sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6550447d2c8cd4cd72571f7daaa3013a43e631cdad5c839121f99f71d81f0a19 | MATLAB | 8,893 | 240 | % Code to produce figure 2
clearvars
close all
load('rainbow_cmap.mat')
load("colour.mat")
%% Load AUTO files
load('KpLCr1.dat')
load('KpLCr2.dat')
% Hopf bifurcations
load('HB1.dat')
load('HB2.dat')
% limit points
load('LP1v1.dat')
% homoclinic bifurcation
load('HOM1.dat')
load('HOM2.dat')
% ... |
9df90b20b3b355cdbf38b464a27b66c251a98367356830a3c83cbcd41990f50c | MATLAB | 8,895 | 183 | clear all
close all
%% Parameter initialization
run('spiking_parameters_simple_dopa.m') %most parameters are stored in this file
plot_var = 1; %set to 0 to turn off trial by trial plotting
%% main program
for l = 1:num_trials
tic
%% initialization
[v_it,v_kt] = deal(zeros(N,1)+v_rest); %membrane po... |
a28276564e8a33cb5017878f3607051c8655172a66d234631225ffa35fa8a3a9 | MATLAB | 8,906 | 196 |
clear all;
globals; initglobals;
FramesInf.act = 0;
FramesInf.noact = 0;
FramesInf.xy00 = 0;
FramesInf.removed = 0;
FramesInf.totalFrames = 0;
DATA_TYPE = 'OF'; %'OF' / 'EM'
DATA_TYPE = 'EM'; %'OF' / 'EM'
switch DATA_TYPE
case 'OF',
base_folder = 'Data\OpenField';
%base_folder ... |
e914d8d6324cf0656f7f12277be0416231473ad6334a6105cf6c8f181292dcd5 | MATLAB | 8,914 | 212 | function [S, varargout] = genCorrelatedSpikeTrains2(spike_opts, varargin)
% function S = genCorrelatedSpikeTrains(spike_opts)
%
% Function to generage a set of correlated spike trains by using a Hawkes
% process, or a discrete approximation of a Hawkes process.
%
% 2017 - Adam Charles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
2f36bc27c34325335e57a869525065dd4ffcc63ce7f05d16d249a46fe3cf3ec7 | MATLAB | 8,915 | 238 | function [montage, cfg] = ft_prepare_ODtransformation(cfg, data)
% FT_PREPARE_ODTRANSFORMATION returns the transformation matrix from
% optical densities (OD) to chromophore concentrations such as (de-)
% oxygenated hemoglobin.
%
% Use as
% [montage] = ft_prepare_ODtransformation(cfg, data);
%
% It is neccessary to... |
6c5be83ab95cdfdaa4f8aeca66afa978309921249a2cd6e34cc35bd88d29e5a7 | MATLAB | 8,915 | 228 | function [dat] = read_neuralynx_ds(dirname, hdr, begsample, endsample, chanindx);
% READ_NEURALYNX_DS reads multiple single-channel Neuralynx files that are
% all contained in a single directory. Each file is treated as a single
% channel of a combined multi-channel dataset.
%
% Use as
% [hdr] = read_neuralynx_ds(di... |
f62e67ef03aac06f1e05b89c82b052e3aaedeb00c5556407b8f1b48ecd87885b | MATLAB | 8,915 | 219 | % findFlyNotMoving.m
%
% Function to find when the fly isn't moving, based on the criteria that
% the 2 midlegs are not moving in X and Y (velocity below threshold).
% Finds based on smoothed velocity below threshold and non-smoothed
% velocity also below (separate) threshold
% Returns indicies of not moving times
%
... |
7029249849d0e70e278c6c827d650098cc51cfc15e7592ebe629759ed99f9203 | MATLAB | 8,919 | 284 | %% Detect EP bursts
mkdir('Bursts');
Events=[];
interval=300000;
i=0;
%%
i=i+1; % Manually for each image
iImage=FileList(i,1).name;
ep=EP(1,i).all; % Load EP.
x = xEP(i,1).all; % Convert to frames
nFrames=frequency(i,3);
figure()
reduce_plot(x,ep); ylim([mEp 20]); ... |
b9586629a0c6c2355375d803ce4e98308e7018c2123a321bf4d8c2df76bf0ad7 | MATLAB | 8,919 | 278 | function [num,status,strarray] = str2double(s,cdelim,rdelim,ddelim)
%% STR2DOUBLE converts strings into numeric values
%% [NUM, STATUS,STRARRAY] = STR2DOUBLE(STR)
%%
%% STR2DOUBLE can replace STR2NUM, but avoids the insecure use of EVAL
%% on unknown data [1].
%%
%% STR can be the form '[+-]d[.]dd[[eE][+-]dd... |
3c8ceb9e93a609655a8f21021f474ac870544c5902c8135d6090564c4444372f | MATLAB | 8,923 | 251 | % findCondYawVelPeaksFT.m
%
% Helper function for saveBallLegStepParamCond_bouts() that takes in
% fictracSmo, cond, and moveNotMove and returns times for valid yaw
% velocity peaks as well as start/end times for corresponding bouts.
% Boolean for whether to extract right or left turns
%
% Adapted from findCondYawVe... |
b71512bd0977f6540e49e7e5d13bb209043f94cf5b320847d0f544b266ef959b | MATLAB | 8,927 | 282 | % plotContLegStepParamCond_bouts.m
%
% Function to plot output of saveContLegStepParamCond_bouts(), compared
% with reference from saveContLegStepParamCond_indpt()
% One figure with 6 subplots, 1 for each leg
% Can select more than 1 output file, will plot on same graph
% Has option to plot reference steps (from saveL... |
297d7364f824992a8e5b5b41591b3b05a52422a1d1346f1aa04138b47b2ebcb7 | MATLAB | 8,937 | 309 | function varargout=buildSectionPreview(sectionToPlot,channel)
% Builds a preview image of the last completed section and sends to WWW
%
% function buildSectionPreview(sectionToPlot,channel)
%
% Purpose
% This function builds a low-res preview image of the first depth, a montage
% of all depths, and a histogram (current... |
098a48ae179d88dc99aecc73db636d4afbdc321822b7193b2b3b2f5e4b672319 | MATLAB | 8,941 | 413 |
classdef My_net_util
methods(Static)
function group_info=gen_group_info_basic(net_config, group_name)
net_config.ref.group_counter=net_config.ref.group_counter+1;
group_info=[];
group_info.child_group_idxes=[];
group_info.net_info=[];
group_info.child_relation='chain';
group_info.group_idx=net_co... |
2ce299c169907c8b900d85fba9c30b51fefdb5d4d6f7fac2a3456d9c5a681e83 | MATLAB | 8,943 | 201 | function data = TDMS_readFileHelper_v1(fid,optionStruct,metaStruct,paramsStruct)
%TDMS_readFileHelper_v1
%
%
% Time stamps in TDMS are stored as a structure of two components:
% (i64) seconds: since the epoch 01/01/1904 00:00:00.00 UTC (using the Gregorian calendar and ignoring leap seconds)
% (u64) positive fr... |
bafde48fbd00279635adf0f899688f7abe354a9849e673aa677b6a1200e35c0f | MATLAB | 8,954 | 249 | function [nsout] = read_neuroshare(filename, varargin)
% READ_NEUROSHARE reads header information or data from any file format
% supported by Neuroshare. The file can contain event timestamps, spike
% timestamps and waveforms, and continuous (analog) variable data.
%
% Use as:
% hdr = read_neuroshare(filename, ...)
... |
4764bfa7a687d6c7341537b7d7dc3ce69cf2ae5431f8715354e522b8e46111fa | MATLAB | 8,959 | 232 | function hdr = read_yokogawa_header_new(filename)
% READ_YOKOGAWA_HEADER_NEW reads the header information from continuous,
% epoched or averaged MEG data that has been generated by the Yokogawa
% MEG system and software and allows that data to be used in combination
% with FieldTrip.
%
% Use as
% [hdr] = read_yokoga... |
c0d95047f260b4ec39d3795b5f7f4114b9bd01b33a5e2e0afdc9f3cd1c7f3c47 | MATLAB | 8,961 | 266 | function spm_preproc_write(p,opts)
% Write out VBM preprocessed data
% FORMAT spm_preproc_write(p,opts)
% p - results from spm_prep2sn
% opts - writing options. A struct containing these fields:
% biascor - write bias corrected image
% GM - flags for which images should be written
% WM ... |
7b25fc5469c2600f7044e101b374fb36063c86d98aa9b507f610c981008cd967 | MATLAB | 8,993 | 231 | %This script allows the user to pick a watershed region in a t-SNE map and
%finds when the animal transitions into that region and plots their
%behavior, not used in paper
%% STEP 1: establish plotting constants
N_rows = 4;
N_columns = 4;
N = N_rows*N_columns;
fps = 14;
frames_before = 5*fps-1;
frames_after = 5*fps;
... |
da699a7f7efd644eaa6e41bf5a5d97e658597119ed4964687ffcfda435fbdba0 | MATLAB | 9,001 | 275 | function [] = ExtDataFig03_DecayRateComparison_PtoS_OptOffset()
% Code for comparing half decay time of the dPR1 neurite GCaMP signals during pulse-to-sine transitions and after the offset of the song driver stimulation in Extended Data Fig. 3g.
GT = 'dPR1NP';
%% pulse-to-sine transitions
DurThre_sine = 5;
DecayRange... |
da72f21c566086e062f169eea6303a3129e2ef58aae51300d2068dd2f30f92b4 | MATLAB | 9,010 | 279 | % mglTestGammaSet.m
%
% $Id:$
% usage: mglTestGammaSet()
% by: justin gardner
% date: 03/06/15
% purpose: Test gamma table setting
%
% 6/1/2018 Seems to be broken again on 10.13 High Sierra. The gamma table that
% gets sets first off seems to be missing the first few values - maybe about... |
8405559c2d3ae5b0abdd87d3d1d39727bb18f5ded196f02b1afe88f4c6b94c53 | MATLAB | 9,014 | 208 | function chanunit = ft_chanunit(input, desired)
% FT_CHANUNIT is a helper function that tries to determine the physical
% units of each channel. In case the type of channel is not detected, it
% will return 'unknown' for that channel.
%
% Use as
% unit = ft_chanunit(hdr)
% or as
% unit = ft_chanunit(hdr, desired)
... |
c7bd7ddbfa38153190f817eaa80196e7037455acc677b00bee5b29e26e6f2c33 | MATLAB | 9,025 | 320 | %% Pre-process the flocking data
% for paper "Inferring stochastic dynamics of complex systems", T.-T. Gao,
% B. Barzel, and G. Yan
clc, clf, clear, close all
tic
% timestamp, x, y, z, dxdt, dydt, dzdt, dxdt2, dydt2, dzdt2, gps_con
N = 9; % birds number
% load the data from different datasets: hf1, hf2,hf3, and hf4
d... |
d2f41d82e94685ce09b298c47c8ba00b54f5ad5b040aab5f1bb0e59b72832d27 | MATLAB | 9,029 | 221 | function script04_2D_images_transverse_to_axons()
% get 2D original/segmented images transverse to the axons
%
% This script needs the original volumes and the results from script:
% script02_proofread_vols.m
% It also needs the information in the text file
% 000_animal_exp_axons_cells_nx_ny_nz_cclims_cglims.txt
... |
d1e3ca00dad89d0d6f171c6dc243ff039b7aad9182610008222e170c8f01c0cb | MATLAB | 9,040 | 262 | function outliers = detect_outliers(X,Y,fig_flag,method)
% Finds univariate and multivariate outliers
% 3 'methods' are available and they can return different
% results
%
% FORMAT outliers = detect_outliers(X,Y)
% outliers = detect_outliers(X,Y,fig_flag,'method')
%
% INPUTS: X and Y are two vectors of the s... |
c948d7ca1ee5215f1f0142302ce387a78ed0a13a8aa3087d1a05445e682a31fd | MATLAB | 9,048 | 246 | function [obj] = ft_convert_units(obj, target, varargin)
% FT_CONVERT_UNITS changes the geometrical dimension to the specified SI unit.
% The units of the input object is determined from the structure field
% object.unit, or is estimated based on the spatial extend of the structure,
% e.g. a volume conduction model of... |
2e242139eee7d1e675b442989caad7abf60c3ae0bc69dd1975e7643f7baaaaaa | MATLAB | 9,073 | 180 | function out = dfa_ripquantpertrial_allphase_NF(index, excludeperiods, rippleskons, trials, pos, varargin)
% Parse through trials; note size and time of each ripple in each trial phase
% Also save whether or not wait trials contain a trigger event (t22) for later exclusion
% For each trial phase, include the trial... |
9679011092a27ea0d5529d5aaf3f87fd5c1c4b23a354b71e1216e11bdf8441d5 | MATLAB | 9,073 | 277 | function [list,sumbytes,varargout] = dirr(chemin,varargin)
%
%
% dirr
% Lists all files in the current directory and sub directories
% recursively.
%
% [LIST] = dirr(PATH)
% Returns a structure LIST with the same fieldnames as returned
% by LIST = DIR(PATH)
% PATH can contain wildcards * and ? after the last ... |
1ba3cda62f86fa89f1caf7401b8ae47922bc215b13171b262db9777de7a435b1 | MATLAB | 9,074 | 217 | clear all; close all; clc
%%%% janine.thome@zi-mannheim.de
%% RF classifier reported in "Classification of amyotrophic lateral sclerosis by brain volume, connectivity, and network dynamics" (HBM)
%% SPECIFY:
groupN = [0,1]; % group coding
groupL = ["Controls"... |
9e94cf7d28267a65f25e7d846fa0d71f33c497c31a19746ad3ee5ee52e16bf85 | MATLAB | 9,077 | 226 | function [event] = read_trigger(filename, varargin)
% READ_TRIGGER extracts the events from a continuous trigger channel
% This function is a helper function to read_event and can be used for all
% dataformats that have one or multiple continuously sampled TTL channels
% in the data.
%
% This is a helper function for ... |
fddaff9ad72f9d3e2d3e652850e8365e4036650a65b0fab5ebe4e4bb1278d2f0 | MATLAB | 9,077 | 188 | function stPred = stPredSimSeqWrapper(params)
% preallocate space
stPred = struct();
stPred.predHRF = [];
stPred.predNeural = [];
stPred.params = [];
stPred.prfResponse = [];
stPred.rf = [];
stPred.hrf = [];
% Use average ROI spatial exponent as static exponent
if params.analysis.useM... |
14b78625a23c7a81c5af6bdbee48c31c32775e20a2ab57671fa06b5eb3c37cc9 | MATLAB | 9,081 | 254 | function script05_align_axons(samplei)
% This script aligns the axons to the z axis, it saves the transformations
% Original->Aligned and Aligned->Original. Instead of rotate coordinates,
% the final rotated volume is "interpolated" using the unrotated volume
% as reference so the original can be recovered in a... |
083b803ffa5632bd119d9a50807465c83f69f3e41bd415deb9b5aacf0f2ac082 | MATLAB | 9,085 | 217 | clear all; close all; clc
%%%% janine.thome@zi-mannheim.de
%% RF classifier reported in "Classification of amyotrophic lateral sclerosis by brain volume, connectivity, and network dynamics" (HBM)
%% SPECIFY:
groupN = [0,1]; % group coding
groupL = ["Controls"... |
6c5a206a2d9e303a35b4964cfb4949f3c71880dceef5c5ad773441e3ade60d7a | MATLAB | 9,089 | 197 | function [mri, hdr] = read_ctf_mri(filename);
% READ_CTF_MRI reads header and image data from a CTF version 2.2 MRI file
%
% Use as
% [mri, hdr] = read_ctf_mri(filename)
%
% See also READ_CTF_MRI4
% Copyright (C) 2003-2010 Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fiel... |
ce451449119ad601508d98f49b37879a861def677847eb5ed64c678423d4d5f7 | MATLAB | 9,094 | 263 | function varargout = filetype_check_uri(filename, ftyp)
% FILETYPE_CHECK_URI
%
% Use as
% status = filetype_check_uri(filename, type)
%
% Supported URIs are
% buffer://<host>:<port>
% fifo://<filename>
% global://<varname>
% mysql://<user>:<password>@<host>:<port>
% rfb://<password>@<host>:<port>
% seri... |
0038720e27e6f2b4301cc86ddaf2b63c131fd630b4a9b485549b9869db3c47d3 | MATLAB | 9,097 | 217 | clear all; close all; clc
%%%% janine.thome@zi-mannheim.de
%% RF classifier reported in "Classification of amyotrophic lateral sclerosis by brain volume, connectivity, and network dynamics" (HBM)
%% SPECIFY:
groupN = [0,1]; % group coding
groupL = ["Controls"... |
b1ab14f67907ecf753f16245c248343c9ff4459f477937470a5c5b9f5ea3ec8b | MATLAB | 9,120 | 226 | % findLegFtCmbNotMove.m
%
% Function that takes in start and end indices for not moving bouts, as
% calculated on leg data and FicTrac data, and returns start and end
% indices for not moving bouts on both datasets, as calculated as
% intersect, union, leg only, or FicTrac only
%
% Helper function for interactGetNo... |
001f59491ea18c2bdef64dc1cfb3a665b7746e2ffbd1b3ccabea254c15b37a45 | MATLAB | 9,123 | 234 | function grad = yokogawa2grad_new(hdr)
% YOKOGAWA2GRAD_NEW converts the position and weights of all coils that
% compromise a gradiometer system into a structure that can be used
% by FieldTrip. This implementation uses the new "yokogawa_meg_reader"
% toolbox.
%
% See also FT_READ_HEADER, CTF2GRAD, BTI2GRAD, FIF2GRAD... |
651a265710a789fddd45424a407f5c23721e75743d29b4399c964828562d3a3f | MATLAB | 9,126 | 207 | clc
ManualMark_on=get(handles.cue_channel,'Value');
if ManualMark_on>1
if isfield(passdata,'cal') && isfield(passdata,'cue')
if isfield(passdata,'correction_data')
if ~isempty(passdata.correction_data)&& ~isempty(passdata.cue)
t=passdata.interval_cal*(1:1:size(passdata.cal,1));
... |
b26144b4849cd55996a07701aecdb7f2e6e55c6c996b879fd9b05444c9b3eb3c | MATLAB | 9,127 | 255 | % plotNormCondLegStepParam_allFlies.m
%
% Function that takes output files from saveLegStepParamByCond_fly() and
% generates a plot of the legStep param for each leg. Plots mean +/- SEM
% for each fly. Different conditions in different columns. Points from the
% same fly are connected by lines.
% Select output fil... |
aa3e9a95544c7b600fd97a4a336b62b531f332ba435c8f8e308f2f7aa5df1ada | MATLAB | 9,138 | 230 | function [recall, precision, info] = vl_pr(labels, scores, varargin)
%VL_PR Precision-recall curve.
% [RECALL, PRECISION] = VL_PR(LABELS, SCORES) computes the
% precision-recall (PR) curve. LABELS are the ground truth labels,
% greather than zero for a positive sample and smaller than zero for
% a negative on... |
888bc1161dff6b2cb227ce5b14e300d3fbc384ad79988bf7ea24117814440960 | MATLAB | 9,148 | 366 |
function train_opts=gen_net_opts_model_type1(run_config, class_info)
train_opts=run_config;
train_opts.eva_param=gen_eva_param(run_config, class_info);
train_opts.get_batch_ds_info_fn=@my_get_batch_ds_info;
train_opts.epoch_model_cache_fn=@my_epoch_model_cache;
train_opts.batch_disp_step=0.2;
train_opts.net_run_ver... |
d39bef6d7babe971a62b89cd5ad2fae6c522987a72b97bdae532372c26c2af97 | MATLAB | 9,163 | 220 | function [perCell, total] = mltp_compute_bfo_general(obj, session, rotDeg, mirrorContexts)
% mirrorContexts should be the same length as the number of contexts
% an entry of 0 means do not mirror, and 1 means to mirror
% this is used because often context 2 has the reward cup mirrored
% Allow the f... |
16634b56b92156678de176f351125a37599414ba4e6878a5c7d9bd0d16d1de1e | MATLAB | 9,173 | 206 |
%function [Spikes,nose,Fs]=getSpikesOF(File);
%getSpikesOF, modified from getSpikes to read OpenField data. ehud, Oct
%2016
%
%1. parse the data according to gaps in Timestamps (> 1s)
%Session_str, e.g.,'20150906Thalamus36\20150906Thalamus36_1to...'
%
%Spikes{Nelecs,Nunits}, cell holding spike times in ms fr... |
8d1f262326508c1d772fe2e3b1ec6168f50da225ba171a4430385bbcdb18d7a3 | MATLAB | 9,176 | 179 | function [] = PlotValidateBehavioralMappingExperimentGroup (TestLNPStats, LNPStats, meanLEDPower, stdLEDPower, L, density, xx)
%Takes in structure LNPStats and plots them depending on the settings; not used in paper
% Detailed explanation goes here
fps = 14;
BTA_seconds_before_and_after = 10;
BTA_seconds_... |
db75250db95102d56435c9d003d292854a26d6b722dcf5bc066a64f870084cf7 | MATLAB | 9,189 | 297 | function [out,scale] = physicalunits(arg1)
% PHYSICALUNITS converts PhysDim inte PhysDimCode and vice versa
% according to Annex A of FEF Vital Signs Format [1]
%
% HDR = physicalunits(HDR);
% adds HDR.PhysDim or HDR.PhysDimCode, if needed
%
% PhysDim = physicalunits(PhysDimCode);
% converts Code of PhysicalUnits... |
dd968fe70808a88b396d6d6fcc884ff828f61ee225cf6d09bbf899b1ea8bbf68 | MATLAB | 9,189 | 259 | % plotHeatmapEphysVYawVelBinFwdAcc.m
%
% Function to plot output of getCorrelationEphysFwdAccYawVel_cond_all() or
% getSlideWinEphysFwdAccYawVel_cond_all() as heatmap.
% Plots yaw velocity on x, forward acceleration on y, normalized spike rate
% in color. Mean spike rate for that yaw velocity+forward acceleration bi... |
e7a74b0125174e20b50eeb6e90c61e69fbc5210ff3de9cf3f14cf07031327f66 | MATLAB | 9,193 | 215 | function params = VOR_Default(params)
%{
VOR_Default
This script takes information stored inside of an smr file and
1) preprocces it
2) run the default sine analysis script
This is a modified version of Hannah Payne's script 'runVOR'.
Requires three files to be stored in the current folder
1. '.smr' data f... |
fa51b098ea376b802ab43ef4a490752c105a4736958b33bbc4248eba58dc2739 | MATLAB | 9,193 | 307 | function varargout=correctZilluminationInDirectory(sectionDirectory,outputDirectory,verbose)
% Correct illumination of different optical sections in a physical section
%
% function stats=correctZilluminationInDirectory(sectionDirectory,outputDirectory,verbose)
%
% Purpose
% Imaging deeper in a physical section results ... |
04d6e94318a298f652db75d358c8013e6c183d5bf36a35c2580a845ce709b50e | MATLAB | 9,196 | 335 | function [succeeded,savename,trx] = convert_units_f(varargin)
setuppath;
fps = 20;
pxpermm = 4;
% parse inputs
[matname,matpath,moviename,ISAUTOMATIC,trx,savename,dosave,readframe_fcn] = ...
myparse(varargin,'matname',nan,'matpath',nan,'moviename',nan,'isautomatic',false,...
'trx',[],'savename','','dosave',true,'... |
dce56c0d412ebef0f8df25b181b73d89588493c12ddc0a74d15f8048e783716b | MATLAB | 9,197 | 222 | %This script allows the user to pick a watershed region in a t-SNE map and
%finds when the animal stays in that region and plots their behaivor, not used in paper
%% STEP 1: establish plotting constants
N_rows = 4;
N_columns = 4;
N = N_rows*N_columns;
fps = 14;
frames_before = 1.5*fps-1;
frames_after = 1.5*fps;
durat... |
c5405eceb4d6bdd7019ca18be8f60bbee861eddb30be9ba964064584c2452388 | MATLAB | 9,204 | 225 | % This script accurately computes and displays electric fields sampled on
% a cross-section (transverse plane) via the FMM method with accurate neighbor integration
%
% Copyright SNM/WAW 2017-2020
bem4_define_planes_big;
bem5_figure_scales_big;
%% Load/prepare data
planeABCD = [0 0 1 Z]; % Equati... |
629df15b94f0a6f546c6b1bafa9a894a80005729d372163f85ac9735cc9613d7 | MATLAB | 9,213 | 283 | %% Figure2 plot of HR and Rossler stochastic dynamics
% for paper "Inferring stochastic dynamics of complex systems", T.-T. Gao,
% B. Barzel, and G. Yan
% Code before line 159 is about HR system, and after line 159 is about Rossler system.
% If user want to generate HR(or Rossler) system's results, please comment
% o... |
c53095685e1c8f8826e34d7472eb6cb8c0c5bbd2e8190a537eca3ae1782e18dc | MATLAB | 9,213 | 318 | function varargout=sigstar(groups,stats,nosort,Yloc)
% sigstar - Add significance stars to bar charts, boxplots, line charts, etc,
%
% H = sigstar(groups,stats,nsort)
%
% Purpose
% Add stars and lines highlighting significant differences between pairs of groups.
% The user specifies the gro... |
16e935e0e4310a0eb5e53d7c5f5382a22e3b46ebd71ca3fe17581dddc2e15b6d | MATLAB | 9,219 | 255 | % getCorrelationEphysContParam.m
%
% Function to extract correlation between spike rate or median filtered
% membrane potential and one or more continous parameters (from continuous
% estimate of step parameters or FicTrac variables. If more than one
% parameter is chosen (i.e. more than 1 parameter and 1 leg), cor... |
42a147629675719bcc115c3131d6c583bf19c9127f5a7e9bc1c83b880cbcb9cc | MATLAB | 9,231 | 207 |
%% Define all three planes (m)
X = 1e-6; % YZ Cross-section position, m
Y = 1e-6; % XZ Cross-section position, m
Z = 200e-6; % XY Cross-section position, m
delta = 70e-3; % 3e-3; % half plane window, m
xmin = - delt... |
bca1b0b9ec87c7d5f6d327f4dd3583b10472369bca354e980a29a6aae70564dd | MATLAB | 9,233 | 242 | % saveSpikerateCond_bouts.m
%
% Function that saves spike rate over time for turning bouts, defined by
% yaw velocity peaks. User can specify FicTrac conditions that yaw
% velocity peaks must meet as well as the initial forward velocity range
% and the change in forward velocity between the start and peak of the
% ... |
c869c7c0073dd2ff3fb8f6ce50c5cbbad23cec9c3aa58fa7dcbf0252663d10e0 | MATLAB | 9,236 | 178 | %% calculates the cross-sectional strain distribution induced during micro-fluctuations of accommodation in the living human crystalline lens
addpath([pwd '/peak_interp'])
namtag='20to25years'; % name of the result files
folder='xxxx'; % path to the results folder
for jj=1:size(complx1_aligned,2);mtrx_aligned(1:size... |
814a586be080817d48ad51eaef952c50819468be5cc350fefdb6c8f84529ac65 | MATLAB | 9,237 | 244 | function festr = fillExport(propertyNames, RawClass, parentName)
exportHeader = 'function refs = export(obj, fid, fullpath, refs)';
if isa(RawClass, 'file.Dataset')
propertyNames = propertyNames(~strcmp(propertyNames, 'data'));
end
exportBody = {strjoin({...
['refs = export@' parentName... |
c6e1504b02610466b943df928b3009a93ceb909b9249c005277e3f1d23303835 | MATLAB | 9,242 | 243 | classdef NwbFile < types.core.NWBFile
% NWBFILE Root object representing data read from an NWB file.
%
% Requires that core and extension NWB types have been generated
% and reside in a 'types' package on the matlab path.
%
% Example. Construct an object from scratch for export:
% nwb = N... |
6cb118107b75ebc6f070a15c808759dad7cbfbbacb3a5fc0d8a1d78e0efb6d8f | MATLAB | 9,243 | 369 | function [maps_out,tmap_th,H] = aedes_fmri_analysis(DATA,varargin)
%
% This function does a quick fMRI analysis in SPM style. No motion
% correction or slice timing at this time...
%
% Defaults
TR = [];
contr = [1];
onset = [];
durat = [];
smooth_kernel = [];
d_cutoff = []; % Don't temporally filter data by defau... |
54d062d8aefa840bcdb2d0135898939f8fd2a60efbb0bbf49e9151f8fe061e75 | MATLAB | 9,251 | 258 | classdef BoundPipe < types.untyped.datapipe.Pipe
%BOUND Represents a Bound DataPipe which must point to a valid file.
properties (SetAccess = private)
config = types.untyped.datapipe.Configuration.empty;
pipeProperties = {};
stub = types.untyped.DataStub.empty;
end
prop... |
0e17c23d102890d9b320582bfefd8b8467d8eff207631bf51dfb31ce6c17cbce | MATLAB | 9,269 | 264 | function varargout=collateAverageImages(theseDirs,deleteOriginalDir)
% Loop through data directories and use saved average files to create grand average images
%
% function collateAverageImages(theseDirs)
%
% PURPOSE
% Create the grand average images that can be used for background subtraction.
% Over-writes any existi... |
941edf8a274aba5ec578464aacb02f55e55f6d2853e58b1b1859f304c56e06ed | MATLAB | 9,269 | 292 | % SUPPLEMENTAL FIGURE 2
%% LOAD FIXED OUTCOMES
if ismac
load('/Users/christianpotter/Desktop/Analysis/pop_analysis_potter2023/fixed_outcomes.mat')
else
load('C:\Users\Runyan1\Desktop\Desktop Code\dimred_event_analysis\pop_analysis_potter2023\Figure 1\fixed_outcomes.mat')
end
%% PLOT INFO ABOUT COMBINATION CO... |
b6bd38c900f09c56f04197aab00ee18feacfe4207cc2253b213ecbef094be188 | MATLAB | 9,275 | 181 | function ds = createDataTable(projectDir,subjnrs,postFix)
%% Function to create voxel data table:
% NOTE: Requires running s_prepareDataForPlotting.m
%
% INPUTS:
% projectDir : base folder where cloned code repo and downloaded data live
% subjnrs : subject numbers (as in the fMRI experiment)
% postFix : fixed se... |
1684913dfa60263799fd2bb2642c541f8bdf3b8094264bcce9270f7bc0c20a87 | MATLAB | 9,277 | 325 | % Generate figure 3
%% Load data
experimentfilename = '/data/experiment_XOR3S2T_0920_ETA=64_VIT=40_[2S2T2G]_23-09-20-15-31-46.mat';
load([cd,experimentfilename]); % cd gives current directory
EXP = experiment;
addpath([cd,'/helper_scripts/'])
%% Set configurations for figure
bxlim = [10^-3,10];
selectti... |
51f920539b1a2e2005bfd7f62a2d96aece2ea1729592924955deb781cf581915 | MATLAB | 9,281 | 302 | % f_GetSignalsNico
%
function [m_EEGSig m_ECGSig m_RespSig] = ...
f_GetSignalsNico( ...
pstr_FullPath, ...
pstr_EEGSigStr, ...
pstr_AveStr, ...
pstr_ECGSigStr, ...
pstr_RespSigStr, ...
ps_FirstSam, ...
ps_LastSam, ...
ps_ScaleData)
if nargin < 2
error('[f_GetSignal... |
ab052c8914e3599049481972db8b528e0dedb3e100528f15b676b019d61d226d | MATLAB | 9,286 | 207 |
showfigs = 0;
%% Define all three planes (m)
X = 1e-6; % YZ Cross-section position, m
Y = 1e-6; % XZ Cross-section position, m
Z = 200e-6; % XY Cross-section position, m
delta = 3e-3; %77.5e-3; % half plane... |
0710b4b17f5295a7444f0c45ca55de53bc99cbb881cf467a220b4fbf672ec1eb | MATLAB | 9,295 | 214 | function buildToSpike2(ops)
%% this function will take a channel of waveforms in either a .txt
% or .mda format and add it to an existing .smr file
%
% See 'options.m' file for various things like file location and initial
% sorting method
%
% - waveform data should be in SAME FOLDER as smr file
% - waveform d... |
a65ee1694db5197ee5a401c5363992924a37b6e55c9c81bdd44c7a4b8aa99e2f | MATLAB | 9,302 | 310 | function Out = aedes_rotateflip(DATA,squareImages)
% AEDES_ROTATEFLIP - GUI for rotating and flipping files
%
%
% Synopsis:
%
% Description:
%
% Examples:
%
% See also:
%
% This function is a part of Aedes - A graphical tool for analyzing
% medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Nis... |
f3dd4a0a7852abbbf000c58e29a5c9832137457dd5613b59218e3d8faebb69e2 | MATLAB | 9,311 | 245 | function [ncs] = read_neuralynx_ncs(filename, begrecord, endrecord)
% READ_NEURALYNX_NCS reads a single continuous channel file
%
% Use as
% [ncs] = read_neuralynx_ncs(filename)
% [ncs] = read_neuralynx_ncs(filename, begrecord, endrecord)
% Copyright (C) 2005-2007, Robert Oostenveld
%
% This file is part of Field... |
217c117bab5867b1c0b88609f5a00a111a39dfca8072929a83c54c83fccb813d | MATLAB | 9,331 | 256 |
% Auto-correct potential identity swaps of tracked flies.
%
% To auto-correct identities, use:
%
% trk = track_auto_id(trk)
%
% where:
%
% trk. - tracking structure obtained from tracker_jobs
% names - names of fields in .data
% data - n_flies x n_frames x n_fields containing raw trackin... |
0e68ae2c09c3bce1163734f4abe3a55a063273e3ad7f60f2121f42e10d77968e | MATLAB | 9,332 | 330 | clear all
close all
clc
% Calculate ID scores of interest for the ISTART project..
% Daniel Sazhin
% ISTART
% 12/09/21
% DVS Lab
% Temple University
%subjects = [1002, 1004, 1006, 1007, 1009, 1010, 1011, 1012, 1013, 1015, 1016, 1019, 1021, 1240, 1242, 1243, 1244, 1245, 1247, 1248, 1249, 1251, 1253, 1255, 1276, 1282,... |
3cc125d87f75d54cf283c87c6cd95d1a4a4553229b972c24a6956e653b84a4c0 | MATLAB | 9,348 | 153 | % run amapOFshow
clear all; runMode = 'batch'; close all;
globals; initglobals;
PRINT_ERRORS = 0; PRINT_INFO=0; PRINT_NAN=0;
DATA_TYPE = 'OF';
%DATA_TYPE = 'EM';
PLOT_TYPE = {'tuning'}; % {'map'}, {'trajectory'}, {'tuning'}, {'map';'trajectory'} ;
%PLOT_TYPE = {'map'}; % {'map'}, {'trajectory'}, {'tuning'}... |
e2ca4388b5357e583811b2a50f4b97ec8cee913ed1a3757271c3f3190120ed88 | MATLAB | 9,352 | 208 | clearvars -except num_meta_tr ff_values tempi value_list valuei value
close all
%% Parameter initialization
run('spiking_parameters_simple_dopa.m') %most parameters are stored in this file
plot_var = 0;
%% main program
Ach = zeros(1,t_total/dt + dt);
for l = 1:num_trials
tic
%% initialization
[v_i... |
9062963069d725b5cf865d89f9f048d1f7117f92f77217211919e7e3a43e74ea | MATLAB | 9,359 | 270 | function [awf, eas, ias] = wmti_parameters(dt, mask)
% Calculation of the white matter tract integrity metrics
%
% -----------------------------------------------------------------------------------
% please cite: Fieremans, Els, Jens H. Jensen, and Joseph A. Helpern.
% White matt... |
1f23514477de132364fb5baca49cffef4a23a1642d9d4364e0eae60305add599 | MATLAB | 9,363 | 268 | %__________________________________________________________________________
% violin.m - Simple violin plot using matlab default kernel density estimation
% Last update: 10/2015
%__________________________________________________________________________
% This function creates violin plots based on kernel density e... |
c70d1ff9772b79ca63188f433f348e4ffde029670154a7d2e2958a2133d25a5a | MATLAB | 9,377 | 265 | function ft_write_event(filename, event, varargin)
% FT_WRITE_EVENT writes an event structure to a file, a message daemon
% listening on a network socked, or to another computer connected through
% the serial port.
%
% Use as
% ft_write_event(filename, event, ...)
%
% The first argument is a string containing the fi... |
09e786d2eb9ce3f21c66ce653786336bb7d840ef4df7e816b28f9e9d73670127 | MATLAB | 9,384 | 227 | clc
if get(handles.EditInputMark,'Value')==1
if isfield(passdata,'cal') && isfield(passdata,'cue')
if ~isempty(passdata.cal) && ~isempty(passdata.cue)
t=passdata.interval_cal*(1:1:size(passdata.cal,1));
color=['r','g','b','c','m','y','k'];
axes(handles.DataPreVie... |
4355d405d2a52e3fa94f38d444a0a636f8724c78f7c27fb8cd95776ca47befba | MATLAB | 9,385 | 258 | clear
clc
close all
main_folder=('/projects/LEIFER/Sandeep/APIData/20200831_RunRailsTriggeredByTurning_Sandeep_AML17_AVA_10ulRet/Data20200831_162748'); %% main folder path
filename='workspace_data_20200831_162748_80uW_5sec_turning.mat';
load(fullfile(main_folder,filename)); %% save the workspace data inside the main f... |
72efddaf5ef3052a2fc5ed8eb941741bc641892de0d5780c77f1b59f87a6d6e0 | MATLAB | 9,386 | 259 | % plotOptomotorOptoDiffLegStepParam_allFlies.m
%
% Function that takes two sets of output files from
% extractOptomotorLegStepParamsOptoCond_fly() and generates a plot of the
% difference in the specified legStep param for each leg, across the two
% sets of data. Matches across flies. Plots mean for each fly as
%... |
9d66fb8d6e292ff63f985d963ca2c023ebd8ccaf6c3e808279bc70dabf314e68 | MATLAB | 9,399 | 154 | % run amapOFshow
clear all; runMode = 'batch';
globals; initglobals;
PRINT_ERRORS = 0; PRINT_INFO=0; PRINT_NAN=0;
DATA_TYPE = 'OF';
%DATA_TYPE = 'EM';
PLOT_TYPE = {'tuning'}; % {'map'}, {'trajectory'}, {'tuning'}, {'map';'trajectory'} ;
%PLOT_TYPE = {'map'}; % {'map'}, {'trajectory'}, {'tuning'}, {'map';'t... |
50c4932d6a3931834c1f17677868a2f688fce04a71666bb691f4fb2023b86e6c | MATLAB | 9,409 | 157 | function [data_struct, parameters, raw_data] = importEyetrackingData(filename, opt)
%IMPORTEYETRACKINGDATA Read the contants in a file and save them as a table
% The expected input is a filename and an option list. The file must be a
% .tsv file with a comma as decimal operator. It is designed specifically
% for ... |
0fc81aaa4a176eac4cde8edc85a5d8758dea330e9559c1f5879d5778a504de9f | MATLAB | 9,410 | 227 | % This script accurately computes and displays electric fields sampled on
% a cross-section (transverse plane) via the FMM method with accurate neighbor integration
%
% Copyright SNM/WAW 2017-2020
bem4_define_planes_zoom;
bem5_figure_scales_zoom; %_alternative;
%% Load/prepare data
planeABCD = [0 0 1 Z]... |
5ffe10818dfd37622b5e38a153c462365afa4f945a51c4d911fb92aeb983fa8a | MATLAB | 9,410 | 351 | function [kspace,data,msg_out]=epi_recon(kspace,Dat,procpar)
% This is a custom VNMR k-space reconstruction code for EPI data used by
% aedes_readvnmr.
% If called without input arguments, return the sequence names that
% this code reconstructs
if nargin==0
kspace = {'epi_se_rapid_sp3','epi','epi_fMRI','epip','epip... |
20b2c28b28ca453df385882f3565452355b1e5406374f589d2b1d906e2c5d684 | MATLAB | 9,415 | 200 | function BurstDetection (peakfolder, end_folder1, end_folder2, end_folder3, nspikes, ISImax, min_mbr, cwin, fs, check)
% Function for producing the Burst Detection files
% INPUT
%
% OUTPUT
%
% by Michela Chiappalone (17 Marzo 2006, 12 Gennaio 2007)
% modified by Luca Leonardo Bologna (10 June 2007) in order to handle m... |
e9bf6535bed3dc6df4d285c1055f23a4ee5d1fa998691cfacee47dad9a8c4554 | MATLAB | 9,422 | 269 | function [awf, eas, ias] = wmti_parameters_savedi(dt, mask)
% Calculation of the white matter tract integrity metrics
%
% -----------------------------------------------------------------------------------
% please cite: Fieremans, Els, Jens H. Jensen, and Joseph A. Helpern.
% Whi... |
3ea1a084fa88be4eb2848b0abc55c57b365baafaba07829a0fb8fc4af4430d52 | MATLAB | 9,435 | 262 | function [Sc,Tree]=hierarchicalConsensus(Ssample,varargin)
% HierarchicalConsensus Compute hierarchical consensus partition.
%
% Syntax
%__________________________________________________________________________
%
% [Sc,Tree]=hierarchicalConsensus(Ssample)
%
% [Sc,Tree]=hierarchicalConsensus(Ssample,alpha)
%
% [S... |
91014b40f3c3223d6bb6b9696a1f3b7b35cd5e2dbb4d022ea7c8f8b9ef5ea51c | MATLAB | 9,441 | 273 | function [type, dimord] = ft_datatype(data, desired)
% FT_DATATYPE determines the type of data represented in a FieldTrip data
% structure and returns a string with raw, freq, timelock source, comp,
% spike, source, volume, dip, montage, event.
%
% Use as
% [type, dimord] = ft_datatype(data)
% [status] = ft_... |
4519c9904aaadf2787a288fd7de93073a7b6fb7f4a0f1ed7ef4cfff6dd8bc211 | MATLAB | 9,454 | 229 | % preprocessLegVidFiles.m
%
% Function to preprocess raw leg video .tiff files.
% Call on date folder.
% Does generates and calls powershell script for renaming .tiff files.
% Does command line call to ffmpeg to generate .mp4 video file for each
% trial with leg video data.
% Generates powershell script and filelist ... |
5d7703acae6638b4aab598b0a19925aece8f628f77f31f8af18129c5076b54aa | MATLAB | 9,457 | 202 | %%% author: SK
%%% date: 28/03/2024
%%% reference :"Neural effects of dopaminergic compounds revealed by multi-site electrophysiology in mice and interpretable machine-learning"
clear all; close all; clc;
%%Specify the directory to save data
save_dir = 'E:\WT Pharmacology Results 2023\SIFT 1KHz Arfit 10s5s'... |
a7819ebf9256136af9a678d9866ad056dea8e02e5be81ce4cac635098db3d695 | MATLAB | 9,459 | 246 | % saveSpikerate_bouts.m
%
% Function that saves spike rate for turning bouts, defined by yaw
% velocity peaks. User can specify FicTrac conditions that yaw
% velocity peaks must meet.
% Extracts bouts that meet FicTrac conditions and accounts for timing of
% step relative to yaw velocity peak
% Extracts both right ... |
c21b57c5eaa5520bc5b611f7ee85fc2c2f78e7c7363acd82727cd877815bbcab | MATLAB | 9,472 | 278 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function make_stabilitybfo90_percell_formatted_for_sigmastats_separated(analysisSettings, analysisResults)
% There will be numDays x 2 = 12 excel files created.
% Each file has one days data, and either within or across.
% Each file ... |
1957cdf25de5c6a4bf4d204d9d06038722a236dc184700675aba81950e2e0d3a | MATLAB | 9,474 | 178 | %% Example pipeline going from raw Neuropixels data recorded with SpikeGLX to curated (with Bombcell) units identified with UnitMatch
%% User Input
%% Path information
DataDir = {'H:\MatchingUnits\RawData'};%{'H:\MatchingUnits\RawDataMonthApart'};% ;%Raw data folders, typically servers were e.g. *.cbin files are stor... |
5d4171915da20cc3661b8139dc42762b83309b99882084d911760161c26a9e24 | MATLAB | 9,488 | 182 | function success = auto_resolve_problems(folder_name)
% automatically resolve centerline problems
addpath(genpath(pwd))
parameters = load_parameters(folder_name); %load experiment parameters
if parameters.TrackOnly
success = true;
return
end
frames_around_problem_to_cut = param... |
fcc4c7a397cfa4c1ded0d03ef863ce811df153b6180a0f4f1b810132333b2a3a | MATLAB | 9,490 | 328 | function fig_fMRI_QA(fMRIName,nan_FD, Xd, nan_DVAR_pre_reg, nan_DVAR_post_reg, nan_DVAR_post_all,path_ex_sum)
%% This function shows gray plots and some extra info required for quick visual inspection of bold data
% Oscar Miranda-Dominguez
%silence warnings
warning('off', 'all')
[r c]=size(Xd);
%% settings
FDvlow_t... |
569cb456210228ed62a3e909eb806ffd6ac8def372a64640018e3a2a284c9e0b | MATLAB | 9,491 | 198 | function [params] = simseq_loadstRetPRFParams(pths, hemi, roi, ...
spatialModel, temporalModel, veThresh, hvol, subFolder)
% Function to select pRF params from toonotopy experiment within ROI
% cd to toon data
cd(fullfile(pths.dataDirToon, pths.toon))
if ~exist('veThresh', 'var') || isempty(veThresh)
veThresh... |
c8d3b07b2b0c0a592af89b8732f47e4b7937e757dfa6674d2015dcdf793a341a | MATLAB | 9,491 | 245 | %averaging Open field data
%Author: Maria Chernysheva
%load the data
close all
clearvars
clc
%give folder with matlab functions
folder_with_matlab_scripts = 'Y:\Chernysheva Maria\MATLAB\Matlab_scripts_AlloLight';
addpath (genpath(folder_with_matlab_scripts))
%give the folder with the data subfolders
main_... |
1b2845c9875205a0732d3a8dcba0c1bc9cf8f72421232169cc2f16affe5524e2 | MATLAB | 9,506 | 328 | function postreg_fig_fMRI_QA(fMRIName,nan_FD, Xd, nan_DVAR_pre_reg, nan_DVAR_post_reg, nan_DVAR_post_all,path_ex_sum)
%% This function shows gray plots and some extra info required for quick visual inspection of bold data
% Oscar Miranda-Dominguez
%silence warnings
warning('off', 'all')
[r c]=size(Xd);
%% settings
... |
a74740e21f6201a942c5728be9a5a8f77175c5c05cb9977c1167d5b9450482dd | MATLAB | 9,516 | 175 | %% s_prepareDataForPlotting.m
% Script to prepare data for "createDataTable" function. Mainly combines
% ROIs (like VO1 and VO2 into VO1/2) and single voxel pRF parameters with
% single voxel model fitting results.
%
% Code written by E.R. Kupers (2024) Stanford University
%
%% Define params
subjnrs = [1,2,3,7,8... |
03a641473e7f65cfdc55242bc785cd01484c07438e5717f32266a9610ca9ab4a | MATLAB | 9,522 | 251 | function success = core_tracker_job_combine(output_per_chamber_track_file_name, ...
output_segmentation_file_name, ...
atomic_track_file_name_from_chunk_index, ...
calibration_or_calibrati... |
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