sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4ef33ffc366264db5242c077e477fd9ed5f56a8a3643fa7fb01af37592390c27 | MATLAB | 3,138 | 158 | function fmri_spm_volumes(infile,outdir,varargin)
% This function reads VNMR EPI data and writes volumes in separate NIfTI
% files for SPM analysis
%
if nargin<2
error('Too few input arguments')
end
% Defaults
if infile(end)==filesep
infile = infile(1:end-1);
end
[fp,fn,fe] = fileparts(infile);
if strcmpi(fn,'fi... |
e499d2b4b3867fa3bb3c09d554fe402649474da933defa7c3e19f79dd67d1532 | MATLAB | 3,139 | 84 | function [map,thismanyhits] = heatmap3ct(traceOrig,DFForZ,camtime,timeFP_frames,startFr,endFr,lowRes)
trace=round(traceOrig/lowRes); %reduce tracking resolution
%% correct non-tracked epochs by carrying forward last measurement
% Cleversys assigns -1 to non-tracked frames
j=1;
traceC=trace;
for j=1:length(trace);
... |
8e4ea7e805cd6a0637b503c4f221f6a04ed6411c5c359382c06ebcd6209bc924 | MATLAB | 3,141 | 117 | %% Sriram Summary OKR BETWEEN ANIMALS
%% Load File
clear;clc;
try
load('diffData.mat')
T = readtable('diffData.xlsx');
catch
warning('No diffData File Found!')
return
end
color = T.color;
conditions = unique(T.condition);
%% For Each Condition
for i = 1:length(conditions)
A = figure(i);clf... |
c60cf5960b9b63cdb3780cb9320aab0802ef8b73b651034fd656f39605f57224 | MATLAB | 3,142 | 97 | function [maskErode,maskLargest,maskThreshold] = create_mask_erode(dataMagnitude,radiusDisk,percentileThresh)
% [maskErode,maskLargest,maskThreshold] = create_mask_erode(dataMagnitude,radiusDisk,percentileThresh)
%
%=================================
% PURPOSE
%=================================
%
% creates a new mask fr... |
d69f95c75528280ec220b0345a9df9892ea1f2b42b7fc074031f32efe5c1689a | MATLAB | 3,145 | 92 | function plotFFTSetupON( obj, varargin )
% PLOTFFTSETUPON
% Plot setup ON LFP recording fourier transform
%
% Syntax:
% PLOTFFTSETUPON( obj, varargin );
%
% Input parameters:
% * obj DBScope object containg streaming data.
% * (optional) ax Axis where to plot.
% * rec Index of re... |
5b80211375521f246ea3740db6b2ebd2d12c2f1b11b112b60a4b5f6bddeea0b3 | MATLAB | 3,146 | 73 | % This demo shows how to use the software described in our IJCV paper:
% Selective Search for Object Recognition,
% J.R.R. Uijlings, K.E.A. van de Sande, T. Gevers, A.W.M. Smeulders, IJCV 2013
%%
fprintf('Demo of how to run the code for:\n');
fprintf(' J. Uijlings, K. van de Sande, T. Gevers, A. Smeulders... |
6960fdd6ea71f553447dd5bb670993d084b193cd751f1c9eb83ade59df1c4988 | MATLAB | 3,147 | 98 | % This example creates a square module with optodes. It then uses MOCA's
% automated createLayout() function to overlay the module over the ROI.
% Once this probe is generated, this demo shows how to toggle individual
% modules on/off, how to translate the probe relative to ROI, and how to
% rotate individual modules.... |
7df5d4e7db265cd65652ca9714290c17e049e53779a06135c005821177e8bb6f | MATLAB | 3,148 | 102 | % plotAllKernels.m
%
% Function to plot all kernels, where those relating the same variables in
% the same direction are plotted on the same subplot. I.e. the yaw
% velocity forward kernel for left, right, sum, and diff. Also shows
% variance explained. Produces 1 plot, with subplots.
% Requires the structs generate... |
943dca7f447de1b28382bf93c3d9a83a54dfaf5def94d563c978e6905da7e884 | MATLAB | 3,149 | 87 | % computeMeansStdErrsFictracOpto.m
%
% Helper function for computeAvgFictracOpto_1Fly() that takes in cell array
% of stimulation reps and returns 2 cell arrays of the same size, one with
% the mean and one with the standard error across reps
%
% INPUTS:
% reps - cell array of size # NDs x # durations, where each e... |
e9f62e14b106d92e7ff15240d2a8a209d0b1aa63353a66a4c5483c5dc8def90b | MATLAB | 3,150 | 110 | function [] = classificationGenerator()
if ~isdeployed
disp('loading path')
%for IU HPC
addpath(genpath('/N/u/brlife/git/vistasoft'))
addpath(genpath('/N/u/brlife/git/encode'))
addpath(genpath('/N/u/brlife/git/jsonlab'))
addpath(genpath('/N/u/brlife/git/spm'))
addpath(genpath('/N/u/brlife/... |
c06f6cadb7ef766b6772cd62d12f0e3c8771eecc9e55f4ca888b5232fcff2ad8 | MATLAB | 3,151 | 74 | function [I Q F]=motif4struct_wei(W)
%MOTIF4STRUCT_WEI Intensity and coherence of structural class-4 motifs
%
% [I Q F] = motif4struct_wei(W);
%
% Structural motifs are patterns of local connectivity. Motif frequency
% is the frequency of occurrence of motifs around a node. Motif intensity
% and coherence... |
c0bcbf5108068638375adb06d6e2689945f947de10c15205c7cf9f9792632383 | MATLAB | 3,151 | 97 | function [ mynii ] = MYnii( vol, varargin )
%MYNII Usage: MYnii(inputvolume). Replaces nifti function, output .mat .dir .dims .voxelsize .data
% MYnii opens .gz files if needed. Accepted input is .nii, .hdr, .dcm (no
% mat available) and .PAR or .REC (no mat available). If anything is
% given after the vol, a par... |
c7d6a80bb818b91f1f2ba5fa7a274fef9437aa53682f4e4266ccaa6813a554ab | MATLAB | 3,151 | 84 | % This script assigns coil position, dIdt (for
% electric field), I0 (for magnetic field), and displays the resulting
% head-coil geometry. It may be be executed several times to adjust the
% coil position
%
% Copyright SNM/WAW 2017-2020
addpath('../../../../FMM3D/matlab');
%% Define dIdt (for ele... |
8c2f73ec07f45b62b294911f2b9602cc9eca54cd675acf262bceae87472cb4b9 | MATLAB | 3,152 | 77 | function [ x, u, energy ] = fcn_optimalControlContinuous( A, B, rho, x0, xT, T )
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This function solve the optimal control problem where
% min_u \int_0^T ||x_T-x(t)||^2+\rho ||u(t)||^2 dt
% s.t. dx(t)/dt = A x(t) + B u(t), x(0) = x_0, x(T) = x_T
%
% ... |
c5c18080d09dc990f19c296494026e5144a5076d95e21b52b2fbf4a5a28fd643 | MATLAB | 3,152 | 81 | %% TOPOPLOT_MODELESTIMATES
% This script creates topoplots based on the model estimates of each
% channel.
%
% INPUT:
% - summary/*/*_channels.csv: summary output table from R containing model
% estimates of each channel for the given condition
%
% OUTPUT:
% - topoplots of the model estimates for each of the conditions... |
a3042e1fccbd1733ec7348d8c48d5430eacb918fa78274b5c9667fa116653b5f | MATLAB | 3,153 | 86 | % segments data from each block into trials from 1s before onset
% to 10s after onset
% and saves it in scr_epo_all.mat
% additionally creates single trial plots so that one can check data
% quality
function skin_conductance_epoch(cfg)
interval = [-1 10]; % trial interval in s relative to heat onset
raw_file_path = f... |
b7182e3dfa2c8ae749d222732036648d16e9e71eb119d380432f0d1cc54b90b3 | MATLAB | 3,153 | 75 | % This script assigns coil position, dIdt (for
% electric field), I0 (for magnetic field), and displays the resulting
% head-coil geometry. It may be be executed several times to adjust the
% coil position
%
% Copyright SNM/WAW 2017-2020
addpath('../../../../FMM3D/matlab');
%% Define dIdt (for ele... |
0123454e6d48ff1dfc51e9f644d59622a2d9c9b184103dff23e5162a968620a2 | MATLAB | 3,154 | 92 | function plotFFTSetupOFF( obj, varargin )
% PLOTFFTSETUPOFF
% Plot setup OFF LFP recording fourier transform
%
% Syntax:
% PLOTFFTSETUPOFF( obj, varargin );
%
% Input parameters:
% * obj DBScope object containg streaming data.
% * (optional) ax Axis where to plot.
% * rec Index o... |
022650d27f5fa7b4fdf19af16509211c9ca802b04bd3b49f6e697e9ad69745a1 | MATLAB | 3,154 | 82 | % mglContextStash: Set aside the mgl state and config, to reactivate later.
%
% $Id$
% usage: contextName = mglContextStash(newName)
% by: ben heasly
% date: 09/07/2022
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: Set aside the mgl state and config, ... |
47976026880f73876dbd73563f150ce4f074c96dbec710d1b94782bdbbb9ce5b | MATLAB | 3,157 | 82 | function data = read_artinis_oxy3(filename, header, begsample, endsample, chanindx)
% reads Artinix oxy3-files into fieldtrip format
% use as
% header = read_artinis_oxy3(filename)
% or
% event = read_artinis_oxy3(filename, read_event)
% where read_event is a boolean. If 'true', the function returns events.
% If... |
6938c0adc473701aefcd02257872be6947c710150989ae6b52f56d7864fa4ba8 | MATLAB | 3,157 | 96 | function [coeffs,mean_data,initialProjection,threshold]=find_dir_subspace(pars,optimW,I_ramp,colour_dir)
%% find_dir_subspace defines a common subspace for trajectories across different directions
% INPUTS
%
% pars: parameters of the simulation set on MCtx_RNN_SOC_common_parameters
%
%optimW: Weights of the network
%
... |
b0bd78d85ce022a84357462b6eed3baa7a1fe5a80280ea3df6a34cef359c3e9f | MATLAB | 3,158 | 98 | function [startstop]=find_startstop_v1(data, events, rot_tra, run, ID, varargin)
% FIND_STARTSTOP_V1
% This function detects the timepoints when a participant starts and stops
% when walking. This was defined as an increase/decrease in horizontal
% pelvis velocity over a threshold of 0.3 m/s after a start/stop signal... |
9938389d6a9d5bee6c7846c1078421e1ec675da6191311a615bfefd487b9ee84 | MATLAB | 3,159 | 86 | % segments data from each block into trials from 1s before onset
% to 10s after onset
% and saves it in scr_epo_all.mat
% additionally creates single trial plots so that one can check data
% quality
function skin_conductance_epoch(cfg)
interval = [-1 10]; % trial interval in s relative to heat onset
raw_file_path = f... |
c65f9db41e478ebe0e82211e73dfa995dafabde94cbba5f3cab036fc6bbff473 | MATLAB | 3,162 | 118 | % Script to compute mean MePD output on the Kp x c_{ie} par. space
clearvars; clc;
addpath("C:/Users/kn356/OneDrive - University of Exeter/Desktop/StandardMATLAB")
load("rainbow_cmap.mat")
load("par.mat")
par.d=0.05;
time_vector = 0:0.1:5e+3;
%%
p1 = [1.6 , 14];
p2 = [0, 65];
n = 150;
% Define the parameter ... |
a46f5b3728ead1a2a594e6ec592949e22567327f6539a2ea4e3fb7c62e2664de | MATLAB | 3,164 | 113 | function polarPlotVectorsGender(File)
% open up csv file containin the gain and phase
[~, ~, array] = xlsread(File);
[row, col] = size(array);
rLimits = [0, .62];
myfig = figure();
% does this file contain gender information?
if col > 4
gen = true;
else
gen = false;
end
% cycle through each entry and plot t... |
da399dda73548ab1781bc7608f418eac339c2e7f82060f02e7c0a4d91ec32bf2 | MATLAB | 3,168 | 82 | function plotCrossCorrVarChronic( obj, varargin )
% Cross-correlation and cross-variance of chronic LFP recordings
%
% Syntax:
% PLOTCROSSCORRVARCHRONIC( obj, ax );
%
% Input parameters:
% * obj - object containg data
% * ax (optional) - axis where you want to plot
%
% Example:
% PLOTCROSSCORRVARCHRONIC( obj... |
e074f8b9bd83560a3e2a4cae348bb726ccffbbf8508ae762532395e7e020863c | MATLAB | 3,171 | 115 | % Script to extract pdf curves for S, T and <S> vs T
% Author: Keshav Srinivasan, March 2023
%% Parameters
tsteps = 1e8; % Number of time steps of the time-series vector
d = 25; % Range of k (time-bin)
%Initalize variables
S = zeros(tsteps/10,d);
T = zeros(tsteps/10,d);
counts = zeros(1,d);
p = 1; % The subsampl... |
5275da27f3338307162b24025d625fd7c81183794618e397ab055dc325b5ce5a | MATLAB | 3,174 | 96 | % getAlignedLegStepsContfromBouts.m
%
% Helper function for saveContLegStepParamCond_bouts() that takes in
% indices of yaw velocity peaks (peak, start, and end) and returns the
% continuous leg step parameter values aligned to the velocity peak
% To allow averaging over different bouts and the inconsistent frame r... |
11e3bc3280be9f8ed66a74af9bb5e8575d74a45a7acb5d8a4a0aa3086aa47429 | MATLAB | 3,175 | 91 | % Coupling of the KNDy network model with MePD outputs
function dx = KNDy(t,x,par)
%% KNDy model parameters
d1 = par.d1; % Dyn degradation rate
d2 = par.d2; % NKB degradation rate
d3 = par.d3; % Firing rate reset rate
k1 = par.k1; % Maximum Dyn secretion rate
k2 = par.k2; % Maximum NKB secretion rat... |
13009e4d9fa123e471a2b11f6a333c926b7e9ce64e803d69e51824e9ca4419df | MATLAB | 3,176 | 94 | data_path = '/Users/celia/Documents/two_context_data'; % change this
load(fullfile(data_path, 'ratemaps-2021_12_1_12_34_49_K1_d4.mat'))
minTrial = 4;
animals = length(extractfield(ratemaps.data, 'animal'));
within = cell(length(animals),3);
across = cell(length(animals),3);
rmDay = cell(length(animals), 3);
for a = 1... |
9dc9ec659b11f2f9b5c61d4e55c01ac1b933e1a32d30e24ef96adf6d1d0cbb66 | MATLAB | 3,178 | 66 | % VL_AIB Agglomerative Information Bottleneck
% PARENTS = VL_AIB(PCX) runs Agglomerative Information Bottleneck
% (AIB) on the class-feature co-occurrence matrix PCX and returns a
% vector PARENTS representing the sequence of compressed AIB
% alphabets.
%
% PCX is the joint probability of the occurrence of t... |
f093d7f5e6d5c3dd581375b3569d687a92a910529c704059b3ac317425bace07 | MATLAB | 3,179 | 109 | function vars = alignmentMethod_Saccade_APP(app, vars)
disp('Calculating Alignment Based on Saccade Overlap...')
%% Prep
badSpots_vid = vars.sacLoc_vid;
alignmentWindow = [-3 3];
alignmentSlots = alignmentWindow(1)*vars.samplerate_Magnet:alignmentWindow(2)*vars.samplerate_Magnet;
rr = 1;
for i = alignmentSlots
if... |
98ac09731ff1ec6591b7f8614068762248abfc9895e8b113a59dec86dc9b42b7 | MATLAB | 3,180 | 55 | clear
file=dir('ACC*uncertain*.mat');
k=1;
for jj=1:length(file)
load(file(jj).name)
gotrial=find(outcome(:,1)==1|outcome(:,1)==2|outcome(:,1)==5);%Go trial,hit/miss/ro
%delte first trial
gotrial(find(gotrial<=1))=[];
nogotrial=find(outcome(:,1)==3|outcome(:,1)==4);%Nogo trial,cr/fa
nog... |
f9f7c59e0e346275598f5f98cb0f3ffdc7a0070a04f3e521b11d1f82a15c4103 | MATLAB | 3,180 | 113 | classdef My_util_dagnn
properties
end
methods(Static)
% -------------------------------------------------------------------------
function layers = simpleFindLayersOfType(net, type)
% -------------------------------------------------------------------------
layers = find(cellfun(@(x)strcmp(x.type, type)... |
0e83b9b6d49c252b9b67f38921e65a74a4abe7ab64745fd568bffc2120504dc4 | MATLAB | 3,182 | 93 | % uSelectROIs.m
%
% Function for the user to select the ROIs and background threshold for a
% single time series. Calculates raw signal (mean pixel intensity) in each
% ROI and performs background subtraction.
%
% INPUTS:
% none, but prompts user for trial folder with preprocessed imaging data
%
% OUTPUTS:
% non... |
7cc3c224645054812076afe0e7a303de4daa93ed97250c3f53dd6e3c9eb99e8c | MATLAB | 3,182 | 81 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [R] = compute_stats_stability_bfo180_sim_curves_days123(analysisSettings, analysisResultsGroupAverages)
SessionsToGroups = load_sessions_to_groups_table(analysisSettings);
SessionsToGroups(~ismember(SessionsToGroups.... |
7619fc31039283b02337170cd9775645329468af63e4b81245031ed192b93f88 | MATLAB | 3,183 | 84 |
function cnn_batch_info_disp(train_opts, work_info_batch)
batch_ds_info=work_info_batch.ref.ds_info;
img_size_str=my_gen_array_str(batch_ds_info.img_size);
img_size_str_input=my_gen_array_str(batch_ds_info.img_size_input);
img_size_str_aug=my_gen_array_str(batch_ds_info.img_size_aug);
f... |
a0748ac00b99278b22710ec845687fd2d3469cc0c4c5a325186b86b2586236b3 | MATLAB | 3,183 | 60 | function Tracks = load_labview_tracks(folder_name, parameters)
if exist([folder_name, filesep, 'labview_tracks.mat'], 'file') == 2 && exist([folder_name, filesep, 'timestamps.mat'], 'file') == 2
loaded_variable = struct2cell(load([folder_name, filesep, 'labview_tracks.mat']));
Tracks = [loaded_varia... |
d832be0d02596337cc17b0149cd112dc1b2b741f33719a30b33cabe1f09180cb | MATLAB | 3,186 | 83 | function handle = restack_dataplots( handle, dataplots )
% restack_last_plot Ternary plot restacking
%
% This function accepts a ternary axes "handle" and another scalar or
% vector structure "dataplots" which contains a field "object" or "obj"
% which is the specific handle of the plot to stack (e.g.
% dataplo... |
6b0180a2c3c4fe9ea53194335e11ae9342f09ae34b61e77087a282d5efad1a77 | MATLAB | 3,188 | 82 | function averageTimeframe(results, name, opt)
all_participants = fieldnames(results);
experiments = opt.experiments;
for experiment = experiments
experiment = experiment{1};
aoi_names = opt.aois.(matlab.lang.makeValidName(experiment)).names;
nb_aois = length(aoi_names.voronoi) ... |
2056e15c59d51fc17d474856bb1899914047a54e4984f20821b1d0069fc38d77 | MATLAB | 3,190 | 109 | % loadKernelYScaleYLabels.m
%
% Function to load y scales and y labels for kernel plotting, for when
% behavioral velocity units are all deg/s or for both mm/s and deg/s
%
% INPUTS:
% whichEphys - string for which ephys variable (spikeRate or medFiltV) to
% return y scales and labels for
% degPerMM - 0 if usi... |
e3ce95138be484a1f54bdb73fad13def9dc9723afdfbad47ff7d6fc61686dafe | MATLAB | 3,190 | 78 | % mglMetalFinishBatch: await results from a completed command batch.
%
% usage: [results, batchInfo]= mglMetalFinishBatch(batchInfo)
% by: ben heasly
% date: 01/12/2024
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: Returns the Mgl Metal to its normal state
%... |
9258743995144eea0e6aaaa39039fc979da867149a3a349eb0d691304d8374c4 | MATLAB | 3,191 | 81 | function mltp_compute_bfo_180_ac(obj, session)
outputFolder = fullfile(session.getAnalysisDirectory(), obj.Config.placemaps.outputFolder);
% Allow the function to run so that other functions do not break,
% but give a warning.
if session.getNumTrialsToUse() < 2
warning('This function requires ... |
7ed6edb8654b33fc59395292c07eb17af03ba212e9a378923df50958aee7d2a8 | MATLAB | 3,192 | 81 | function status = fillGroupsInformation( obj, data )
% Fill groups information
%
% Syntax:
% status = FILLGROUPSINFORMATION( obj, data );
%
% Input parameters:
% * data - data from json file(s)
%
%
% Example:
% status = FILLGROUPSINFORMATION( obj, data );
%
% Available at: https://github.com/NCN-Lab/DBScope
% Fo... |
d22f58165ae15fa033da5a96a8d1ff6770dc2d54d82e6621f10ae82efd48b4a3 | MATLAB | 3,193 | 73 | clear;
tbl_dir = pwd;
tbl_name = fullfile(tbl_dir,'S3_Data.xlsx');
[~, sheetNames] = xlsfinfo(tbl_name);
groupStr = {'Young','Old'};
condStr = {'Correct','Incorrect'};
%% Fig.3B, require https://www.mathworks.com/matlabcentral/fileexchange/23661-violin-plots-for-plotting-multiple-distributions-distributionplot-m
rainc... |
bba3dc3dc37dd41263b45e483cb5f7e9b77a7ca1952b717b2b164b58cddf2fcb | MATLAB | 3,196 | 103 | function [st3, rez] = standalone_detector(rez, spkTh)
% Detects spikes across the entire recording using generic templates.
% Each generic template has rank one (in space-time).
% In time, we use the 1D template prototypes found in wTEMP.
% In space, we use Gaussian weights of several sizes, centered
% on (x,y) posit... |
365a994d665173ca38e90db2a50d2df067b7c0f0c6ee57d79b3a9b419c72c888 | MATLAB | 3,197 | 115 | % windows() - Symmetric window functions
%
% Usage:
% >> h = windows(t, m);
% >> h = windows(t, m, a);
%
% Inputs:
% t - char array 'rectangular', 'bartlett', 'hann', 'hamming',
% 'blackman', 'blackmanharris', 'kaiser', or 'tukey'
% m - scalar window length
%
% Optional inputs:
% a - scalar or vector wi... |
e1ddeb7c922a7b7ee7fbfbe4c160c1eda201c6006728694971cd4b83cd5add2c | MATLAB | 3,197 | 83 | %% Burst Network Starting
clear all
clc
% Load file to compute BNL index and to identify the compartments
[filename, pathname] = uigetfile({'*.mat'},'Select NetworkBurstDetectionFile with all electrodes');
if isequal(filename,0)
return
else
col = ['gray ' 'green ' 'red ' 'cyan ' 'yellow ' 'violet ' 'blue '];
... |
d39c3fc76738aed49c7fda640ffd7cdc6288897bc26138479b3b042df7b7e8ee | MATLAB | 3,198 | 104 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
% This function reads in the excel files and then plots them since they
% were previously plotted in Excel. This is so that a reviewer doesn't have
% to plot them manually. Makes Figure S15A (mfr).
close all
clear all
clc
% Paths
r... |
e2563ebc29e50a1c96712f97f888ee3b395e224e0a6e7fa37c54d28849b21c2f | MATLAB | 3,198 | 105 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
% This function reads in the excel files and then plots them since they
% were previously plotted in Excel. This is so that a reviewer doesn't have
% to plot them manually. Makes Figure S15B (pfr).
close all
clear all
clc
% Paths
r... |
86d6921bee73807afe48dd2a8da5596dfbc60ca4f9595833f096d66f5078fe3e | MATLAB | 3,199 | 95 | function [zValues,zCosts,zGuesses,inConvHull,meanMax,exitFlags] = ...
findTDistributedProjections_fmin(data,trainingData,...
trainingEmbedding,parameters)
%findTDistributedProjections_fmin is called by runEmbbedings to find the
%optimal emb... |
5709e917b1e5d3f0b1daab563f0f2a4830b3f99df3638b452b9815cd0b06ad72 | MATLAB | 3,200 | 131 | function plot_motion_1d(FD,n,FD_TR,time_min)
[r c]=size(FD);
if r==n
FD=FD';
end
raw_FD=FD;
th_min=floor(time_min*60/FD_TR);
FD(FD<=th_min)=0;
FD_sorted=FD;
ticks=size(FD,1);
fds=linspace(0,0.5,ticks);
survivors=sum(FD>0,2);
neighbors=(-3:3)*.5; %lapsed time in minutes
n_neighbors=length(neighbors);
ths=time_min+n... |
dde0a3a59005d5fe8cf08f12388a7802bf36efc86eacda7fc6aa05625e2f03a6 | MATLAB | 3,201 | 73 | % mglContextActivate: Activate mgl state and config previously stashed by mglContextStash.
%
% $Id$
% usage: swappedOutName = mglContextActivate(toActivateName, swappedOutName)
% by: ben heasly
% date: 09/07/2022
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% p... |
25c6767c496099426a482fa9a441f747b81e35b40838142a70b787afb8cc3fde | MATLAB | 3,202 | 90 | % isPreSyn.m
%
% Function that returns whether each element of a source neuron list is
% presynaptic to at least x elements of a target neuron list
%
% INPUTS:
% sourceNeurons - single string or cell array of presynaptic neurons, by
% name
% targetNeurons - single string or cell array of potential postsynapt... |
85de9b53ecfff099a9200e2b8ddaea54fc80fc94d90173409f8ba586d0f798b6 | MATLAB | 3,204 | 97 | function [edge_usage,percent_usage] = fcn_get_edge_usage(L)
%FCN_GET_EDGE_USAGE calculate edge usage in shortest paths
%
% [edge_usage,percent_usage] = fcn_get_edge_usage(L) takes as input a
% cost matrix and returns the number of times an edge {i,j} was
% traversed across all shortest paths and the fraction ... |
e50fb11440ffeed7a92b7fe5fffc7c9dc0a6d057ee2efc20fe4ada69ebaaa8d2 | MATLAB | 3,204 | 75 | function newRect = OffsetRect(oldRect,x,y)
% newRect = OffsetRect(oldRect,x,y)
%
% Offset the passed rect matrix by the horizontal (x)
% and vertical (y) shift given. You can also pass in column vectors x and y
% with e.g., n different "shifts" and the function will return n copies of
% oldRect, each shifted by one of ... |
252b6133b892980bff9fc5004935fac328ea60c55def68e1dfbb699d9217408a | MATLAB | 3,206 | 102 | function [ guessA , guessb ,loglikes] = hmm_training( seqs,pi,guessA,guessb,info )
%% Train Hidden Markov Models (HMMs) using the Baum-Welch algorithm.
%% authors: Stefano Diomedi
%% date: 22nd February 2024
%
%% Inputs:
% - seqs: Emission sequences for training.
% - pi: Initial state probabilities.
% - guessA... |
c5a03eaf90884b44949cd4aa61fe4d42792bc9e4b2f53e31b41beb4285fcc5f7 | MATLAB | 3,207 | 129 | function generate_productjson(fg_classified)
tract_info = cell(length(fg_classified), 2);
fibercounts = zeros(1, length(fg_classified));
possible_error = 0;
num_left_tracts = 0;
num_right_tracts = 0;
for i = 1 : length(fg_classified)
name = fg_classified{i}.name;
num_fibers = length(fg_classified{i}.fibers);
... |
c8763d500dc05d755875650b170b9508b85eace7431b8ab18ddeec25b7821a4d | MATLAB | 3,208 | 120 | function [x, f, cost] = beads(y, d, fc, r, lam0, lam1, lam2)
% [x, f, cost] = beads(y, d, fc, r, lam0, lam1, lam2)
%
% Baseline estimation and denoising using sparsity (BEADS)
%
% INPUT
% y: Noisy observation
% d: Filter order (d = 1 or 2)
% fc: Filter cut-off frequency (cycles/sample) (0 < fc < 0.5)
%... |
1428405e6b94ecc483baf2990bd203127c4ac789a584e88455765453341472c6 | MATLAB | 3,209 | 120 | function [SepParticles,markers] = ParticleSeparation(MnonConv,minMarkerSize,Convthresh)
% Ultimate Erosion of Convex Shapes (UECS) based particle separation of non convex particles
% based on the discribtion of
% Park, C. and Ding, Y. (2021) Data Science for Nano Image Analysis, Springer Nature, Cham, Switzerla... |
26a438960c6885947bd02be21fdfa8fc696418505c9477cbf391fe24aec0367b | MATLAB | 3,209 | 99 | function [hdr, dat] = read_mpi_ds(dirname)
% READ_MPI_DS reads all DAP files from a directory containing files or
% alternatively a single DAP file and returns it in a simplified FieldTrip
% format. The analog channels and spike channels are both returned in a
% continuous format.
%
% Use as
% [hdr, dat] = read_mpi_... |
036cf9c5894236c6e733910291951b110a2a90f2cc56dac4b6f4ecf83a362530 | MATLAB | 3,215 | 81 | classdef SpikeEventSeries < types.core.ElectricalSeries & types.untyped.GroupClass
% SPIKEEVENTSERIES Stores snapshots/snippets of recorded spike events (i.e., threshold crossings). This may also be raw data, as reported by ephys hardware. If so, the TimeSeries::description field should describe how events were detecte... |
3b079d34aa17b8cf008885468cebd9b2424d38719947d34eea73fc03e546304f | MATLAB | 3,215 | 69 | function axon_params = check_axon_params(axon_params)
% axon_params = check_axon_params(axon_params)
%
% This function checks the elements of the struct axon_params to ensure
% that all fields are set. Fields not set are set to a list of default
% parameters. The struct checked is:
%
% - axon_params - Struct co... |
1b5fbbeacbdf0ce6693a9c0f220c181e8d7da4fbde2c5631a1dfee45a016705a | MATLAB | 3,218 | 100 | %% Script to obtain centiles by PE diagnosis (suspected, definite, and clinical)
% Copyright (C) 2023 University of Seville
% Written by Natalia García San Martín (ngarcia1@us.es)
% This file is part of Neurobiology Centiles Psychosis toolkit.
%
% Neurobiology Centiles Mapping toolkit is free software:
% y... |
5daf2b9f4e2912d889056b44a3bedc1f1a05bca53f1da956ccdd339645ef49cc | MATLAB | 3,218 | 100 | function [file] = read_ctf_ascii(filename);
% READ_CTF_ASCII reads general data from an CTF configuration file
%
% The file should be formatted like
% Group
% {
% item1 : value1a value1b value1c
% item2 : value2a value2b value2c
% item3 : value3a value3b value3c
% item4 : value4a value4b v... |
165b1fbb616cae416726d679f77dc1abf1e9d34ab57d01589cdf84dcb705133f | MATLAB | 3,219 | 81 |
% poorly written, please forgive!
commonSpikes = ones(1, length(data.default(2,:)));
% this removes the NOT common spikes, reset justTimes to contain running
% list of common spikes. If a spikes doesn't exist in a particular file, it
% will be removed.
justTimes = data.default(2,:);
length(justTimes)
commonSpikes ... |
e36be88bbe3faea71c6b7a3fb29549c2a9293e15cf0b1155a1b4f9c7e4821814 | MATLAB | 3,219 | 107 | function [A,W] = gretna_R2b_MST(Original,Stype,Ttype,Thr)
%==========================================================================
% This function is used to threshold a weighted matrix into a binary matrix
% and weighted matrix by identifying the minimum spanning tree subgraph
% first, followed by adding new conne... |
ff7da9489aeabc751e7faac9cdb5b3ccfcb1cac98ce9f8497f2f107acb3f8c6d | MATLAB | 3,220 | 98 | function [dat] = read_wdq_data(filename, hdr, begsample, endsample, chanindx)
% READ_WDQ_DATA reads data from wdq files
%
% Use as
% [dat] = read_wdq_data(filename, hdr, begsample, endsample, chanindx)
% or
% [dat] = read_wdq_data(filename, hdr, 'lowbits')
% Copyright (C) 2011, Jan-Mathijs Schoffelen
%
% This file ... |
9b202355d0743f5ae709599a80333e0d693fa18dea182fe6816d5ebca00511d5 | MATLAB | 3,222 | 103 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [T] = get_bestaligned_registered_rotated_maps(BestAligned, MapsData, registeredCellName, doNormalization)
cdata = BestAligned(ismember(BestAligned.registeredCellName, registeredCellName),:);
numSessions = size(cdata... |
5bee8a36711f8183b6b2eca4eaa6f086fd4a4e685f7ee581f4170255e179e86a | MATLAB | 3,223 | 124 | %
% Adaptive Edge Weighting for Label Propagation
%
% INPUT
% X: d (features) times n (instances) input data matrix
% param: The structure variable containing the following field:
% max_iter: The maximum number of iteration for gradient descent
% k: The number of nearest neighbors
% sigma: Initial width par... |
0397c119868ad0fea4127a87a04b901036f8bcf9510355117175da8de7702723 | MATLAB | 3,224 | 96 | function trainTree( opts, stream, ftrs, labels, treeInd )
% Train a single tree in forest model.
% finalize setup
treeDir = [opts.modelDir '/tree/'];
treeFn = [treeDir opts.modelFnm '_tree'];
% TODO: comment to prevant loading pre-compute tree
if(exist([treeFn int2str2(treeInd,3) '.mat'],'file'))
fprintf... |
f62d114bacd7a7caa70558d54c64a77fe0d99cf3e940844a77a9ba54798f6ef0 | MATLAB | 3,226 | 71 | % This script computes the induced surface charge density for an
% inhomogeneous multi-tissue object in an external time-varying magnetic
% field due to a coil via a BEM/FMM iterative solution with accurate
% neighbor integration
%
% Copyright SNM/WAW 2017-2020
%% Parameters of the iterative solution... |
dfdaa112048c19fa8175e5ed70fec5cc7cf5b7af7c467ccf2214c54c137797cb | MATLAB | 3,227 | 85 |
outputFolder = 'output';
if ~isfolder(outputFolder)
mkdir(outputFolder);
end
fid = fopen(fullfile('output', 'coherency_table.csv'), 'w');
fprintf(fid, '%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s\n', 'animal', 'day', 'contextA', 'contextB', 'trialA', 'trialB', 'digA', 'digB', 'animalSessionCellName', 'isStable', 'b... |
000f9472c774de0e908070ce391187bfe08e58b16f9a1761ec81cbe4240e87dd | MATLAB | 3,229 | 79 | function [result] = ml_egomaps_batch_compute_with_egotable(...
pop_cell_activation, ...
RADIUS_CM, EGOMAPS_CM_PER_BIN, EgoTable)
% This code processes more than ones cells activity and doesnt make any
% plots, but can with a callback with simple changes needed.
numCells = size(pop_cell_activation,2... |
c07e397bc92c793bdaa77771e7e8b2e77851c9fa02a5a253dda70e57e5971e49 | MATLAB | 3,230 | 110 | function remain = assignopts (opts, varargin)
% assignopts - assign optional arguments (matlab 5 or higher)
%
% REM = ASSIGNOPTS(OPTLIST, 'VAR1', VAL1, 'VAR2', VAL2, ...)
% assigns, in the caller's workspace, the values VAL1,VAL2,... to
% the variables that appear in the cell array OPTLIST and that match
% the ... |
d033be21ec17322ef81f7a7dbb1e484bf500c58e2adbd2ea52bbb788ea1f06a7 | MATLAB | 3,233 | 88 | %% stable/reverse/restable
clear
% file=dir('ACC*-stable*.mat');
file=dir('ACC*-restable*.mat');
% file=dir('ACC*-reverse*.mat');
nn=0;Cellid=[];
p=strfind(file(1).name,'-');
populationname=file(1).name(p(1)+1:p(2)-1);
k=1;
for j=1:length(file)
load(file(j).name);
label=str2num(file(j).name(4:5));
... |
e7c84ab7d89da2876ff288af1d1e1b24c8f63d02a29d6e129eb526f45b8f2355 | MATLAB | 3,233 | 96 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [T] = get_bestaligned_registered_rotated_maps_all(BestAligned, MapsData, doNormalization)
T = [];
k = 1;
registeredCellNames = unique(BestAligned.registeredCellName);
for iCell = 1:length(registered... |
726debbe67c8b9020501843eedfeee22689824a7ea43c01a399b168d15445094 | MATLAB | 3,234 | 92 | classdef network_project_superclass2
% superclass for all network project stuff. Not meant to be used directly.
properties (Constant)
% location of relevant folders
Directory = 'C:\Users\Durian Lab\Documents\MATLAB\Continuous_Network/'
% experiments run
ExperimentFol... |
be27f2d90bcb95712648f9eb872a8c89f96466fe4b7f1e97134d6c1e42f1b996 | MATLAB | 3,234 | 124 | %
% Adaptive Edge Weighting for Label Propagation
%
% INPUT
% X: d (features) times n (instances) input data matrix
% param: The structure variable containing the following field:
% max_iter: The maximum number of iteration for gradient descent
% k: The number of nearest neighbors
% sigma: Initial width par... |
4d326bf0e12f757ed96e407fecc9c427059f7a08b28c069d736037d15ee04dc5 | MATLAB | 3,236 | 80 | function thermalNoiseRemoval(filein, name, ofolder)
% Make sure that the following has been done:
% - you have downloaded the most current nonlocal mppca repo from github
% (https://github.com/NYU-DiffusionMRI/mppca_denoise)
% - you have FSL installed and know where its Matlab functions are located
% - you have set up... |
d9ce0e6f2c2b3b8460efd197727118a22efb8848a541a36fe879e81cf19f796d | MATLAB | 3,239 | 79 | function [ LFP_filtdata ] = applyFilt_ordered( obj, LFP_ordered, fs, filterType, order, varargin )
% This function returns the filtered data given the parameters that define
% the desired filter.
%
% Use with streaming recordings of LFPs;
% Sampling Frequency for Streaming = 250Hz.
%
% Depending on the type of the filt... |
f115cb4e68039f4329d62a4b9b80cdda0ff664b585a0e24c964d74429b1f8712 | MATLAB | 3,240 | 77 | function [DATA_and_MARKER_binned, info] = binning_and_cutting(DATA, MARKER, bin, condition, marker, m_time, p_time,info,str_save_append)
%% Function to bin spike times and event markers for each neuron and trial
%% authors: Stefano Diomedi
%% date: 22nd February 2024
%
%% Inputs:
% - DATA: Raw spike data
% - M... |
f4b67f53cd89dc68f4ddd18cda55cf937866897f10e573b70e626c8c1fe1b1d1 | MATLAB | 3,240 | 73 | function [cnmf, pcaica, suite2p, est] = correlateAllSegmentations(cnmf, pcaica, suite2p, est, neur_act2, varargin)
% [cnmf, pcaica, suite2p, est] = correlateAllSegmentations(cnmf, pcaica, suite2p, est, neur_act2, varargin)
%
% Function to pair the components from different segmentation algorithms
%
% 2018 - Adam Charl... |
26e447281fcbe892a33a93d68cdccbee08a05cb7ce9be0710e78477e8eec775d | MATLAB | 3,241 | 127 | function [estParams, LL] = fastfa(X, zDim, varargin)
%
% [estParams, LL] = fastfa(X, zDim, ...)
%
% Factor analysis and probabilistic PCA.
%
% xDim: data dimensionality
% zDim: latent dimensionality
% N: number of data points
%
% INPUTS:
%
% X - data matrix (xDim x N)
% zDim - number of factors
%
% OUTPUT... |
50e4dcfa2ad171ab0c7856d02f0e15b9db8fdfb2237278031136be6875db8a0c | MATLAB | 3,243 | 105 | function [fid, sens, label, sens_label] = read_zebris(Fname_zeb,skip)
% Reads Zebris files:
% fiducials locations, and
% either sensor file or headshape file or both
%
% FORMAT [fid, sens, label] = read_zebris(Fname_zeb,skip)
% Input:
% Fname_zeb - Zebris ASCII file containing sensor locations (mm)
% ... |
a58850b7a4354c713360a6bc938ad04149a948a2a0f1383db9348f25997f3daf | MATLAB | 3,244 | 96 | function corra = corrH(Var,LFP,Fs,elec)
% compute corr Head*Var.
% for now - corra.plot - node.o * var
% LFP is expected to hold the nose var, when called from corrHead
% var is the frames vector of tuning var.
% LFP
%
globals;
% CORRPAR.lags = [-500, 500]; %ms
% CORRPAR.maxF = 100; %Hz. low-pass filtered... |
c062552f6e9732e9851a1ad880249e4cfed2605697533895c25ef2f36f9e8309 | MATLAB | 3,246 | 81 | function mltp_make_trial_position_plots_raw(obj, session)
if obj.isVerbose()
fprintf('Making position plots\n');
end
% Make the folder if it does not exist
folder = fullfile(session.getAnalysisDirectory(), obj.Config.trial_nvt_position_plots_folder);
... |
2cbbc8929ef0c5800a9149689d4368d20ee57cd1eb383113177a3a069d1bcc9a | MATLAB | 3,247 | 85 | clear
cd ./stable-cuelight
% C1S2:loop;C1S3:go cue;C1S4:go judge;C1S5:no gocue;C1S6:nogojudge;
% C1S7:go Hit;C1S8:go miss;C1S9:no go CR;C1S10:airpuff;OUT1:reward;OUT2:airpuff;
% C1S11:light on;C1S12:light off
control=dir('C*.mat');%control
inhibit=dir('I*.mat');%inhibition
performence=[];
for ii=1:length(contro... |
778f4b81a8faa5e01e0452adc8d193de58cb17e1343f6c7fe33dfd78921f50ec | MATLAB | 3,248 | 106 | %
% Draw hop plot in function of time.
%
% PARAMETERS
% $network
% $type "full" or "split"
%
% INPUT FILES
% dat/hopdistr_time.$type.$statistic.$network
% dat/hopdistr_time_runtime.$type.$statistic.$network
% dat/stepsi.$network (full only)
% dat/steps.$network.mat (split only)
%
% OUTPUT FILES
% plot/hopdistr_tim... |
80ea69ee6d6d69b71bf5fb4ee6cab42a527826fe0dc114ab6e3cab3b413a91bd | MATLAB | 3,248 | 86 | function [On Ar] = reorder_mod(A,M)
%REORDER_MOD Reorder connectivity matrix by modular structure
%
% On = reorder_mod(A,M);
%
% This function reorders the connectivity matrix by modular structure and
% may hence be useful in visualization of modular structure.
%
% Inputs: A, connectivity m... |
291e8941ee15f9644c76263c6d163c067dc820151e857966c394ccf8bb2d3b99 | MATLAB | 3,253 | 58 | %%
fs = filesep;
handles.fs = fs;
%% Defaults to calculate connectotyping
handles.connectotyping_settings.default_frames=60; % set the number of random frames included to connectotype, subjects with fewer frames will be excluded from this environment
handles.connectotyping_settings.repetitions=10; % if a participant ha... |
80a4db437ea890ef32bb4861dd9754e621038817b46cc251352b6432d204a88a | MATLAB | 3,253 | 77 | f_fin = OPT_S.f_fin.*SC.mask_f_cam;
FOV.max_ramp_y = FOV.max_ramp;
FOV.max_ramp_x = FOV.max_ramp;
ramp_max = max(FOV.max_ramp_x,FOV.max_ramp_y);
n_big_area = round(ramp_max/SC.dx*2);
N_big_area = 2*n_big_area+1;
%% settings
ramps_big_fov_x = (-FOV.max_ramp_x :FOV.d_ramp :FOV.max_ramp_x);
ramps_big_fov_y = (-FOV.max_ram... |
17faaa69feb3f78d5d31792f57867848df4b7f54454e55346cdabd9792d37695 | MATLAB | 3,257 | 131 | function J = vl_imarray(A,varargin)
% VL_IMARRAY Flattens image array
% J=VL_IMARRAY(A) creates a mosaic J from the array of images A. A
% can be either a M*N*K array, storing one gray-scale image per
% slice, or a M*N*3*K or M*N*K*3 array, storing a true color RGB
% image per slice. The function returns an im... |
6d974eb34878d740532a065f5ad8deb07c49992fef3aedb27082618cd6801fd2 | MATLAB | 3,258 | 94 | classdef OpticalChannel < types.core.NWBContainer & types.untyped.GroupClass
% OPTICALCHANNEL An optical channel used to record from an imaging plane.
% REQUIRED PROPERTIES
properties
description; % REQUIRED (char) Description or other notes about the channel.
emission_lambda; % REQUIRED (single) Emission wav... |
c9e94341304ced997d35f13c52d593cd32b2f909ea5a3fc5f490483866e4cc26 | MATLAB | 3,258 | 132 | %
% Apply a spectral transformation to a central matrix.
%
% PARAMETERS
% d (r*r) Central matrix
% curve Name of curve to apply
% values Parameters of the curve
%
% RESULT
% d_new (r*r) New central matrix
%
function [d_new] = curve_apply(d, curve, values, data_decomposition)
r = size(d,1);
pivot = pivotize(data... |
222d97171a2ba88f6afe790e3a401b1c88d6e52916501f6c5bd43abfbc991502 | MATLAB | 3,259 | 96 | function vl_plotss(ss, varargin)
% VL_PLOTSS Plot scale space
% VL_PLOTSS(SS) plots the scale space SS. SS is a structure
% with the following members:
%
% ss.firstOctave::
% The index of the first octave in the scale space.
%
% ss.lastOctave::
% The index of the last octave in the scale space.
%
% ss... |
5da65af5d06ff5fd532394fc1c11d346a2c33a2857ad0576dde183d0e5081338 | MATLAB | 3,259 | 101 | % getFANCcontributions.m
%
% Function to read in output of csvFancChangeLog function (in R), to get
% user contributions to all neurons in specified folder. Each neuron is a
% single CSV file
% Returns table of users, user affiliations, user IDs, number of edits,
% number of neurons
%
% INPUTS:
% changeLogFolderP... |
93a4affb6a0ec15039b5043ff1817bedabbbab5a04d6994688bbbbcc8040513b | MATLAB | 3,259 | 93 | function [state, B, A] = denss(X_or_state, parameters)
% Main DSS algorithm
% [state, B, A] = denss(X or state)
% [state, B, A] = denss(X or state, [params])
% [state, B, A] = denss(X or state, {param1, 'value1', param2, 'value2', ...})
% X Mixed signals
% state Existing or new algorithm s... |
f83474d947a54f11547e159e1ce3361e5b12c2fc9ddf40d7b3121989a41adaa4 | MATLAB | 3,259 | 95 | % getAlignedLegXYfromBouts.m
%
% Helper function for saveLegStepParamCond_bouts() that takes in indices of
% yaw velocity peaks (peak, start, and end) and returns the leg X and Y
% positions aligned to the velocity peak
% To allow averaging over different bouts and the inconsistent frame rate,
% interpolate to speci... |
fe2a832b61e0b725b6277397d36d7bd93ca3b0afe41c26ee32bcddbceb6486e6 | MATLAB | 3,260 | 108 | %firws() - Designs windowed sinc type I linear phase FIR filter
%
% Usage:
% >> b = firws(m, f);
% >> b = firws(m, f, w);
% >> b = firws(m, f, t);
% >> b = firws(m, f, t, w);
%
% Inputs:
% m - filter order (mandatory even)
% f - vector or scalar of cutoff frequency/ies (-6 dB;
% pi rad / sample)
%
% O... |
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