sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a78a7532e579b919193d7401c0fc2fe3c66583927ba0614f6677509112dc369e | MATLAB | 2,748 | 76 | function out = LK_CueObjAnalysis_prefObjTest_20230923(cfg)
%
% LK_CueObjAnalysis_prefObjTest_20230923 computes a cell's strength of
% object tuning.
%
% Steps:
% - Estimate the firing rate per object;
% - Identify the preferred object;
% - Test whether the firing rates associated with the preferred object are
% highe... |
3f1667224cec86a6655ae370663755003ba9f9417938a57b48a4eab2f3ab4c26 | MATLAB | 2,750 | 112 | % BCT_TREE Creates a tree from a BCT string.
% (trees package)
%
% tree = BCT_tree (BCT, options)
% ------------------------------
%
% Finds the directed adjacency matrix from a BCT vector (0: terminal, 1:
% continuation, 2: branch), uses a stack.
% Creates a fake tree (see "xdend_tree").
%
% Input
% -----
% - BCT ... |
cde6ba135567957831475068e48dd99f5d72bdc032d6c07eb2b193f817f0ac4a | MATLAB | 2,750 | 68 | % util unit test
%
% mv_select_train_and_test_data
tol = 10e-10;
% Random data
N = 100;
ntime = 30;
X = randn(N,40,ntime);
clabel = randi(3, N, 1);
train_indices = [1:N/4, 80:N];
test_indices = setdiff(1:N, train_indices);
n_tr = numel(train_indices);
n_te = numel(test_indices);
is_kernel_matrix = 0;
[Xtrain, train... |
ccc070520e1618f78062ba07657cee59e62cd8aad11e50849832c31c77400623 | MATLAB | 2,752 | 81 | %decc_plotFig1
% Related to Viswanathan, Stein, Nieder, PLOS Biol, 2024
% PV 2024
load('DECCdataFig1.mat')
% Figure parameters
lcolor = [0 0.3 0; 0 0.5 0; 0 0.7 0];
dcolor = [0.0 0.0 0.6; 0.6 0.0 0.0];
ls = ['-.';'--'];
% Figure 1
for m = 1:2 %for monkey
%Tuning curve plot (Figure 1B top)
figure1 = figure('Co... |
95849655d8145f820d199ebdee540943e7d1b9e2aa7d9590b612ac687f5eaf64 | MATLAB | 2,755 | 109 | function [h2, se, p_wald, p_perm,v_w] = get_heritability(Y, X, K, se_flag, n_perm)
% Heritability analysis of multidimensional traits
% Reference: https://www.nature.com/articles/ncomms13291
%
% Input:
% Y: an Nsubj x Ndim matrix of multidimensional traits
% X: an Nsubj x Ncov matrix of covariates
% K: an Nsubj x Nsubj... |
22f9b26054086d88a9d1ea44931fe9d003a39fca11676750f1cc9cfaaa6e14c9 | MATLAB | 2,756 | 82 | classdef Test_Calc < matlab.unittest.TestCase
%TEST_CALC Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
properties
end
% ================================================================== %
... |
76cc449075514bcf5fa1d439de05e53365167b004bc7be9c8a81422e638c353f | MATLAB | 2,759 | 83 | %sim_steam.m
%Jamie Near, McGill University 2014; Dana Goerzen, McGill University 2021
%
% USAGE:
% out = sim_steam(n,sw,Bfield,linewidth,sys,te,tm)
%
% DESCRIPTION:
% Simulate the STEAM sequence using ideal (instantaneous) RF pulses. To
% remove unwanted coherences, coherence order filtering is employed
%... |
2a9257a6a0dfee38c8e9837637c60c3b7e6def3837e369175388d93f6450338d | MATLAB | 2,764 | 90 | function aperiodic_sensitivity(arrayID)
baseFolder = '/lustre04/scratch/nbrake/data/simulations/trend_peak_interaction2';
funPath = '/lustre04/scratch/nbrake/code/simulation_code';
addpath(funPath);
fid = fopen(fullfile(funPath,'mod_files','default_parameters.json'));
str = char(fread(fid,inf)');
fclose(fid);
pars = ... |
0b749dce35c72f1fe35ca75b5a233d083486b073dba479692ccced198f7238aa | MATLAB | 2,767 | 80 | clear; clc;
%% Add paths now..
loadpath;
%% Dataset details now..
datasetname = ['27072018_SponSleep']; %'', '27072018_SponSleep','14092018_SponSleep',
%'17092018_SponSleep','30102018_SponSleep',
%'01112018_SponSleep'... |
f914398930b94f47843f90dfe4b82dfed7526b947e4bb66dc9052591f03279e4 | MATLAB | 2,770 | 86 | function sftptomatlab(userName,hostName,password,remotefilename,localfilename)
%sftptomatlab connects Matlab to a remote computer and uploads
%a file using the SFTP protocol
%
% STATUS = SFTTOMATLAB(USERNAME,HOSTNAME,PASSWORD,LOCALFILENAME,REMOTEFILENAME)
%
% Inputs:
% USERNAME is the user name required for the rem... |
6f03f89c07878e7142dfd35fbf33d813f9ad3966c0959dd9546757e6cc642a3d | MATLAB | 2,772 | 93 |
function rgb = hcl2rgb(h, c, l)
%HCL2RGB Convert a HCL (i.e., CIELUV) color space value to one
% in sRGB space.
% RGB = HCL2RGB(H, C, L) will convert the color (H, C, L) in
% HCL color space to RGB = [R, G, B] in sRGB color space.
% Values that lie outside sRGB space will be silently corrected.
% Code... |
49f62a431cfaf6c2cd4c60d0919744165e1b989a0242d3caa20ba8bf17452062 | MATLAB | 2,776 | 71 | function [errMat, subCoords] = fillErrMat( iFrame, ...
chSeq, refImg, maxDy, maxDx, Ny, Nx, numLines)
%fillErrMat - helper function conforming to parfor
% This function calculates absolute error of all possible considered ...
%vertical and horizontal shifts
totLines = (numLines - 2*maxDy);
subCoords = zeros(totL... |
8893742056965338ec7a5f6046fa9be7c900e4dd8942fc4c78523a55dabdd523 | MATLAB | 2,781 | 139 | clear
close all force
imSize = [733, 977];
pix2deg = 34.910;
load('a7_2_createAvergedNOTMorphedHeatMapsLoad.mat', 'hmAll')
load a0_0_bhv2trialStrct.mat
%%
%hmAll = zeros(733, 977,nMuscimol, nMonkey, numel(NIm), 'double') from a7_2;
% UMuscimol = [0, 12 (r),9(l) ,4,1];
%iMuscimol =
%1: base
%2: rig... |
d0f778a29b46009c2a3b6e054a746da5f271a55cc0f36bf4777fbe2c3aaf1df9 | MATLAB | 2,784 | 68 | function ch_calc_ratio(self, chNums, varargin)
%ch_calc_ratio - Calculate the ratio of two image channels
%
% ch_calc_ratio(OBJ, CH_NUMS) calculates a new channel based on the ratio
% of two existing image channels, and merges it into the existing image
% data. CH_NUMS must be a length 2 vector specifying the ima... |
f77f5186b2b3e3321c1fdf8f43a196ecf2fa1c3b2b5c09958992307d9b7a5db8 | MATLAB | 2,786 | 115 | clear;
clc;
close all
%% Figure12
subs=30;
frequency=1:1:60;
condition=2;
load([pwd,'\temporary data\fbtrca.mat'])
ac=fbtrca_ac.*100;
% -------------------------------------------------------------------
colors={[51 103 161],[150 68 71]};
name1=['Stimulus Frequency (Hz)'];name2=['Accuracy (%)'];name3=['ITR... |
ccc3a9a0b22c870e310f1ccede004fcfbd3fbafa4b624f6dfbe671a6a64c1c52 | MATLAB | 2,789 | 68 | %% Export Continuous Data To Binary File
%
% <html>
% Import continuous data into Matlab using TDTbin2mat <br>
% Export the to a binary file (f32 floating point or 16-bit integer) <br>
% Channels are interlaced in the final output file <br>
% Good for exporting to other data analysis applications <br>
% </html>
... |
c95d72080efbd378383e4b945a8c467d3441e749ca53174e5a332cf4a3ef8288 | MATLAB | 2,791 | 85 | function varargout = plot(self, objPI, varargin)
%plot - Plot a figure
%
% plot(OBJ, OBJ_PI) plots the default figure for the CalcDiameterLong
% object OBJ using the ProcessedImg object OBJ_PI.
%
% plot(OBJ, OBJ_PI, AX, FIG_NAME) plots the figure on the specified axes
% handles AX, and the particular figure spe... |
a43d10ab2e6be10825b3f67ca908d4764a3544480ec5a800288fde29a360cd93 | MATLAB | 2,795 | 89 | function roiImg = plot_3D_masks(varargin)
%plot_3D_masks - Helper function to plot 3D masks
%
% This function is not intended to be called directly.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms... |
33aeb5bd074a7becfa6acdd8b55ecd5df79e08d70f8889c0cc6c274ceeeba5a1 | MATLAB | 2,796 | 102 | % PLOTSECT_TREE Plots a selected path along a tree.
% (trees package)
%
% [HP, indy] = plotsect_tree (intree, sect, color, DD, options, ipar)
% -------------------------------------------------------------------
%
% Draws a line through a section out of a tree. The section must be a
% directed path away from the root... |
f85995de49aaab371594627065d47891bb2cfbd872cb4b8276fc2b77710869ad | MATLAB | 2,800 | 80 | %% Define all relevant parameters and known number of tiles per round
% This is the CA1 complete hippocampus acquired on July 9th-July 14th
% Numbers are from metadata and examining the raw data folders
numTiles = 170;
numRows= 10;
imgSizeXY = [2048, 2048];
imgResXY = .1625; % in um, Taken from the .ims properties re... |
8b53a05b17478096b799c10c9171ffaef9e4979ac989b1372801ee79141fb742 | MATLAB | 2,804 | 157 | function [All,outVars] = ExpressionTypeIdentifier(All,outVars)
numExps = numel(All);
mouseNameList = {
'I127_1'
'HB40_1'
'HB47'
'I132_2'
'I135_1'
'I136_1'
'W4_3'
'I137_3'
'I138_1'
'W20_1'
'mora_tre'
'w14_1'
'w21_1'
'i139_2'
'HB95'
'i140_... |
31e1679fb0cb7b659c616aa05dc8e7e19e080906bcaf867b86a456962ace22b4 | MATLAB | 2,808 | 60 | %%==========================================================================
% This is the function part of codes for the reciprocity model proposed by Gao, X., Jolly, E., Yu, H., Liu, H., Zhou, X., & Chang, L. J. (2020). The hidden cost of receiving favors: A theory of indebtedness. BioRxiv, 2020-02. doi: https://doi.... |
bf0a20ef80f731250699e3bfb0db89014a1127695a97bdfd556f789442dc3076 | MATLAB | 2,808 | 110 | %==========================================================================
% This script extracts behavioral information from the logfiles.
%==========================================================================
% start
clear; clc; close all;
% paths
behPath = 'E:\OpenField\Beh_20201215\';
dataPath = 'E:\... |
7754cdba494b159c04d8d3f0758d05b40b03088803c6a780ca087fc6cdf45a45 | MATLAB | 2,810 | 103 | % CVOL_TREE Continuous volume of segments in a tree.
% (trees package)
%
% cvol = cvol_tree (intree, options)
% ----------------------------------
%
% Returns the continuous volume of all compartments [in 1/um]. This is
% used by electrotonic calculations in relation to the specific axial
% resistance [ohm cm], see ... |
c175bc2af47fb7b36ea26f71689e942ddf8fd846c03dcd4dbe4b4031d4194841 | MATLAB | 2,812 | 76 | % SHOW_STACK Show maximum intensity projection of an image stack.
% (trees package)
%
% HP = show_stack (stack, options)
% --------------------------------
%
% Show the maximum intensity projections of a stack on a 3D patch (see
% "load_stack" for a description of a stack structure and see "cgui_tree"
% stk_ panel).
... |
cf3f9f5f7c6907613c2d6199b5f92dd91e77b2acf7964e1ae2b01c007ffb77fb | MATLAB | 2,816 | 133 |
close all force
clear
load('a0_0_bhv2trialStrct.mat');
%%
% non faces
NImage{2} = [...
2
4
5
6
8
10
12
13
17
18
19
20
26
29
35
];
NImage{1} = [...
7
11
25
27
38
39
40
47
49
53
56
60
9
22
28
... |
5d6d3560a205fd834505018d48338b648c6f136de082d5719297ad23877d7def | MATLAB | 2,817 | 83 | %io_CSIwritelcm.m
%Brenden Kadota, Sunnybrook Research Institute 2022.
%
% USAGE:
% RF=io_CSIwritelcm(in,outfile);
%
% DESCRIPTION:
% Takes MRSI data in matlab structure format and writes it to a text file
% that can be read by LCModel (LCModel RAW format). Namely, "One voxel's
% data is immediately concatenated to t... |
afc8b47e06442686abe65aaadfeedaa76cc31f3358b0c0443dd4d24ace404187 | MATLAB | 2,817 | 73 | %%==========================================================================
% This is the function part of codes for help rejection model proposed by Gao et al., 2021, The hidden cost of receiving favors: A theory of indebtedness
% This script should be used in combination with the main file:
% Help_rejection_model_ma... |
a1955d709ff6b5de2fa834b5091abcddc57159d7fd242bf02a3e6cf2c35684cc | MATLAB | 2,818 | 84 | %% Code for orientation decoding analysis
clear;
addpath './Tools';
protoDir = '';
%% Ground truth analysis
load('Saved_maps_groundtruth.mat')
Cond90 = TS.Header.Index.iValidBLKCond{6};
Cond0 = TS.Header.Index.iValidBLKCond{3};
map0_gt = DataTrialBand(:,:,Cond0);
map90_gt = DataTrialBand(:,:,Cond90);
[DP_... |
27800a0bebd150c8813b8e552f3e8d406419c6cd51d433d72793aedbcc2f0f8a | MATLAB | 2,822 | 70 | function ch_calc_sum2(self, chNums, varargin)
%ch_calc_sum2 - Calculate the sum of two image channels
%
% ch_calc_sum2(OBJ, CH_NUMS) calculates a new channel based on the sum
% of two existing image channels, and merges it into the existing image
% data. CH_NUMS must be a length 2 vector specifying the image chan... |
4ccc594a8d197631093f497cfe42d54872b556d95bc8915ffcc45ede85513592 | MATLAB | 2,824 | 72 | classdef test_qc < matlab.unittest.TestCase
methods (Test)
function motionQcComputesSelectedSvdR2(testCase)
outDir = tempname;
mkdir(outDir);
cleanup = onCleanup(@() rmdir(outDir, 's'));
motionFile = fullfile(outDir, 'motion.txt');
motion = [(1:8)... |
d10f1c8f39c7b1304624902544150e56a347640c9434ec03964a3459b8ece5a8 | MATLAB | 2,824 | 87 | function varargout = plot(self, varargin)
%plot - Plot a figure
%
% plot(OBJ) plots the default figure for each element of OBJ.
%
% plot(OBJ, H_FIG, FIG_NAME) plots the figure on the specified figure
% handle(s) H_FIG, and the particular figure specified by FIG_NAME.
% FIG_NAME must be one of the following:
%
%... |
7c461a4e8017ef1b10003a7050ac63a6320525d2a5ba47c851159c78dee375cb | MATLAB | 2,829 | 95 | function varargout = plot_PCspectrum(self, objPI, hAx, varargin)
% CellsortPlotPCspectrum(fn, CovEvals, PCuse)
%
% Plot the principal component (PC) spectrum and compare with the
% corresponding random-matrix noise floor
%
% Inputs:
% imgSeq - input image sequence
% CovEvals - eigenvalues of the covariance matrix
%... |
c29fe4eae56a65151f4d064726bdb855a0a5462a156b9380ab7ed8c6b8f3f9a9 | MATLAB | 2,834 | 71 | function x = readSBX(path, info, firstScan, Nscan, pmt, z)
%
if nargin < 2
[pathDir, pathName, ~] = fileparts(path); % pathExt
[~,infoPath] = FileFinder(pathDir, 'type','mat', 'criteria',@(x)(strcmp(x,pathName))); %
fprintf('\nNo info structure was provided. Loading %s', infoPath{1})
info = MakeI... |
24ebaf231910d76625abdde0f35db71ab0a85c46658ad12e5cd371a20facfdfd | MATLAB | 2,840 | 101 | function drawROI_Callback(obj,~,~)
% Draw a ROI to image a sub-set of the full FOV
%
% Purpose
% This callback allows for imaging a sub-set of the full FOV
% Disable button until ROI has been drawn
obj.ROIButton.Enable='off';
obj.ResetROIButton.Enable='off'; %There is a callback on ROI size... |
d7f1e0e1e2df2e9a6498c9d8180bf8797e8fb0acc4825094af31b04e55127d35 | MATLAB | 2,845 | 67 | %Written for the first splintr barcode dataset from Oz
% FOLDER_NAME = 'ExSeqAutoSlice';
FILEROOT_NAME = 'PrimerNPCCCframe7';
DIRECTORY = '/mp/nas0/ExSeq';
offsets3D = [6,6,5]; %X,Y,Z offsets for calcuating the difference
roundnum = 1;
BEAD_ZSTART = 120;
%Load all channels, normalize them, calculate the cross corr o... |
d4a6ef81edeb1e723ebae6ddca672aa954307226e4ec21329ec0d483079bc994 | MATLAB | 2,846 | 123 | % io_readlcmraw_dotraw.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=io_readlcmraw_dotraw(filename);
%
% DESCRIPTION:
% Reads LCModel .RAW model spectrum file into the FID-A data structure format in MATLAB.
%
% INPUTS:
% filename = filename of LCModel raw file.
%
% OUTPUTS:
% out = Input metaboli... |
0d4a127820ea0d9a716082176c599b32c57b4b51e85314c6884d9a5a8e0fd67d | MATLAB | 2,847 | 109 | % EUCL_TREE Euclidean distances of all nodes of a tree to a point.
% (trees package)
%
% eucl = eucl_tree (intree, point, options)
% -----------------------------------------
%
% Returns the Euclidean (as the bird flies) distance between all points on
% the tree and the root or any other point.
%
% Input
% -----
% -... |
29ffae7ab6ff3fb28ee8a88ddc370a54e9a54e9c63c093777ec7e7b65fc8510d | MATLAB | 2,851 | 90 | function result = mergeimports(data, verb)
import zapit.yaml.*;
if ~exist('verb','var')
verb = 0;
end
result = recurse(data, 0, [], verb);
end
function result = recurse(data, level, addit, verb)
import zapit.yaml.*;
indent = repmat(' | ',1,level); % for debugging
if iscell(data)
result = i... |
48d1c89862e0f7968d12b06d8826bfad430687cfdaf1a2c37fed35ced466fbab | MATLAB | 2,851 | 55 | function [EMG_Channel1MovementTimeInSec,EMG_Channel2MovementTimeInSec,EMG_Channel3MovementTimeInSec,...
EMG1DataIn2000HzNormalized,EMG2DataIn2000HzNormalized,EMG3DataIn2000HzNormalized]...
=AnalyzeEMGSensorsData_01_01_2020(EMG1Data2000Hz,EMG2Data2000Hz,EMG3Data2000Hz,StartTriggerTimeInSec,EMGThresh... |
47b39679d532122d835d74a9187fddc5f54fb410837ce941cd203b2cbbd86f56 | MATLAB | 2,852 | 79 | function initialize_network(masterFolder)
addpath('/lustre04/scratch/nbrake/code/simulation_code');
[sa,X] = network_simulation_beluga.getHeadModel;
locations = sa.cortex2K.in_from_cortex75K;
% dp = zeros(2001,3,100);
% for arrayID = 1:10
% for j = 1:10
% i = 10*(arrayID-1)+j;
% folder = fullfile... |
0279c5765fd72407a901c3248b3fc772e6d624b760023df9a64a52c83b8eb573 | MATLAB | 2,855 | 82 | function chName = choose_channel(varargin)
%choose_channel - Choose an image channel
%
% CH_NAME = choose_channel() prompts the user to specify what is shown on
% a given image channel from a list of all the known channel types.
%
% CH_NAME = choose_channel(CH_OPTS) provides the user only those options
% listed... |
59d8fad8c90b25af8249088d671fa101d3bbd1a1cb44bf3db8858dc0d3564f14 | MATLAB | 2,856 | 93 | function roiNames = create_ROI_names(maskROIs, varargin)
%create_ROI_names - Helper function to create ROI names
%
% This function is not intended to be called directly.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
%... |
95d0932ccfd9970df34737c871193f838d63de9c90b98a6ea8fa4252ec9c3de7 | MATLAB | 2,856 | 100 | % SSE_TREE steady-state electrotonic signature of a tree.
% (trees package)
%
% sse = sse_tree (intree, I, options)
% -----------------------------------
%
% Calculates the steady state matrix containing the current transfer from
% every node to every other node in the tree, i.e. each column i is the
% potential dist... |
8e81d8241151437b186d8ba26df4ec8c2ad470b62c0e5eac4660e394ac4a4f46 | MATLAB | 2,859 | 96 | function shf_sig = shuffle_esc(sig, Fs)
% function shf_sig = shuffle_esc(sig, Fs)
%
% This function shuffles a signal using random insertion type shuffling.
% The signal 'sig' is divided into a number of sections, equal to the
% number of seconds of data or 1000, which ever is smaller. These sections
% are of random ... |
f37faff41cc4493ac0762e571e90fcf37dc26ef4799c818ed65a96786ab77478 | MATLAB | 2,860 | 125 | % this code will read all the gaze files from the trials and covernt them
% to the image coordinate.
clear
close all force
warning on
hWB = waitbar(0,'checking the trials ...');
%load tirals info
load('a0_0_bhv2trialStrct.mat');
load('a0_11_insideFace.mat', 'inFaceTimeSumAll')
timeOnEyeAll = inFaceTimeSumAll;
... |
8a7e193b1617d87996415eb81d7eb74594f025dcc5b985d407e932d8b8179748 | MATLAB | 2,861 | 142 | close all force
clear
load a15_0_SacOnEye.mat
load('a0_0_bhv2trialStrct.mat');
NIImage_Individual = [7
9
11
22
25
27
28
38
39
40
41
42
43
44
47
49
52
53
55
56
57
59
60
]';
%group
%
NIImage_Group = [
36
37
45
... |
cb31bd420b751337aac8aea1a4424796378ec8de21493a88f356beb1ca600c31 | MATLAB | 2,861 | 77 | function [C,pp,pe] = pcfit_v5(data,lambda,peak_guess,ran,span)
% pcfit_v5: Fits peak's centroid position (version 5). The function also finds peak (max) position and peak extinction.
% algorithm details: Article below
% - Improving the instrumental resolution of sensors based on localized surface plasmon resonance
% ... |
a6862ad8ec9e4561472cc415cc480bdef7877039f5da8407b592133891dfe93b | MATLAB | 2,862 | 108 | % TRAN_TREE translate the coordinates of a tree.
% (trees package)
%
% tree = tran_tree (intree, DD, options)
% --------------------------------------
%
% Translates the coordinates of a tree, per default sets tree root to
% origin (0, 0, 0).
%
% Input
% -----
% - intree ::integer:index of tree in trees or structur... |
88b3682c5ff7581044271c2dfc2a3e2879398fd1fce613a11ad61512364ad204 | MATLAB | 2,864 | 131 |
close all force
%{
clear
load('a0_0_bhv2trialStrct.mat');
load('a19_2_distWithinAndBetweenEachTrial.mat', 'distToMeanSameCondition', 'distToGrandMean')
load('a19_0_downSizeAverageHeatMaps.mat', 'hmAll105x140')
%}
%%
% non faces
NImage{2} = [...
2
4
5
6
8
10
12
13
17
18
1... |
316a28f0d31348dd157afb2b113b2e78f529bce632ed1b7937df4048f2c07c35 | MATLAB | 2,871 | 86 | classdef Test_CalcFindROIs_params < matlab.unittest.TestCase
%Test_CalcFindROIs Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
properties (TestParameter)
classCFR = utils.find_subclasses('CalcFin... |
d1c7b1eedd682eaf2191c96e8f45a74e60a81910e721501d63844272d099ca77 | MATLAB | 2,871 | 112 | % this code will read all the gaze files from the trials and covernt them
% to the image coordinate.
clear
close all force
warning on
hWB = waitbar(0,'checking the trials ...');
%load tirals info
load('a0_0_bhv2trialStrct.mat');
load('a0_8_timingLeftVsRight.mat')
load('a0_3_2_findFaceAndEyeLocatoins.mat')
%%
IFa... |
d3e437ee06bfaef19b17624a7973110dc3e08b1ec74ed2b43d408a2b3048d385 | MATLAB | 2,871 | 79 | function [varargout] = t2n_getPP(neuron,tree,pp)
% This function plots the locations of a given NEURON point process onto each
% morphology and optionally returns these values, too;
% INPUTS
% neuron t2n neuron structure or cell array of structure (see
% documentation)
% tree TREES toolbox morphologie... |
7e5351bb653bacd5790401b69d5504822c87f37eadd2381378d157cb4a7631e4 | MATLAB | 2,875 | 105 | function[P, S, X, E] = fit1DGabor( tag, dat, P, S, X, E, n, N )
% number of iterations for fitting
niters = 200;
% load symbolic equations for Gabor and first derivate
define_Gabor_tuning_curve;
% convert disparity and mean responses to row vectors
x_orig = dat(:,1)';
resp_orig = dat(:,2)';
% interpolate dispariti... |
e8568768e7f8f9fdd41415bf834ac4d829b857fa2623110bba6eadc1f1354504 | MATLAB | 2,876 | 75 | function [ListOfAnalyzedChannels,PSD_OfAllAnalyzedChannels,LFP_PSD_TimeBins,LFP_PSD_FrequencyBins,NoiseTimePointsAllChannel]...
=Analyze_LFP_data_20_8_2017(filenameLFPMEAData,NonActiveElectroChannels,StartTriggerTimeInSec,NoisePeakDetectionThreshold)
ActiveElectroChannels=[]; %%%% Output from Intan RHA onl... |
083a5b8a5fd9c8ea5d71e3ce631e141c1013f79ef5f1e5fc0b0cf1fc22e0c1d9 | MATLAB | 2,880 | 76 | function [plotROIs, nROIs] = get_plotROIs(self, plotROIs)
%get_plotROIs - Check and/or return the ROI numbers to plot
%
% ROIS = get_plotROIs(OBJ) returns a vector containing the ROIS that can
% be used for plotting. In most cases, this will be all the ROIs that
% were detected.
%
% ROIS = get_plotROIs(OBJ, RO... |
baea3875b96717b845fdbce26fd6e99a8cec39462d04771766ef7fec5adc2ab9 | MATLAB | 2,881 | 113 | % IDCHILD_TREE Index to direct child nodes in a tree.
% (trees package)
%
% idchild = idchild_tree (intree, ipart, options)
% -----------------------------------------------
%
% Returns the indices to the direct child nodes for each individual node in
% the tree.
%
% Input
% -----
% - intree ::integer: index of tr... |
f9d3dcf9d871f9b486e7a85e449e44a1d6e78198746abedb173203020f9e3e1f | MATLAB | 2,885 | 104 | clear
close all;
clc;
subs=2;
freq_band=3;
stime=0.1:0.1:5;
condition=2;
load([pwd,'\temporary data\fbcca_stime.mat']);
ac_stime;itr_stime;
% 30 subject *2 condition *3 frequency_band *50 data_length
%% Figure 10a-----------------------------------------------------------------
%ACC
name1=['Accuracy (%)... |
5a6cd8bcfdd603f055197103dc491eb1711fa7e350a1c940510eb307c3013ae7 | MATLAB | 2,888 | 107 | function varargout = prfsi(val, varargin)
%prfsi - Check that the value is a positive, real, finite, scalar integer
%
% prfsi(val) checks that val is a positive, real, finite, scalar integer.
% If it is, nothing else happens; if it is not, the function throws an
% exception from the calling function.
%
% prfsi(... |
ed3c3d075952347366e2d43e7244c5924983982e9691fe25cf745052ef6a662f | MATLAB | 2,888 | 88 |
%% Pipeline for getting breathing belt regressor for fMRI processing
%
% Use: Run the script, a dialog box will open and you can choose the
% physlog file you want to process. It will process and plot, and save the regressor matrix. then you
% can load the breathing reg matrix into conn
% 15 May 2024
% Editors (alpha... |
496514a5194820052562fc16e6162a18a1445ea1fc8bf5a568dbb891d6cd46b0 | MATLAB | 2,892 | 121 | function pasteBrainThenScale(atlas_data)
% First click places bregma of border brain at clicked location
% Mouse motion: brain scales and rotates to follow cursor
% Second click places second ref point and brain stops moving
uF = uifigure;
uA = uiaxes('Parent',uF);
b = atlas_data.whole_brain.b... |
ecddc3908378abe9265f14f87e78cd8a4ec5c0c6c336e865680d170e1d6bbc40 | MATLAB | 2,894 | 86 | function varargout = numel(val, num, varargin)
%numel - Check that a value has an exact number of elements
%
% numel(val) checks that val has exactly two elements. If so, nothing
% else happens; if not, the function throws an exception from the calling
% function. val must be a vector or an array.
%
% numel(va... |
26013383ebf30ef16884f92ddef6911c5d764fc6c37c525a888d641ccb55de1c | MATLAB | 2,896 | 86 |
clear
close all force
warning on
hWB = waitbar(0,'checking the trials ...');
hWB1 = waitbar(0,'checking the trials ...');
%load tirals info
load('a0_0_bhv2trialStrct.mat');
I = arrayfun(@(x) isfield(x.analyze,mfilename), dataTrl);
if any(I)
I(I) = arrayfun(@(x) x.analyze.(mfilename) , dataTrl(I));
end
NTrial =... |
4be1b57be11272e14a6bef401b4df24d3298af4da392163846314531376f511c | MATLAB | 2,900 | 136 | %% This script plot histology bar graphs
% goodF condition
clear;clc;
% load('raw_data.mat')
load('raw_data_individual.mat')
goodF.Reelin = mean(goodF_R);
goodN.Reelin = mean(goodN_R);
badF.Reelin = mean(badF_R);
badN.Reelin = mean(badN_R);
goodF.Cal = mean(goodF_C);
goodN.Cal = mean(goodN_C);
badF.Cal =... |
277047afc4a241c59360ae1fbb34745605de26c6e6d642d44a714ddd44ce4d31 | MATLAB | 2,906 | 115 |
load(fullfile(dataFolder,'simulations','trend_peak_interactions','parameter_changes.mat'));
f = 0.1:0.1:500;
rhythms = load(fullfile(dataFolder,'simulations','trend_peak_interactions','rhythm_spectra.mat'));
rhythms.psd = rhythms.psd([1,5,3,4,2]);
P3 = zeros(length(f),5,5);
P3(:,:,1) = mean(P2(:,:,1:5),2);
P3(:,:,2... |
cc4f9eef980ade0742e2a6d9bd7d9e8ae6615ef30a93311f9f48eab737540ac9 | MATLAB | 2,907 | 71 | function prop = t2n_pnode(neuron,tree,node)
% This function returns all properties (mechanisms and point processes)
% that have been set at a specific node. This is similar to psection() in
% NEURON and useful for validation of set parameters.
%
% INPUTS
% neuron t2n neuron structure (see documentation)
% tree ... |
f6c52a514be08353ef4d75a401131325d880307dd1a52f7138b3f22c5a36729b | MATLAB | 2,909 | 1 | function [time0]=countDown(display,cdStartSecs,cdStartScan, triggerType)
% function [time0]=countDown(display,cdStartSecs,cdStartScan, [triggerType])
%
% time0 is the time (GetSecs) at which the scanner started.
% cdStartSecs is the (integer) number of seconds for the entire countdown sequence
% cdStartScan is the (rea... |
f59ab3f2134d327c7cdc8abb0ae0f877164d198c5f437e05a1ad53d2ffeb2027 | MATLAB | 2,910 | 80 | % Preprocessing unit test
%
% average_samples
tol = 10e-10;
N = 256;
X = randn(N,1);
% Get default parameters
pparam = mv_get_preprocess_param('average_samples');
%% if a class has less than group_size samples, it should disappear from the averaged sample
pparam.group_size = 5;
clabel = ones(N,1);
clabel(N-30:end)... |
be823ba2b5da2379715a980849066666cac762eaabde6f25d405c70b2a79dcc6 | MATLAB | 2,911 | 67 | function f = LK_PlotRippleCorrelationsWithBeh_20231030(dt)
%
% LK_PlotRippleCorrelationsWithBeh_20231030 plots the correlations between
% ripple rates and different behavioral properties including memory
% performance and trial index.
%
% Lukas Kunz, 2023
% create figure
f = figure('units', 'centimeters', 'position', ... |
1602369a6c50fbb75c7d466289bb84c0fffaec80eadd7b947b4cfe79607307d2 | MATLAB | 2,912 | 91 | function [unlabeled] = extractUnlabeled(data,options)
nDomains = size(data,2);
switch options.un
case 0
% Unlabeled 'labels' vector
for i = 1:nDomains
L = zeros(size(data{1,i}.X,1),1);
eval(sprintf('[Xtr%iu Ytr%iu] = ppc(data{1,%i}.X,L,options.puT,options.real);',i,i,i... |
4f509581ef05579de0448c1336278c2df330fd93cb9e0aad9331949b4f308977 | MATLAB | 2,912 | 122 | function [DPrime, DMean, STD, dpSignal, dpNoise] = CalculateDPrimes(Signal,Noise,Dim)
%% function DPrime = CalculateDPrimes(A,B,Dim)
% Calculate d' between A and B in the dimention of DIM
%
% A and B must have same sizes in all dimentions but DIM
% DIM refers to the dimention of repetation, default = 3
% DPrime is the... |
47429f0b209f566504f0852137d35bc821e643186325bde898716dca0ef43019 | MATLAB | 2,913 | 75 | % op_CSIrose_shiftKcoords.m
% Jamie Near, Sunnybrook Research Institute 2024.
%
% USAGE:
% [shiftedKTable, ind]=op_CSIrose_shiftKcoords(kFile, in);
%
% DESCRIPTION:
%This function adjusts the k-space coordinates in a rosette MRSI
%acquisition to account for any offsets due to gradient imperfections.
%Each petal has ... |
040360000e87954a4a748131454a0a37f3fc08cd83731f9fb6da533957a635f4 | MATLAB | 2,914 | 74 | % Converts MATLAB format SC files into a txt file format that can be read
% by the hybrid brain network model implementation
%
% USAGE:
% generate_input_SC(SC, output_filestem)
%
% INPUTS:
% SC - [N,N] array that contains connection weights for all
% NxN region pairs
% output_files... |
3a74d0b98fd636ea988b81123441500cf982515a19a3d038b9e4243b9f558d4b | MATLAB | 2,917 | 59 | function P_value = permutation_test_ttest(ctrl_mtx, case_mtx, Wp, CID, Clist, M, threshold_GT, Method)
% Conducts a permutation test using the t-test to assess the statistical significance
% of a test statistic derived from control and case matrices compared to a permuted dataset.
% Inputs:
% ... |
e9849538713f3ccf9ebd65dc56a57c47482d7c26a568407016252e36b34c688b | MATLAB | 2,918 | 96 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [dist_obj] = distance(input,output,num_params)
%DISTANCE Records Wasserstein distance between spike trains
if nargin<3 || isempty(num_params)
num_params=struct;
end
if ~isfield(num_params,'n_tri... |
75324d4abbd0ae0f640c6b366fcda629e2eae85716bb71b333ad7c60aaabcba8 | MATLAB | 2,920 | 98 | % sim_onepulse_shaped.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out = sim_onepulse_shaped(n,sw,Bfield,linewidth,sys,RF,tp,phCyc,dfdx,G)
%
% DESCRIPTION:
% %This function simulates the effect of a frequency selective or slice
% selective excitation, followed immediately by the acquisition window.
% This ... |
c9c3d35f145e10bfd42b74d959a0673bc1d6a4b59f13f6e2ef58e16f34f2b7ac | MATLAB | 2,921 | 86 | function b = datatypesize(c)
% B=DATATYPESIZE(C)
% return number of bytes B based on string C.
% extended with cpx types for complex, see also freadbk.
% -1 is returned for unknown type
%
% help fread
% MATLAB C or Fortran Description
% 'uchar' 'unsigned char' unsigned character, 8 bits.
% ... |
34160f32a392d05913edae5b1232d24b107d4c021ddaec7b443f26874aaf258b | MATLAB | 2,923 | 68 | function MakeSbxPartial(expt, sbxInfo, varargin)
% Apply only the some components of the affine transform
IP = inputParser;
addRequired( IP, 'expt', @isstruct )
addRequired( IP, 'sbxInfo', @isstruct )
addParameter( IP, 'outPath', '', @ischar )
addParameter( IP, 'sbx', true, @islogical )
addParameter( IP, 'overw... |
8d5c04fdaa59bc810e942c6f7d0843ebcf6e9c5f91a8564e8c0c47a9bbbf7565 | MATLAB | 2,926 | 74 | classdef listenerExample < handle %The class "listenerExample" inherits the built-in class "handle"
% This file defines a simple example class called "listenerExample"
%
% Prerequisites
% If you aren't familiar with OO, first look at simpleOOexample.
% Also, you should look at anonymousFunctionExa... |
1e5df4885919460c5d7ddcd6a25dcbb61e6326836c0418f96bd9a3f25db4a44e | MATLAB | 2,929 | 72 | function loadConfig(obj,fname)
% Load a YAML config file
%
% zaptit.stimConfig.loadConfig(fname)
if ~exist(fname)
fprintf('No config file found at "%s"\n', fname)
return
end
data = zapit.yaml.ReadYaml(fname);
ind = 1;
obj.stimLocations = struct(...
... |
721c5c2f6ca32cf7fc4949c72849172cba0d18fe7d4f24ce38c56dfc1c400642 | MATLAB | 2,930 | 94 |
clear
close all force
warning on
imSize = [733, 977];
imSizeCent = fix([733, 977]/2);
y1 = imSizeCent(1)+(-130:70);
x1 = imSizeCent(2)+(-120:0);
y2 = imSizeCent(1)+(-130:70);
x2 = imSizeCent(2)+(0:120);
hWB = waitbar(0,'checking the trials ...');
%load tirals info
load('a0_0_bhv2trialStrct.mat');
load('a0_3_0_extr... |
dd815f3ea17016f7907b575be054628a1ee841eeea01836090de7c21bb337bd5 | MATLAB | 2,930 | 80 | %% Stream Plot Example
%
% <html>
% Import continuous data into Matlab using TDTbin2mat <br>
% Plot a single channel of data with various filtering schemes <br>
% Good for first-pass visualization of streamed data <br>
% </html>
%% Housekeeping
% Clear workspace and close existing figures. Add SDK directories... |
a4527c0b50690823ca0edb8cff6fd00adde6cbd54abbbc40587c674de2a51830 | MATLAB | 2,931 | 60 | function f = LK_PlotRipplePSTHPerPhaseStart_20231030(dt)
%
% LK_PlotRipplePSTHPerPhaseStart_20231030 plots the ripple PSTH and
% time-resolved average ripple rate per trial phase. Good and bad trials
% are separated. Data is locked to the start of the trial phases.
%
% Lukas Kunz, 2023
% create figure
f = figure('unit... |
bc90c200750326789c0ae3cadc645a0148d947f95b65817b570f7b73ded56443 | MATLAB | 2,931 | 80 | %% Stream Plot Example
%
% <html>
% Import continuous data into Matlab using TDTbin2mat <br>
% Plot a single channel of data with various filtering schemes <br>
% Good for first-pass visualization of streamed data <br>
% </html>
%% Housekeeping
% Clear workspace and close existing figures. Add SDK directories... |
5f6748fdce5b02640b7305c74d65d14d182e9be1271237d74bff6bb9089b1637 | MATLAB | 2,932 | 60 | function f = LK_PlotRipplePSTHPerPhaseEnd_20231030(dt)
%
% LK_PlotRipplePSTHPerPhaseEnd_20231030 plots the ripple PSTH and
% time-resolved average ripple rate per trial phase. Good and bad trials
% are separated. Data is locked to the end of the trial phases.
%
% Lukas Kunz, 2023
% create figure
f = figure('units', 'c... |
76020ba4caf4f066c6b173c4e0d3f083ad44ee2162b7f40ff39e85bba367dc34 | MATLAB | 2,934 | 65 | function unpresentable = returnUnpresentableConditions(obj)
% Return indices of conditions that can not be physically presented
%
% unpresentable = zapit.stimConfig.returnUnpresentableConditions()
%
% Purpose
% A stimulus condition can not be presented if the beam-blanking at each point
% tr... |
208fb890371260e38d6506061bf836c287f778e359f8a3643caae0a6391c74ea | MATLAB | 2,936 | 105 | function [out] = EEGfMRIPav_cbm_mod06_osap(parameters,subj)
% Standard Q-learning model with delta learning rule and Go bias and
% Pavlovian response bias and separate learning rate for salient Go
% responses (action priming model).
% ----------------------------------------------------------------------- %
%% Retrie... |
81f294b85c680632353fc5cc9f34d789291f2460062af59e5e0a58ff8dbf0861 | MATLAB | 2,937 | 98 | function LK_SigLine(x, y, p, varargin)
%
% LK_SigLine plots a significance line.
%
% Input:
% x: all x values
% y: two y values that indicate the position of the horizontal lines
% p: p-values (if float, then the significance level is indicated via
% different shades of gray; if logical, all significant tim... |
90f73e20dd0bd5298846c0c4d25c849842c2de8956ef3bd13ce5f2c359a703ea | MATLAB | 2,940 | 84 | function hAx = plot_windows(self, ~, hAx, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version... |
a13c230f2c4863dcbd45d47683c177bec7619839f26d2083596f9cef50801767 | MATLAB | 2,942 | 83 | function cfrdObj = from_mask(varargin)
%from_mask - Load ROIs from a mask or binary image
%
% OBJ = from_mask() prompts the user to select a file containing
% the mask and will create a ConfigFindROIsDummy object using the
% provided information. Supported file types are as follows:
%
% - MAT-files containing... |
03a19761ed720568ca2a6323cf23b8c2d1bd8451b42281d3fb66a498d64afa27 | MATLAB | 2,944 | 98 | %% Comparison of SVD components between subjects
% Michelle Medina
% August 8, 2022
%% Load saved data
close all;
clear all;
sub_M03 = load('sub_M03_fl_var.mat');
sub_M08 = load('sub_M08_fl_var.mat');
sub_M29 = load('sub_M29_fl_var.mat');
%% Plot histograms by plotting the time-course of the 2nd SVD coefficient and... |
f25890efeb4fdad8ee26a06c121b65d59f2e8ee0d4b1d921e24b81d5bd60f6c1 | MATLAB | 2,944 | 70 | function tree = add_axon(tree,type)
% Adds an axon to the morphology. Soma region needs to be already defined.
if (nargin < 2) || isempty (type) % if the number of function input arguments is less than 2, or the input 'type' is empty
% {DEFAULT: case 'MainenSejnowski'}
type = 'MainenSejnowski';
... |
6914581bc7c1489a6ab24a6eb6e2c283a4be7e66ed78cad0a811059745d6e931 | MATLAB | 2,949 | 130 | function plotSphericalHarmonics(shmat,time, filename)
PS = PLOT_STANDARDS();
C = distinguishable_colors(16,'w');
% Plot Each Coefficient of Varying Order
figure()
tl = tiledlayout(4,1,'TileSpacing','compact');
% Order 0
nexttile
yyaxis left
ylabel({'Field Fluctuation'; '[ppm]'});
yyaxis right
h1 = plot(time,shma... |
4b4626981dfdce02c3d67d03f5bea8bd83eca43c583027c0bc4d49ab62b5080c | MATLAB | 2,961 | 74 | function [lambda_out, cut_out] = param_tuning(Wp, method, prctile_vec)
% parameter tuning function
% Input:
% Wp: Original shuffled (observed) adjacency matrix (-log(p-values))
% lb: lower bound for lambda_0
% ub: upper bound for lambda_0
% By default, lb and ub are set to be lb = 0.5, ub... |
b5854f1307788d99fe8a7130912bbea6aff445fec65f936e84aa0ce0753a80be | MATLAB | 2,961 | 86 | % op_CSIZeroFill.m
% Brenden Kadota, SunnyBrook Hosptial 2021.
%
% USAGE:
% [out]=io_loadspec_rda(rda_filename);
%
% DESCRIPTION:
% Zero fills in the spatial domain
%
% op_CSIZeroFill pads zeros to the spectral domain. If the padded zeros
% result in an odd number of points, it will always pad onto the left side.
%
... |
d0cd1cc4b516fff91b263adb7fcf549de8f35f8f35fbabdce83b8b6ef33a8420 | MATLAB | 2,962 | 88 | %% Import data
index = importdata(['..' filesep '..' filesep 'Results' filesep 'NEURON' filesep 'locs' filesep 'index.dat']);
locs = importdata(['..' filesep '..' filesep 'Results' filesep 'NEURON' filesep 'locs' filesep 'locs_all_seg.txt']);
diams = index.data(:,1);
locations = locs(:,1:3);
parent_locs = locs(:,4:6);... |
ef6010d08bcafbbb9ce45a1da3225251a9ec1b02c6f6f8c054f61167f8892313 | MATLAB | 2,963 | 67 | function [trainBoutsInd, testBoutsInd] = GetTrainAndTestInd(MouseIDs,contextLabel,sessionNames)
miceIdClasses = unique(MouseIDs);
contextLabelVec = unique(contextLabel);
trainBoutsInd = [];
testBoutsInd = [];
useMouseForTrain = true(length(miceIdClasses),1);
useMouseForTest = true(length(miceIdClasses),1);
f... |
d7d627b3d75b9ed36ec39f1822a2efa47b5c9bb609e5088f4cd994dda2cb3f6f | MATLAB | 2,967 | 89 | function imp = Array2ij(array, typestr, name)
%IJARRAY2PLUS Converts MATLAB array to ImageJ ImagePlus object
% imp = ijarray2plus(array, typestr)
% array size [nRows,nCols,nFrames,nPlanes]
% $Id: ijarray2plus.m 475 2009-03-20 20:43:13Z kenichi $
% Edited by Arthur Sugden 180731
% Nam... |
92e74246109874651d56cf8d039593136049f567599b393a34a0296453c2d5e9 | MATLAB | 2,968 | 56 | %% Extract all sbx files within a folder
% Clear any previous variables in the Workspace and Command Window to start fresh
clear
clc
% Set the directory of your 'sbx' files
mainDir = 'D:\2photon\AB40\221004\';
% add '\' to mainDir if it is not included
if mainDir(end) ~= '\'
mainDir(end+1) = '\';
end
... |
49c273f29be2bc41c84e41f1d93b3471039c8b4a6517d2ed3a71ebb009bfa69e | MATLAB | 2,984 | 81 | % Compute artificial alpha input (10 Hz sine wave)
% First part: ~10 minutes of activity with short alpha burst
% Second part: ~10 minutes of activity with slow power
% modulation (0.01 - 0.03 Hz)
function generate_artificial_input()
%{
Generate first part: 10 minutes with short alpha burst
%}
% G... |
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