sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5698a32b7dfcc8903bba42e86ec5b49d552eecdd13d9dc9308a09eca64da7ef4 | MATLAB | 9,528 | 448 | function [dat] = read_neuralynx_sdma(dataset, begsample, endsample, chanindx);
% READ_NEURALYNX_SDMA read specified channels and samples from a Neuralynx splitted DMA dataset
%
% Use as
% [hdr] = read_neuralynx_sdma(dataset)
% [dat] = read_neuralynx_sdma(dataset, begsample, endsample, chanindx)
%
% The splitted ... |
cf809955db33c337a6e385c688e7af2e7a042b57a1db84e36982d4df5225be91 | MATLAB | 9,531 | 343 | %figS4_eval_synthetic_highFR.m
%
%%
clear all;
close all;
clc;
%% addpath if not added yet
% assumes script run within local directory
scriptdirs = {pwd;
'..\..\plot';
'..\..\helper_functions';
'..\..\analyze';
};
addpath(scriptdirs{:})
datadir = pwd;
nSS = 1000;
ssfile = 'subsample1000_highFR_stdRP.mat';
sspath = f... |
37e6dd8095d0709d905d7923c9242a68219bcfe86b284dd4a8ed267155a849a6 | MATLAB | 9,533 | 260 | function convertUG_BIDS_2021_pmod_debug(subj)
maindir = pwd;
usedir = '/data/projects/istart-data/';
%try
% 11-18-21 | This is the code I am using for the bids converter.
% Plan now is to use the BIDs converter for only the simple regressors. Ie:
% Export the endowments (cue onsets) and the decision phases
% (accep... |
1c1aeb86f6ac73e9e70d7e013b21bb3ec55aac237ffa1dce7c8de04d92049f52 | MATLAB | 9,538 | 261 | function convertUG_BIDS_2021_pmod(subj)
maindir = pwd;
usedir = '/data/projects/istart-data/';
%try
% 11-18-21 | This is the code I am using for the bids converter.
% Plan now is to use the BIDs converter for only the simple regressors. Ie:
% Export the endowments (cue onsets) and the decision phases
% (accept/reje... |
84a055d2e0f8eec602b23eb7d6707a5cb3aa5c55ba4390cc14c6f6a674742809 | MATLAB | 9,538 | 374 |
% This configuration here (gen_net_opts_model_type2.m) applies random sampling for epoch construction and image crop generation.
% This setting doesn't require the classification information, like the class statistics for each image.
% In contrast, the configuration in file gen_net_opts_model_type1.m uses class val... |
ac76c935ac423320f9680184b90e9613e29c9a17ff5a0e87ba5e4bfe04cf7e85 | MATLAB | 9,540 | 262 | function output = analyze_network(G, option)
%analyze_network takes in a network and outputs standard graph analyses
% Usage: output = analyze_network(G,option)
% options: 'local','global','both'
if ~exist('option','var')
option = 'both';
end
[n, m] = size(G);
if n ~= m
error('Input matrix mu... |
2d6646488c34a0a158c1d1b62a0b7358b30ef6f3edf2359024a7ebf7a29be18b | MATLAB | 9,546 | 215 | function write_plexon_nex(filename, nex)
% WRITE_PLEXON_NEX writes a Plexon *.nex file, which is a file
% containing action-potential (spike) timestamps and waveforms (spike
% channels), event timestamps (event channels), and continuous variable
% data (continuous A/D channels).
%
% Use as
% write_plexon_nex(filenam... |
4f934c74733e9d21a8e911704934f099b76e59d39a43e92a57771790cd22a72d | MATLAB | 9,546 | 206 |
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; % half plane window,... |
5ac2f99d51249361030855ad4c749ba04297094afa5de80fbfdaa8343cdad875 | MATLAB | 9,558 | 331 | function [omitH, omitCenters, eye_pos_filt, eye_vel_pfilt] = desaccadeVel3(eye_pos_raw, samplerate, presaccade, postsaccade, freq, params, fit1)
% REMOVE TRANSIENTS
transient_threshold = params.transientThreshold;
eye_pos_raw = removeTransients(eye_pos_raw, transient_threshold);
% LOW PASS ON POSITION
N = 4;
fc = para... |
d2eb2000a7152287338171f1e800cc15854d18fcc76933ac26624afbe2e60ae2 | MATLAB | 9,560 | 256 | % runEphysExpt.m
%
% Top level function for running electrophysiology experiments on the
% updated 2P deux two-photon scope.
% Sets up folder structure for organizing data (date/fly/cell),
% prompts whether this is new cell or additional trial(s) for cell. For
% new cell, prompts for experimental condition, asks ... |
cbc7ea85e4738a13c0d03bb57795994caf6494ee4d51913845df907ed5d33201 | MATLAB | 9,561 | 258 | function getSpikesStepComboPhase_cell(cond, tDelay, numPhaseBins, ...
postStimExclDur, pDataPath, pDataFNames, saveFileName, saveFileDir)
% preallocate matrices for binning spikes and phase
numDelays = length(tDelay);
spikeCounts = zeros(numDelays, numPhaseBins);
phaseCounts = zeros(numDelays, numP... |
e9a86364a23a0170178df07433d4161eb98e83000c17f7de3027458b993b0616 | MATLAB | 9,582 | 258 | function [SMVdata, background] = iRSHARPv1(phaseMap, wrap_raw, mask, Params, handles)
% =========================================================================================
% function [SMVdata, background] = iRSHARPv1(phaseMap, wrap_raw, mask, Params, handles)
%
% Inputs:
% phaseMap - unwrapped pha... |
337f6cc6777fbecf0cd8f3c4a6d970032cd0c336dccaf44347b42e82a9b20408 | MATLAB | 9,588 | 292 | function [animal_facing_angle_deg] = ml_clean_headdirection_data(animal_facing_angle_deg, animal_pos_t_mus, showFigures)
animal_pos_t_s = animal_pos_t_mus ./ 10^6;
animal_pos_t_s = animal_pos_t_s - animal_pos_t_s(1);
if showFigures
figure
plot(animal_pos_t_s, animal_facing_angle_deg, 'k.-')... |
a68c281ae10938a30dffc22e00cdee1d9360199bc66ad7d26a19d3ddb49520b4 | MATLAB | 9,591 | 225 | %{
Provides comparison of various filtering on learned component traces.
INSTRUCTIONS:
1. Set "Current Folder" to the one containing the excel file.
2. Ensure data is in the first sheet, with "time" as the last column.
3. Modify the five variables below as needed.
4. Run script.
Generates figures displaying raw a... |
911a54b1b6cf80c4eff99a297b112874e9c4f9cee75156ad7a0ced6a45589c79 | MATLAB | 9,592 | 194 | function plot_individual_worm_videos_post_analysis_function_1(main_folder,output_video_frame_rate,save_excel_file,path_history,demo_mode,parameters,count_number_of_reversal_trial_rails,count_number_of_reversal_trial_turns,stimulus_intensities,test_stimulus_duration,current_tracks,fps,behavior_colors,stim_color)
close ... |
c880b485d49ae2973415486604f099d2766c5f6b7170a9a2c9da7f1dbbe8863a | MATLAB | 9,597 | 196 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: OptoDoseResponse_PooledOverall_2023
% Cohort: PFC dLight1.3b with opto
% May 2023 - Marie Labouesse, marie.labouesse@gmail.com
% 1- POOLED GRAPHS AND MEASUREMENTS
% loads FP data previously analyzed (with: OptoDoseResponse_DataExtraction then Op... |
8f1abcf4d74f1b3af7c8c017a089e7ba49075be81c27f130ddc2b9ec91d0312e | MATLAB | 9,609 | 254 | %script MatAFNI_Demo
%
%
%
%Purpose:
% Demonstrate the use of the matlab AFNI library
% The script is echoed onto the screen but it is best
% you read through it with a text editor.
%
%
%Input:
% You must have the data sets
% ARzs_CW_avvr+orig, ARzs_CW_avvr.DEL+orig and ARzsspgrax+orig
% in the worki... |
1e34646f7e3cedec0c566744dca9c2d6d9a075e02ce20dc27ae4b54065ae1f86 | MATLAB | 9,618 | 237 | function [nev] = read_neuralynx_nev(filename, varargin);
% READ_NEURALYNX_NEV reads the event information from the *.nev file in a
% Neuralynx dataset directory
%
% Use as
% nev = read_neuralynx_hdr(datadir, ...)
% nev = read_neuralynx_hdr(eventfile, ...)
%
% Optional input arguments should be specified in key-val... |
7ddf8adc972acde4cca3d9febd72f07bed69c12e05c9076f1b95c86dca4a36d5 | MATLAB | 9,630 | 210 |
%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... |
2dd10cf6dfd7f2b64945540644a3cc573584875771ff35abc54693a48debf0ae | MATLAB | 9,637 | 280 | % Fig.3 VIP Cells Analysis
% Run config.m
% Process data for each animal using the processAnimalData function
[psth, response, visI] = processAnimalData(cell_activity_allday, stim_type_allday, trials, nanimals, nstim_type, win, threshold, ngratings);
%% fig.3c - Plotting PSTH for VIP cells
% Define limits for the p... |
3c8569b3caa4a5dcab82660a830e44f838cf5d87df89d40175a52afbfdace099 | MATLAB | 9,637 | 220 | function varargout = motion_survival_plot(varargin)
% MOTION_SURVIVAL_PLOT MATLAB code for motion_survival_plot.fig
% MOTION_SURVIVAL_PLOT, by itself, creates a new MOTION_SURVIVAL_PLOT or raises the existing
% singleton*.
%
% H = MOTION_SURVIVAL_PLOT returns the handle to a new MOTION_SURVIVAL_PLOT or t... |
0db31f61e50ace03eca6ab02d8c3881575ae1f496f5587c81fc4a3739aed6e99 | MATLAB | 9,643 | 328 | %% Experiment 12: Noise Stability Ananlysis
%% Perturbation:
rng('shuffle','twister');
U_Scales_Noise = struct('scale',[],'noise_sigma',[],'UU_diag_SC_vs_SCnoisy_all',[],'all_combo_diagonals',[]);
d = 2.5e-4;
std_multiplier_list = 0:2.5e-4:0.05;
var_multiplier_list = std_multiplier_list.^2;
k_multiplie... |
34b0e935a2b3f0dd6159651ff98cf468b55a6fd7bc54b11fca9138b8798a249c | MATLAB | 9,643 | 222 | function plot_model(model_name,data,x,empirical_coeffs)
mouseNames = unique(data.mouseName);
nSims = 20;
% simulate the model with parameters x
switch model_name
case 'multi_trial_belief'
value_init = ones(2,4) * 0.2;
for iSim = 1:nSims
% loop... |
b616e6f969e8bdd029c64f7d96118df232c7ab5e59ee1fa1c934ce49c74cd92f | MATLAB | 9,657 | 368 | clear all
close all
clc
%% Behavioral Data analysis
% 03/29/2020
% Daniel Sazhin
% This script takes a participant's responses and collapses them into a
% dollar amount for analysis.
% Update the subjects list with up-to-date subjects
maindir = 'C:\Users\danie\Documents\Github\istart\UGDG'; % set on computer doing... |
6dd230fb40b80ac39e89e42ee29bd2e875f0d8b6845b265778d7218aebb689a6 | MATLAB | 9,662 | 208 | % ==========================================================================
% script : MIBI_linearRegression
% --------------------------------------------------------------------------
% purpose : linear regression TSC and brain mask for quantification
% input : ROIs and postprocessed data
% out... |
ba320d00bc2bb49abafd74aed71d98d4e086040d4266fceae8415209408da5ee | MATLAB | 9,672 | 270 | function ellipse_t = fit_ellipse( x,y,axis_handle )
%
% fit_ellipse - finds the best fit to an ellipse for the given set of points.
%
% Format: ellipse_t = fit_ellipse( x,y,axis_handle )
%
% Input: x,y - a set of points in 2 column vectors. AT LEAST 5 points are needed !
% axis_handle - optional.... |
1e76566a847f04c73a1b67fb3213d1ad1e41f0a0bb050b608f42d458b56e6b09 | MATLAB | 9,674 | 255 | function [ellipse_t, rotated_ellipse] = fit_ellipse_altMethod( x,y,axis_handle )
%
% fit_ellipse - finds the best fit to an ellipse for the given set of points.
%
% Format: ellipse_t = fit_ellipse( x,y,axis_handle )
%
% Input: x,y - a set of points in 2 column vectors. AT LEAST 5 points are needed !
% ... |
9e1f2bfa6e39fb57a6387e0946b220836af89ccf6d6133eef27bc60878318dde | MATLAB | 9,678 | 260 | function [coords,direction,lifetime]=dotMotionFrame(coords,direction,lifetime,stimParams,timeSinceLastUpdate,displayParams);
% [coords,direction,lifetime]=dotMotionFrame(coords,direction,lifetime,stimParams,timeSinceLastUpdate,displayParams);
%
% Displaces input device coordinates coords corresponding to one motion fr... |
43358007fd79bd48df9e78afc5c53dabaacfd77b43c6299cab5076c399706ae5 | MATLAB | 9,685 | 204 | function make_no_autocorrelation_env(handles)
%% Internal variables
fs=filesep;
env_folder=[handles.env.path_gagui fs ...,
handles.env.name{2} fs,...
handles.func_data_name fs,...
handles.env.group];
if ~isfolder(env_folder)
mkdir(env_folder);
end
change_permissions(handles,env_folder)
n_parcel=length(... |
17b36a99bfa23dfa334a44c959815a79ad41e4cd926af23f080e6dd79f2e11b7 | MATLAB | 9,689 | 260 | function [assignment, cost] = assignmentoptimal(distMatrix)
%ASSIGNMENTOPTIMAL Compute optimal assignment by Munkres algorithm
% ASSIGNMENTOPTIMAL(DISTMATRIX) computes the optimal assignment (minimum
% overall costs) for the given rectangular distance or cost matrix, for
% example the assignment of tracks (in... |
ad1a193cfc199da1d518db6470bb1a085fa71d3d62175a5d5c02efbbb5fdf414 | MATLAB | 9,690 | 208 | function compute_mcmappy_shrunk(obj, session, trial)
% Call this one for the maps using the actual geometry (like a
% rectangle).
%experimentDescriptionFilename = fullfile(obj.RecordingsParentFolder, 'experiment_description.json');
% cm_per_bin = obj.Config.placemaps.cm_per_bin_rect_both_dim;
% cm_... |
c126f049cdf04ce75dc72415fa093dd5f24636f8db4da32a41f8c18e60a98b2a | MATLAB | 9,697 | 229 | function run = nirs_preprocessing(run)
% NIRS_PREPROCESSING
% This function performs the preprocessing steps on the fNIRS data
%
% INPUT:
% - run: matlab structure containing the raw nirs & motion data of each run
%
% OUTPUT:
% - run: same as input, but with the preprocessed data in the field
% run.data_nirs.data_prepr... |
734cce5ac1c6ff98f2c2c7cd45ce6c0f05d989bae30a37b1d8ce34515c9ec72e | MATLAB | 9,706 | 274 | % processLegTrack.m
%
% Call this function to process leg tracking data output from APT
%
% Takes .trk file output from APT and returns processed leg tracking data.
% Leg positions, velocities, step parameters
%
% NOTE: work in progress as additional analyses added
%
% INPUTS:
% none, but GUI prompts throughout
%
% ... |
e74797de6e4dbe0e4080d760e7f1f714db92575a9b1b812feb40c3efa7743783 | MATLAB | 9,722 | 271 | function data = LoadBinary(filename,varargin)
%LoadBinary - Load data from a multiplexed binary file.
%
% Reading a subset of the data can be done in two different manners: either
% by specifying start time and duration (more intuitive), or by indicating
% the position and size of the subset in terms of number of r... |
e350a92dd7ef73d0d4a70d20a69a92a9de0a37781118bb4eda40b6b09ef508b1 | MATLAB | 9,727 | 190 | % mglDigIO.m
%
% $Id: mglDigIO.m 438 2009-01-30 04:46:05Z justin $
% usage: mglDigIO(command,<arg1>,<arg2>)
% by: justin gardner
% date: 06/30/09
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: This is a mac specific command that is used to control a NI... |
aa26559e96ff900cb8cb3dcf34613bcc6f24faf751fe36dd03e1eb65e3674338 | MATLAB | 9,729 | 237 | function [perCell, total] = mltp_compute_bfo_general_placey(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
% Allo... |
0f8bbf21ea23473a37abb161e368ac4b8dc62de2482d7843feab2f7d3ebdf7b6 | MATLAB | 9,730 | 252 | % p_HFOWaitFigure
function st_output = p_HFOWaitFigure(st_intput,pstr_Field,pFieldValue)
if nargin ~= 0
if nargin == 3
f_WriteFields(st_intput,pstr_Field,pFieldValue)
else
error('p_HFOWaitFigure:argChk','Wrong number of input arguments');
end
return
end
%% Variables
% Figure Background ... |
aba753f026c5334861013dddf8171faf6f6dc2546a22b8fd5138730351062fd6 | MATLAB | 9,730 | 376 |
function group_output_info=gen_network_refine_group(train_opts, net_config, group_input_info)
multi_refinenets_group_info=My_net_util.gen_group_info_basic(net_config, 'refinenets');
layers=cell(0);
[one_layers, net_input_info]=gen_input_path_merge_net(train_opts, group_input_info);
layers=cat(2, layers, one_... |
dcf40252a60dc4cd9521db7375aff06c2c177467b2406709d823a2d65a2ea72b | MATLAB | 9,737 | 264 | % saveContLegStepParamCond_indpt.m
%
% Function that saves continuous leg step parameters for all steps that
% meet the user specified conditions on bodytraj
% Treats all time points as independent, as long as bodytraj condition(s)
% are met, unlike saveContLegStepParamCond_bouts.m
% Modification of saveLegStepParam... |
be85172d4d5c19b6ef18df3748d8e1ed24bf98c3eb4aefc44c1e3f62f0942bab | MATLAB | 9,744 | 370 | clear all
close all
clc
%% Behavioral Data analysis
% 01/16/2022
% Daniel Sazhin
% This script takes a participant's responses and collapses them into a
% dollar amount for analysis.
% This script is to deal with two subjects with different input folders.
% Update the subjects list with up-to-date subjects
maindi... |
5754fdbbdae93d6731a9a618d6cd0f8622275b3071ed956a2fc4e5a459ce520b | MATLAB | 9,754 | 332 | function []= report_events_parameters (ds_events,ds,nparams,specify)
%% UNPACK STRUCTURE
all_mchw=[];
all_mchws=[];
all_mchwe=[];
all_mchp=[];
all_mcho=[];
all_tdtw=[];
all_tdtws=[];
all_tdtwe=[];
all_tdtp=[];
all_tdto=[];
n_mch_events=[];
n_tdt_events=[];
%% MAKE TITLE STRINGS
params=ds_events.params;
nparams=... |
d97591ba0b89264a7bb047e89852e3cea761d762c22ce3b772b941d50b23048f | MATLAB | 9,756 | 263 | function fout = waitbar(x,whichbar, varargin)
% Updated to support scProgressBar in sigTOOL
%
%WAITBAR Display wait bar.
% H = WAITBAR(X,'title', property, value, property, value, ...)
% creates and displays a waitbar of fractional length X. The
% handle to the waitbar figure is returned in H.
% X should be be... |
c1846cb76a15bf87d4ca73c936465d2d768403d62f9512a6c0d9fed0abfa4c25 | MATLAB | 9,757 | 251 | function [h, coordsys] = ft_headcoordinates(fid1, fid2, fid3, fid4, coordsys)
% FT_HEADCOORDINATES returns the homogeneous coordinate transformation matrix
% that converts the specified fiducials in any coordinate system (e.g. MRI)
% into the rotated and translated headcoordinate system.
%
% Use as
% [h, coordsys] =... |
14df97d21f9e8fcb703cd9391feecfe3a9e9a38123496642504ce58a934f3d66 | MATLAB | 9,769 | 217 | clear all
close all
%% Parameter initialization
run('spiking_parameters_simple_dopa_m_c.m') %most parameters are stored in this file
plot_var = 1;
%% main program
Ach = zeros(1,t_total/dt + dt);
for l = 1:num_trials
tic
%% initialization
[v_it,v_kt] = deal(zeros(N,1)+v_rest); %membrane potentials
... |
7ba113e52176eaf6b70cf8846ebaf6a7fc1b0b9a93f723c5baaa5b4befcc4cd6 | MATLAB | 9,774 | 258 | % This is a mesh processor script: it computes basis triangle parameters
% and necessary potential integrals, and constructs a combined mesh of a
% multi-object structure (for example, a head or a whole body)
%
% Copyright SNM/WAW 2017-2020
%clear all %#ok<CLALL>
% set tissue_dim <---
[~,name,~]=fileparts(pwd... |
44a09dcdffb4b3f07f7ac5877d2af3e5095995593851b5f89ebc06efc086b1e0 | MATLAB | 9,788 | 418 | %
% Perform curve fitting.
%
% PARAMETERS
% $NETWORK
% $DECOMPOSITION
%
% INPUT
% dat/info.$NETWORK
% dat/decomposition_split.source.$DECOMPOSITION.$NETWORK.mat
% dat/split.$NETWORK.mat
% dat/means.$NETWORK.mat
%
% OUTPUT
% dat/fit.$DECOMPOSITION.$NETWORK.mat
% curves Struct by name of curve of parameters in colu... |
dcb522a401909a82a9d8f51b4040b8315a1a5a28fe5437976cc06dee8e30eb7e | MATLAB | 9,789 | 248 | % mglMovie.m
%
% $Id: mglMovie.m,v 1.1 2007/10/23 22:21:23 justin Exp $
% usage: movieStruct = mglMovie(filename,position) or mglMovie(movieStruct,command,<argument>);
% by: justin gardner
% date: 12/23/08
% purpose: Used to display quicktime movies. This *only* works on 64 bit mac for now.... |
b90d12a8767296b0d16a5272b46863c94d13d5955636083968e76c048cb84ae4 | MATLAB | 9,797 | 257 | function [hdr, record] = edfread(fname, varargin)
% Read European Data Format file into MATLAB
%
% [hdr, record] = edfread(fname)
% Reads data from ALL RECORDS of file fname ('*.edf'). Header
% information is returned in structure hdr, and the signals
% (waveforms) are returned in structure reco... |
77c369ae65661255d916b775e0003efa9cf365f7a3e8b2faff21ebbab33e8d28 | MATLAB | 9,799 | 190 | classdef MLExperimentBuilder < handle
properties (Constant)
ExperimentDescriptionFilename = 'experiment_description.json';
SessionRecordFilename = 'session_record.json';
end % properties
methods (Static)
%%
function [experiment] = buildFromJson(config, sessionsP... |
7976a39dbaa7228417fe4d0b98e2f18990be6bf58d91003238284fe00aa855d0 | MATLAB | 9,802 | 311 | function theAxis = scrollsubplot(nrows, ncols, thisPlot)
%SCROLLSUBPLOT Create axes in tiled positions.
% SCROLLSUBPLOT(m,n,p), breaks the Figure window into
% an m-by-n matrix of small axes, selects the p-th axes for
% for the current plot, and returns the axis handle. The axes
% are counted along the top r... |
e56d527acbfb1fd0b228d0af64c9c302e71bf44da9a4cf2807362091e81993f2 | MATLAB | 9,802 | 205 | function [] = PlotDirectionalBehavioralMappingExperimentGroup (LNPStats, meanLEDPower, stdLEDPower, L, density, xx)
%Takes in structure LNPStats and plots them depending on the settings
fps = 14;
BTA_seconds_before_and_after = 10;
BTA_seconds_before = BTA_seconds_before_and_after;
BTA_seconds_after = BT... |
2aa927489651a21da8068f9582257b18f639f8a9eda8a3f4d97b8009b3a19185 | MATLAB | 9,818 | 114 | function [ opt ] = internal_parameters( opt )
% *-* 25.11.2019: the'internal_paramters.m' script was converted to a
% function
%% This function performs SPATIAL TEMPLATE MATCHING for CaT detection.
% ---------------------------------------------------------------------------
% Internal_parameters
%
% This scrip... |
3a20a32d3da9b6da308da04b7739541109afd498f7082c49a19cb0eda45c17f0 | MATLAB | 9,819 | 151 | clc, clear
% ------------------------------------------------------------------------
% Human batch options that can be changed in the GUI or here directly
% ------------------------------------------------------------------------
% set the number of cores for parallel processing
try
numcores = max(cat_get_defaul... |
67b7ab921686a64b840af218fba86bc20277cc47968b36b640797a75175e57db | MATLAB | 9,824 | 275 | function freezeColors(varargin)
% freezeColors Lock colors of plot, enabling multiple colormaps per figure. (v2.3)
%
% Problem: There is only one colormap per figure. This function provides
% an easy solution when plots using different colomaps are desired
% in the same figure.
%
% freezeColors freeze... |
cc66740241852995cc088a2c403508745847db3ea4e6509ce07b994ddd22bb4f | MATLAB | 9,834 | 210 |
showfigs = 1;
%% Define all three planes (m)
X = 1e-6; % YZ Cross-section position, m
Y = 1e-6; % XZ Cross-section position, m
Z = 0.5e-3 + 200e-6; % XY Cross-section position, m
delta = 3e-3; %1.6e-2; % ... |
9a4d1d724f6543d94976a5612f8d3ccf5645eff041286b16c0b96920f6a98162 | MATLAB | 9,835 | 278 | function h = plotLFPTrendLogs( obj, varargin )
% Plot LFP band power and stimulation amplitude accross time from LFPTrendLogs
% works as an auxiliar method to the extractTrendLogs.
%
% Syntax:
% h = PLOTLFPTRENDLOGS( obj, ax );
%
% Input parameters:
% * obj - object containg data
% * ax (optional) - axis where ... |
f0309cc4e8cf0569afd1c90e22d11397fa9633869c2ae63706519766adeedcab | MATLAB | 9,841 | 308 | % upDownStaircase.m
%
% $Id$
% usage: upDownStaircase(nup,ndown,initialThreshold,stepsize,<stepRule=0>)
% by: justin gardner
% date: 06/20/05
% copyright: (c) 2006 Justin Gardner (GPL see mgl/COPYING)
% purpose: implements a upDownStaircasecase
%
% e.g.: to start a 1up-3down upDown... |
dd3b8289dd2578a0c00183ab7faae29c328062fa67eb776076210f68513c0ff0 | MATLAB | 9,857 | 280 | function [dat] = read_neuralynx_dma(filename, begsample, endsample, channel)
% READ_NEURALYNX_DMA reads specified samples and channels data from a Neuralynx DMA log file
%
% Use as
% [hdr] = read_neuralynx_dma(filename)
% [dat] = read_neuralynx_dma(filename, begsample, endsample)
% [dat] = read_neuralynx_dma(... |
2e4997d1d506e354a7d0ef3d48b940cdb0d9d35638ab3c5358bcff062be7faea | MATLAB | 9,863 | 278 | function HDR=bv2biosig_events(EVENT)
% BV2BIOSIG_EVENTS converts VMRK marker information BioSig Event codes.
% according to biosig/doc/eventcodes.txt.
% Currently, the convention of the BerlinBCI is implemented and supported.
%
% HDR = bv2biosig_events(arg1)
%
% arg1 can be an HDR-struct containg HDR.EVENT.D... |
4b2a8078dfaf67f48e689f2f908207a0996f66f91a9a1f57ea808ca004806fa4 | MATLAB | 9,869 | 238 | % stats_grid_memory (data_dir, read_from_excel, show_plots)
% this function prints stats into the console and
% generates some figures
%
% INPUTS:
% data_dir (str): path to source data
% read_from_excel (bool): load data from .xlsx? (as opposed to .mat)
% show_plots (bool): visible plots?
%
% Mackay... |
ae839fd512fb770c90ebf70c14c78d25970b3eb8b86d21748ccf2b8c5ee92931 | MATLAB | 9,870 | 188 | % f_GetIcons.m [As a part of HFO Detection Project]
% Written by:
% Miguel G. Navarrete Mejia
% Electrical Engineering MS candidate
% UNIVERSIDAD DE LOS ANDES
% Colombia, 2012
% mnavarretem@gmail.com
function st_Icons = f_GetIcons
[m_icon,m_map] = imread('./Icons/open.gif');
m_map(find(m_map(:,1)+m... |
7ea203ab2fb2e9c59b5934b4990c2cf4249fd07a8704af68e6de460aaf6d18c7 | MATLAB | 9,896 | 313 | function saveastiff(data, path, options)
% options.color
% : true or FALSE
% : If this is true, third dimension should be 3 and the data is saved as a color image.
% options.comp
% : 'no', 'lzw', 'jpeg' or 'adobe'.
% Compression type.
% 'no' : Uncompressed(Default)
% 'lzw' : lossless LZW
% ... |
883c39fc07c4df2ab8fb9669b35cd2649494c6ba291e44d21e14a06db400eabe | MATLAB | 9,905 | 267 | % plotLegStepsHist.m
%
% Function that plots histograms of leg step parameters. Multiple
% histograms per figure, by specified conditions (iInj or opto).
% Works on multiple pData files. Select through GUI. Should be for 1 fly.
%
% INPUTS:
% whichParam - which parameter to plot, as string; must match field of
% ... |
94036b98a98750388e7955683792d0e526960a54e93b58c27ad4c7d4840d1eba | MATLAB | 9,909 | 261 | % This is a mesh processor script: it computes basis triangle parameters
% and necessary potential integrals, and constructs a combined mesh of a
% multi-object structure (for example, a head or a whole body)
%
% Copyright SNM/WAW 2017-2020
%clear all %#ok<CLALL>
[~,name,~]=fileparts(pwd); L = length(name)+1;
i... |
fd6e8a8a8e9c2eca71aa87d35bb2934ae55ac2726b1b53616549971de7d7b280 | MATLAB | 9,960 | 262 | % plotAEPPEPbyFictrac.m
%
% Function to plot mean and standard deviation of leg AEPs or PEPs (user
% specified), colored by values of a FicTrac variable (yaw, forward, or
% lateral velocity; user specified).
% User specifies number of bins in which to divide the FicTrac variable or
% the edges of the bins. If num... |
67e14d80383bdb55f0d03ab15d210f86c72ccb7496ba7a3dee1d9b1c99aec722 | MATLAB | 9,961 | 329 | clear all
close all
clc
%% Before you run any code
% The script implements many of the analyses from Tanner et al. That
% manuscript contributes a simple method for estimating weights on
% already-defined edges in a structural connectome. Specifically, we use
% linear regression to explain the future activity of node... |
69901826f47b2d5fe22c0efb140fec405fb4934c243371c86a1c3189ec0c9726 | MATLAB | 9,967 | 221 | function plotCrossCorrVar( obj, varargin )
% PLOTCROSSCORRVAR Plot cross-correlation and cross-variance for LFP online streaming mode
%
% Syntax:
% PLOTCROSSCORRVAR( obj, varargin );
%
% Input parameters:
% * obj - object containg data
% * ax (optional) - axis where you want to plot
% * data_type (optional)... |
88f2135e54b5eac1ba297a40842c91092768b3bc2f6e8844737c553ac1ae596e | MATLAB | 9,969 | 266 | % This project is a general project to perform the analysis
% on a general experiment (nothing too specific).
% It will make placemaps, and perform correleations.
close all
clear all
clc
tstart = tic;
% Don't change these
projectCfgFilename = fullfile(pwd, 'project_config.json');
pipeCfgFilename = fullfile(pwd, 'pip... |
95edac6d2a3ba3177d0dc866b68f6ed6276a1e136032f3d199774f0a9ef27a70 | MATLAB | 9,983 | 218 | clear all; close all;
RUNSIMPLE = 1;
SAMPLETIME = 40; % ms
zeroIdx = 21; %101;
binEdges = -20.5:1:20.5; %-100.5:1:100.5;
load ('Alon_maxCorrValAndIdx_normalized_multi_minAndMax.mat');
% maxCorrIdx
% vStim
% vTrial
% do2Stim
% do2Trial
binCenters = binEdges(1:end-1)+floor(mean(diff(binEdges)... |
fac0bf1e496a17fcc7f293a25e8adda801f386caaa3cd94c84e3df29269fc431 | MATLAB | 9,987 | 349 | %% Script to visualize functional projection of eigenmode regimes
% Necessary for Ternary Plot:
addpath ternary_plots/data_plots/
addpath ternary_plots/axes_creation/
addpath ternary_plots/utilities/
%% Projection Analysis:
scale = 200;
filename = sprintf('MICA_schaefer%d_SCFC_struct.mat',scale);
load(f... |
fc53e4121175134b8e576f7729c687ffe63c741572a8569a00af38777b59c1d5 | MATLAB | 9,992 | 177 | function [] = C2_ROISelection_RFT(badSubs,ROI_num)
% ROI analysis -> Calculates ROI for RFT based on grand average
%inputs:
% badSubs: subjects you want to reject
% ROI_num: number of sensors to constitute the ROI for each side & config
%% Load clean MEG file
% data_folder='/rds/projects/j/jenseno-avtemporal-att... |
cab91365ffb7cecacb17d67fcef4348181380f6e2ff238ee1b07dee7ec6213b0 | MATLAB | 9,999 | 218 | %%% demo of the full MIN1PIPE %%%
clear
warning off
gcp;
% To disable parallel processing, change "parfor" to "for", and change "min1pipe_h5_vary_nopar" to "min1pipe_h5_vary"
% if isempty(gcp('nocreate'))
% parpool;
% end
min1pipe_init;
addpath(genpath('../ANE'))
%% Set data and folder
patch_dims = [160,160];
li... |
dc0b567e293c2406d69d953cb1986bb27b6e02f8573815a84a0d686a68ba8887 | MATLAB | 10,003 | 285 | function [spike] = ft_read_spike(filename, varargin)
% FT_READ_SPIKE reads spike timestamps and waveforms from various data
% formats.
%
% Use as
% [spike] = ft_read_spike(filename, ...)
%
% Additional options should be specified in key-value pairs and can be
% 'spikeformat' = string, described the fileformat (defa... |
74658c2d0d8aa3b68798c7fa8c4ebcb05a99f26731b38523d5d658ca592f73ef | MATLAB | 10,009 | 206 | %% FOG_EVENTS
% Analyzes the FOG events and provides descriptional statistics of the
% observed FOG events
%
% INPUT:
% - *run.mat files (contains all events)
%
% OUTPUT:
% - descriptional statistics in the command window
% - plots of the descriptional statistics
% - FOG_events_all.mat: table of all events of all part... |
cf71426ea1e89bd3e43085985b393b97c2fa4feae24a2e0f05e08936a4448728 | MATLAB | 10,013 | 362 | %
% Draw a plot that tests whether a given vector of numbers follows a
% specific distribution, i.e., a Q-Q plot between the given data and
% a known distribution.
%
% PARAMETERS
% type String representing the type of distribution that is
% tested against; see below for possible values
% x The vector of values
% no_... |
33194d7001e13b6387d55e5e63bb73f76b02beaf3e1a1aa0c563fce88d700b0e | MATLAB | 10,019 | 263 | function fout = waitbar(x,whichbar, varargin)
% Updated to support scProgressBar in sigTOOL
%
%WAITBAR Display wait bar.
% H = WAITBAR(X,'title', property, value, property, value, ...)
% creates and displays a waitbar of fractional length X. The
% handle to the waitbar figure is returned in H.
% X shoul... |
d6c1d7a7cad01043066a371c08e047ae24fa61905a0f6d63fb92eb6fe00c22e9 | MATLAB | 10,036 | 240 | function gretna_Vol_ROI_signal(Data_path, File_filter, Template_path, Template_filter, RoiIndex, Output_path, Level, Num_thres)
%==========================================================================
% This function is used to extract signals for each voxel within each ROI.
%
%
% Syntax: function gretna_Vol_ROI_si... |
01c957e26b1e1defd11398255d5dafe00fd3fde13ba9461eb63fb58346748519 | MATLAB | 10,039 | 175 | function varargout = times_from_profs(mov, NeurProf, lambda, varargin)
% [x_est, x_bg] = times_from_profs(mov, NeurProf, lambda, {BGprofs, batch_size, bin_mask})
%
% Find time traces from ROIs and a movie. This function uses the TFOCS
% library to find ROIs and time traces using either non-negative least
% squares, ... |
65e214e9b7718aab36305cd3c1a8aa6abe08b55d989e5acf75fae4575c29e124 | MATLAB | 10,041 | 177 | % s_selectAndSaveCSTfixPredictionsMatchingVoxels.m
projectDir = fullfile(simseqRootPath);
baseDir = fullfile(simseqRootPath,'simseq/results/');
subDir = 'preprocData_stRet_matchingVoxels_1ch-glm';
subSaveFolder = 'savedPredictions_fixedPRF_combT';
fitName = {'gridFit2','stRet','stRet'};
betaFolder = 'be... |
822f359a056856f168f589599fbbffde6e1eb7ac139af904c81db608c8f1719e | MATLAB | 10,071 | 183 | classdef Units < types.hdmf_common.DynamicTable & types.untyped.GroupClass
% UNITS Data about spiking units. Event times of observed units (e.g. cell, synapse, etc.) should be concatenated and stored in spike_times.
% OPTIONAL PROPERTIES
properties
electrode_group; % (VectorData) Electrode group that each spike ... |
3eac1ff15f4749e187f416bc6360ebc761bb45af41829eb58cdf22a929cbe56d | MATLAB | 10,092 | 219 | %%% demo of the full MIN1PIPE %%%
clear
warning off
gcp;
% To disable parallel processing, change "parfor" to "for", and change "min1pipe_h5_vary_nopar" to "min1pipe_h5_vary"
% if isempty(gcp('nocreate'))
% parpool;
% end
min1pipe_init;
addpath(genpath('../ANE'))
%% Set data and folder
patch_dims = [160,160];
li... |
744451e76d5bad16b1e00db8774fbf5971e6c3ded14f4a710ad122be6cc75e17 | MATLAB | 10,095 | 273 | function mltp_plot_rate_difference_matrices(obj, session)
mltp_plot_rate_difference_matrices_helper(obj, session, 'peakFiringRate', 'PFRS', false)
mltp_plot_rate_difference_matrices_helper(obj, session, 'meanFiringRate', 'MFR', true)
mltp_plot_rate_difference_matrices_helper(obj, session, 'informationRate', 'IC', fals... |
192697055fe36c746e1bdf9fc1ef75dc94dfa86370130adf5ca04d4096e452bc | MATLAB | 10,098 | 290 | function convertUG_BIDS_2021_debug(subj)
maindir = pwd;
usedir = '/data/projects/istart-data/';
%try
% 11-18-21 | This is the code I am using for the bids converter.
% Plan now is to use the BIDs converter for only the simple regressors. Ie:
% Export the endowments (cue onsets) and the decision phases
% (accept/rej... |
d9011893522c1c0160e79ae0149db515d2871977e2552cf848925d5bee5bac25 | MATLAB | 10,113 | 265 | function [tpr,tnr,info] = vl_roc(labels, scores, varargin)
%VL_ROC ROC curve.
% [TPR,TNR] = VL_ROC(LABELS, SCORES) computes the Receiver Operating
% Characteristic (ROC) curve [1]. LABELS is a row vector of ground
% truth labels, greater than zero for a positive sample and smaller
% than zero for a negative o... |
2e9adbffdbc7f6e1d997002baa5321bb764842ce81567686d566e2c07b73a3f4 | MATLAB | 10,115 | 226 | %Output results of Mass Univariate Toolbox t-test to a spreadsheet.
%
%EXAMPLE USAGE
% >> ttest2xls(GND, 1, 'results.xslx')
%
%REQUIRED INPUTS
% GND - A GND variable with t-test results
% test_id - The test number within the t_tests field of the GND
% struct
% output_fname ... |
2e3f21c0a2ed571f0a2cc9318cb76f8f6a7a9e32632494f85973c930fc1ea998 | MATLAB | 10,116 | 255 | function [HZmvntest,P] = HZmvntest(X,c,alpha)
%HZMVNTEST. Henze-Zirkler's Multivariate Normality Test.
% Henze and Zirkler (1990) introduce a multivariate version of the univariate
% There are many tests for assessing the multivariate normality in the
% statistical literature (Mecklin and Mundfrom, 2003). Unfortunatel... |
cf72eb010b59c9bf2d8cbf9bf77f8d9c121d2949aab53518676fe534a1fb4dad | MATLAB | 10,117 | 272 | % multiLinRegEphysFTContParam.m
%
% Function to perform multiple linear regression where an ephys parameter
% is the independent variable and FicTrac and continuous step parameters
% are the dependent variables. Specifically, dependent variables are one
% FicTrac parameter and one or more continuous step parameters... |
8c64e6af95de65a0cf1922dbc4433ad8ed43d4fb11e82bd0820a52be241de441 | MATLAB | 10,133 | 277 | % Function f_EqualizerFreqFilter.m
%
% Description:
% This function performs a kind of spectral equalization by removing a
% polynomial tendency to the magnitude of the signal spectrum estimated via
% the FFT. The procedure changes the FFT magnitude but conserves the
% original phase.
%
% Inputs:
% pv_InSignal: input... |
fc28d25c6420baf0399ec98d736e9bab331d5c84c35809289a3bd73e14d4a03c | MATLAB | 10,150 | 223 | %%% demo of the full MIN1PIPE %%%
clear
warning off
gcp;
% To disable parallel processing, change "parfor" to "for", and change "min1pipe_h5_vary_nopar" to "min1pipe_h5_vary"
% if isempty(gcp('nocreate'))
% parpool;
% end
min1pipe_init;
addpath(genpath('../ANE'))
%% Set data and folder
scale_lowBG = 5e3;
scale_no... |
b584bae176da3b8a4b5b3daeafcc6894c7bcfa57fe95aa8e1a1023a0ffb0816e | MATLAB | 10,156 | 273 | % scatterMoveCondData.m
%
% Function to generate a scatterplot of movement conditioned data, the
% output of moveCondPairData().
% Specify data on x-axis and data on y-axis by field name. Can run for any
% combination of fictrac or imaging fields.
% Plots multiple flies either on same plot or on different plots
% Pl... |
8262b76e927d64f7f238120a69a0aa09aea137c57713f448cad6832518cbf9be | MATLAB | 10,161 | 239 | function varargout = resolve_problems_gui(varargin)
% RESOLVE_PROBLEMS_GUI MATLAB code for resolve_problems_gui.fig
% RESOLVE_PROBLEMS_GUI, by itself, creates a new RESOLVE_PROBLEMS_GUI or raises the existing
% singleton*.
%
% H = RESOLVE_PROBLEMS_GUI returns the handle to a new RESOLVE_PROBLEMS_GUI or t... |
c9e78dca3c086f0169276f64f70859c38d5cbb75f0728bed049037213be7c5ca | MATLAB | 10,167 | 258 | % getSpikesStepPhase_cell.m
%
% Function to get timing of spikes relative to leg step phase
% Bins spikes by phase during step cycle, then normalizes by time spent
% during each phase. Specify number of bins of phase, delay between
% behavior and ephys. Bins separately for each leg
% Can condition on behavioral param... |
eab6e3cc8f5b49412ddf36e005b78fecfa309ef808cb38a80cb867dd21ed0f02 | MATLAB | 10,168 | 222 | %%% demo of the full MIN1PIPE %%%
clear
warning off
gcp;
% To disable parallel processing, change "parfor" to "for", and change "min1pipe_h5_vary_nopar" to "min1pipe_h5_vary"
% if isempty(gcp('nocreate'))
% parpool;
% end
min1pipe_init;
addpath(genpath('../ANE'))
%% Set data and folder
patch_dims = [50,50];
list... |
e4d2ea4020eb2d42134d394c1dce3b01c8df449e4831f90a870256c9a48e1f3c | MATLAB | 10,180 | 283 | %% Script to plot (1) neurobiological similarity matrix,
%% (2) co-vulnerability to psychosis matrix, and (3) their correlation
% 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... |
ce3f843123fbc0c64a6e57736baf6d642a4045531f9da3e73fcbd601aabfd84e | MATLAB | 10,182 | 282 | function validationStr = fillValidators(propnames, props, namespacereg)
validationStr = '';
for i=1:length(propnames)
nm = propnames{i};
prop = props(nm);
% if readonly and value exists then ignore
if isa(prop, 'file.Attribute') && prop.readonly && ~isempty(prop.value)
... |
d31f37fbb21d53a278e3b4027cff8994b381b1ff3898c6a9fd9b58e151e352b5 | MATLAB | 10,200 | 337 | %% CREATE VARIABLES
activity_length=120;
bin_size=10;
start=0;
ex_thresh=2;
type='Peak';
load('Y:\Christian\Processed Data\Event Analysis\standard_ds_onsets_full.mat')
corrs=cell(2,length(ds_events));
rand_corrs=cell(2,length(ds_events));
vars=cell(2,length(ds_events));
rand_vars=cell(2,length(ds_events));
mea... |
1e7efd020519822c94000e34d812d8c8f04e70c551ad6b66dc705468b7ef11b3 | MATLAB | 10,201 | 275 | function ClusterStates_MakeFigure(SleepState,basePath,noprompts)
%Check needed here if Sleep state has the right stuff
v2struct(SleepState.detectorinfo.detectionparms.SleepScoreMetrics)
v2struct(SleepState.detectorinfo.StatePlotMaterials)
v2struct(SleepState.detectorinfo.detectionparms.SleepScoreMetrics.histsandthre... |
c253c3299685fbb53e81c5f091004803f3d64be894ecd37bb389f6641466b691 | MATLAB | 10,206 | 287 | function [mri, hdr, cpersist] = read_ctf_mri4(filename)
% READ_CTF_MRI reads header and imnage data from CTF format MRI file
%
% [mri, hdr] = read_ctf_mri(filename)
%
% See also READ_CTF_MEG4, READ_CTF_RES4
% Copyright (C) 2008 Ivar Clemens
%
% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtr... |
c42089fd85808285936e7488d537f25c783e71093de3714cc0a4157b8de0af2d | MATLAB | 10,223 | 162 | function [neur_locs,Vcell,Vnuc,Tri,rotAng] = sampleDenseNeurons(neur_params,vol_params,neur_ves)
% [neur_locs,Vcell,Vnuc,Tri,rotAng] = sampleNeurons(neur_params,vol_params,neur_ves)
%
% Function to sample the shapes and locations for all somas in a volume.
% The inputs to this function are:
% - neur_params - Struct ... |
9bf62dd7b14310a622db0f18a3e4d8a4090a092e8b9593b271d7b8feeb2baa44 | MATLAB | 10,227 | 272 | function Test
close all
h = figure('units','pixels',...
'position',[270,350,150,300],...
'menubar','none',...
'name','TestFig',...
'numbertitle','off',...
'resize','off');
uicontrol('Parent',h,'Style','pushbutton','String',char([36816,34892,20195,30721]),...
'Position',[10,150,50,20],'callback',... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.