | %{
# speaker sound pressure calibration
speaker_id : int # some number that identifies the speaker
rig : char # setup name
location : tinyint # 1 = Left, 2 = Right
trial : int # trial number of calibrati... |
1a62fba09cf574f2d8f661b7b881f55ab07abe7a6868ddf5b71be01eced2d491 | MATLAB | 1,076 | 40 | function [D] = euclproj_trialwise(data,angs,foldvar,timelist)
% [D] = euclproj_trialwise(data,angs,foldvar,timelist)
%assign stimulus variable for decoding
sortvar = angs;
nbin = 2;
pbin = 1/4;
D = zeros(size(data,1),size(data,3));
ft_progress('init','text');
th = [];
folds = unique(foldvar);
nfold... |
7c614f4790943e2fc74a7c38060fbe495688f0be09ffc17a20f7a49f868f7dd3 | MATLAB | 1,076 | 38 | %% Parameters
rawDataFolder = '/media/timothysit/Elements/MAT_files/MPT_MEC/';
fileName = 'MPT200108_2B_DIV14.mat';
channelNameToPlot = 14;
plotTimeRange = [0, 60]; % in seconds
filterTrace = 1; % 0 : plot raw trace, 1 : plot filtered trace
filterLowPass = 600;
filterHighPass = 8000;
traceColor = 'black';
data = l... |
8292c6c4b495fe79774d40bd229bae077896d24ed81654590eea5533add48a14 | MATLAB | 1,076 | 33 | classdef SprottF < Environment
% SprottF system.
% ALSO RATHER DIFFICULT TO FIND WELL-BEHAVED ATTRACTOR. EXPLODES FOR LONG
% TIME SERIES.
properties
D = 3; % system dimension
Ranges = [3, -2;
4.5, -4;
5, 0]; ... |
8693b7eeb592e1c9e247cc3ffc5ebff48ff0ca4d8af26b2e720241c59d02fcd4 | MATLAB | 1,076 | 33 | function [tpl, str] = parse(tpl,target,handle,append)
%TEMPLATE/PARSE Fill in replacement fields with the class properties
% [TPL, STR] = PARSE(TPL,TARGET,HANDLE) fills in the replacement field
% HANDLE using previously defined variables of template TPL and store
% it in field TARGET. HANDLE can also be a cell array... |
c72ae8e57f34fbe56a3e93f01f2d8bd4993b44a628dd1631699315e458648038 | MATLAB | 1,076 | 49 | function afni_niml_write(p,fn,format)
% simple function to write niml files in ASCII format
%
% AFNI_NIML_WRITE(P,FN) writes a NIML struct to file FN. P should be in the
% form as returned by AFNI_NIML_READ.
%
% The order of the arguments may be reversed. If FN is numeric, then it is
% assumed to be a file identifier. ... |
0c0ed3c7b5eea1784ac2dc863d075c98ae31309778dfc8d2ad37340706d1b45c | MATLAB | 1,077 | 42 | %A partir del S_index vectorizado compara todos los renglones para
%determinar cuales son diferentes. El numero de renglones diferentes
%constituye el numero total de estados de la red. LC Mayo 2010.
function [Edos_vector]=Nedos_b(S_index)
N=size(S_index,2); %Número de picos
S_indext=S_index>0.2; %Considera los vecto... |
2cc2559184bebbf35b0d09400640f9b5bbf5874f98ad5b83104fbca50e49975a | MATLAB | 1,077 | 34 | function wait_time_mean = waittime_20ul_by_previous_vol_SS(A, inferredMixArg)
% Wait times for 20ul trials conditioned on whether the previous trial was
% <20 or >20
% INPUTS:
% A - .mat file with rat data
% OUTPUT:
% wait_time_mean - Average wait time for < 20 uL and > 20 uL
[~, rew] = convertrewa... |
bc0300b8eabd40dc0c7b4979c68761429ee8a2716927624869c1dd1f7cdb264d | MATLAB | 1,077 | 23 | function params = preprocNonLinearOut_GetMetaParams(argNum)
% Usage: params = preprocNonLinearOut_GetMetaParams(argNum)
%
% Get preset arguments for preprocNonLinearOut
%
%
params.class = 'preprocNonLinearOut';
switch argNum
case 1
% Original params recommended by SN
params.gainControl = []; % Br... |
23038515e929bb11cced440f3355d5cc1d59ca7cdd49e1e4fcf29cc43ace04b1 | MATLAB | 1,078 | 55 | function map = arr2map2(arr,ROI)
dim = size(ROI);
idx = find(ROI);
%assume arr is a 3d map in 1xN form; if 4d timeseries with M timepoints,
%arr will be MXN form
%dim should have 3 dimensions
if size(arr,1) == 1 || size(arr,2) == 1
if size(arr,1) < size(arr,2)
arr = arr';
end
end
% f... |
6f3a58736619c79a64e0837f881fa5909dc9d88c20bd4bd6df3636a27dd399f1 | MATLAB | 1,078 | 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: 01 December 2025 by Taechang Kim @ SNU (sakkar2@snu.ac.kr)
%
% DO NOT change the variable names, update the variable value instea... |
c1a082dbc6b3740f88f5edd66655e79c2a00bda6f5bd494b7b08e64288aff94e | MATLAB | 1,078 | 40 | %islscalar - Test if parameter is a (pseudo) logical scalar.
%
% USAGE
%
% test = islscalar(x)
%
% x parameter to test
%
% NOTE
%
% To be considered logical, the scalar should be equal to 0 or 1, but it does
% not need to actually be of class 'logical' (class(x) could be e.g. 'double').
%
% ... |
12802c4c9a30f28aafd0049528caaf036f6542ce3cc16d2b5be22859b6aaf525 | MATLAB | 1,079 | 37 | function [name,file] = hlp_getcaller(indirection)
% Find the name & file of the calling function.
% [Name,File] = hlp_getcaller(Indirection)
%
% In:
% Indirection : optional level of indirection (default: 1)
%
% Out:
% Name: MATLAB name of the calling function, if any
% File: file name of the calling function, i... |
5730dd9508cba3becd0120e19adb4456d464f8cc9c5a5c739bf87cb6080b769c | MATLAB | 1,079 | 35 | function defaults = get_additional_constructor_inputs(this)
% Returns additional (non-property) inputs that can be set in constructor
% of MrDimInfo, e.g., 'firstSamplingPoint', along with their defaults
%
% Y = MrDimInfo()
% Y.get_additional_constructor_inputs()
%
% This is a method of class MrDimInfo.
%
% IN
%
% ... |
77b285c46a6ac1027428722e1c9030a31203cf8a93d601a5becf0549698b5d3d | MATLAB | 1,080 | 34 | function getTriggers_emoReco_answer(params)
% finds events when subject answered correctly (= right) or wrong
% (c) Jiri, Mar16
display([' - finding events for: ' params.thisCategory]);
%% per session: load trials, find events and save
for sess = 1:size(params.storage.sessionCacheFiles,2)
% load trials
... |
99787c38c1ad78d5e2688e543ecf57414ae58d722e5b620d3d1b947d658f77d3 | MATLAB | 1,080 | 34 | function c = redblue(m)
%REDBLUE Shades of red and blue color map
% REDBLUE(M), is an M-by-3 matrix that defines a colormap.
% The colors begin with bright blue, range through shades of
% blue to white, and then through shades of red to bright red.
% REDBLUE, by itself, is the same length as the current... |
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