sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d1edb5de51a19ec6142dc8e706bd366895deb9a4d1011eb443742c9a0719328d | MATLAB | 560 | 31 | % op_complexConj.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_complexConj(in)
%
% DESCRIPTION:
% take the complex conjugate of the data;
%
% INPUTS:
% in = Input data in matlab structure format.
%
% OUTPUTS:
% out = Output following conjugation.
function out=op_complexConj(in);
fids=in.fids;
fid... |
ffb0ba41dc299dd3831342a207472b8410843a9828179d86dffcac6afb748b5e | MATLAB | 560 | 18 | function dphidmu = rspnsFuncDeriv(trp, tau, a, b, sigma, k2)
% Derivative of neuron's current-frequency response function
%
% Input:
% trp - refractory period time
% tau - membrane time constant
% sigma - standard deviation of synaptic noise
% a,b,k2 - constants provided ... |
b0d233676c11630fe371dcee5927ca38b85927ce623f65bb05227fc7c7ab6faf | MATLAB | 561 | 30 | function varargout = isDAQmx_Assembly_added
% Return true if NI .NET assembly has been added
%
% function isAdded = nidaqmx.isDAQmx_Assembly_added
%
% Inputs
% None
%
% Outputs
% isAdded - true if NI DAQmx assembly has been added. false otherwise
%
%
% Rob Campbell - SWC 2022
assemblies = System.AppDomain.CurrentDomai... |
91002c35650b7e91d9ce13ffbb1cee26a68d0ed17d92acabf90637ae96f11a59 | MATLAB | 562 | 17 | function runThroughAllStimPoints
% Present stimulus at each location for one second
hZP = zapit.utils.getObject; % Get API object from base workspace
if hZP.isReadyToStim == false
return
end
for ii = 1:length(hZP.stimConfig.stimLocations)
% Does not wait for a hardware trigger: st... |
dbed7659288479da2ee54a6c97799d1fa8b975aaeac4134c60a1fbeddfbe5880 | MATLAB | 562 | 16 | function [U, S, V, variances, pcaCoords, dataReduced] = doPCA(data)
% This uses other function than the matlab default. Data has samples in
% rows and variables in columns.
% For reproducible results.
rand('seed', 4);
% PCA of centered data. Here 20 components only.
[U, S, V] = pca(data - mean(data), 20);
% Calc... |
67bfc9394531c1ed0dae0ec3f84b2ad56e001144a167f01af7e29e9e5779d485 | MATLAB | 563 | 22 | % op_CSIapplymask.m
% Emile Kadalie, Sunnybrook 2025.
%
% USAGE:
% out=op_CSIB0Correction_v2(in);
%
% DESCRIPTION:
% Applies precomputed brain mask to MRSI data to spatially remove
% surrounding lipids.
%
% INPUTS:
% in = MRSI struct
%
% OUTPUTS:
% out = MRSI struct with masked data
function MRSIStruct = op... |
b545c4b539510d1b2665345e6c547345fd283a1c97486a2b573fe1d493b450d3 | MATLAB | 563 | 17 | function figure5(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
b86c907e7206132caf7725f6948c2ecacdb74136c8837d32b46ab45d4f20c378 | MATLAB | 563 | 24 | %% check_dA_tree
%% test 1
clf; hold on;
axis off
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 10
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
dA_tree (tree, rand (1, 3));
end
end
%% test 2
clf;
dA_tree (sample2_tree, [1... |
076bde752920e26e10ff606582ccfaacf4ea329e5e155c193ee9b7a0274cd579 | MATLAB | 564 | 19 | function varargout = figureNB(x,y)
if(nargin==0)
x=8.9;
y=8.9;
end
set(0,'units','centimeters');
SS = get(0,'screensize');
fig = figure('color','w','units','centimeters','ToolBar','none');
fig.Position = [SS(3)/2-x/2,SS(4)/2-y/2,x,y];
set(fig,'PaperPositionMode','Auto','Pape... |
536b212f715531c4926a3530f80c9033ec46cc6ab33f6f443bd89f870989e05c | MATLAB | 566 | 12 | function [T, G, Map, Ang, Pos, wake, rem, sws] = load_mouse_data(data_path, mouse_name)
% Load data from all electrodes
[T, G, Map, ~] = LoadCluRes([data_path mouse_name '\' mouse_name]);
Ang = LoadAng([data_path 'AngFiles\' mouse_name '.ang']);
Pos = LoadPos([data_path 'PosFiles\' mouse_name '.pos']);
... |
54b417096ab37e1af47d5ea8c49165f8388c9c5e239cb376d978abf3d4b2373f | MATLAB | 566 | 17 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [RR_sum] = compute_RR(joint_distribution,input_distribution,output_distribution)
id_norm=sum(input_distribution(:));
od_norm=sum(output_distribution(:));
jd_norm=sum(joint_distribution(:));
PXY=... |
8c436413a07fba8824af61448441b9063a94a22aef9cc094d631b202693e1a65 | MATLAB | 567 | 25 | %% check_flatten_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 10
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
flatten_tree (tree, 'none');
end
end
%% test 2
flatten_tree (sample_tree, '-m');
%% test 3
flatten_tree (sample_t... |
d5ddf1edf0beb9cd8cc2177c29a16cfcf2290c12cb7f562636ec630283860263 | MATLAB | 567 | 21 | function idx = LK_log2idx(logVec)
%
% LK_log2idx converts a logical vector into an n x 2 matrix with indices
% that denote the start and end samples of true values in the logical
% vector.
%
% Lukas Kunz, 2021
% check whether input is logical
if ~islogical(logVec)
error('Input is not logical.');
end
% check wheth... |
f6d871ec61ea94717226241cc67cdc4ceddf553ebbd81e09c2f080c52c4951a4 | MATLAB | 567 | 17 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [MI_sum] = compute_MI(joint_distribution,input_distribution,output_distribution)
id_norm=sum(input_distribution(:));
od_norm=sum(output_distribution(:));
jd_norm=sum(joint_distribution(:));
PXY... |
23999fd1e4509ec453faf95380a8c59c9688e1eeaf447a364d4346cc76355f79 | MATLAB | 568 | 32 | classdef utils_tests < matlab.unittest.TestCase
% Simple tests of the utils module
properties
end %properties
methods(TestClassSetup)
end
methods (Test)
function getDesktopPathExists(obj)
obj.verifyEqual(exist(zapit.utils.getDesktopPath,'dir'),7)
end
end... |
810ce70565c894c453dec00b8e5b32d1c0a1518e7ac1ba2dbc42e711b50d64c6 | MATLAB | 568 | 13 |
% load('PINES.mat')
[~, stats] = predict(discovery, 'algorithm_name', 'cv_svr', 'nfolds', 1, 'error_type', 'mse');
% Haufe_pattern = cov(discovery.dat')*stats.weight_obj.dat/cov(stats.weight_obj.dat'*discovery.dat);
% however, the covariance matrix is huge and we probably couldn't get it
% done in this
% ... |
340c69b14b4c903d0891efff633bdd0b091d54a2fd52fcc4b493ac312df20aaa | MATLAB | 570 | 36 | %%
clear; close all; clc
fig = openfig('channel21Pulse0002s10Hzstim7_simplified.fig');
%%
scaleX = 30000;
dataObjs = axObjs.Children;
Y = dataObjs(1).YData';
Y = Y(round(min(xlim)):round(max(xlim)));
X = dataObjs(1).XData';
X = X(round(min(xlim)):round(max(xlim)))/scaleX;
outData = [X Y];
... |
3aebc0e194044bb958ec6284833122fff047aa883c96d16650fcaaef7ae874b1 | MATLAB | 570 | 25 | function [inter_mod_LD, rho, pval] = longDistanceConnections_modules(net, coords, comm)
N = size(net, 1);
ind_conn = find(triu(net,1));
[row, col] = ind2sub([N N], ind_conn);
ED = EuclideanDistance([coords(row,1) coords(col,1)],...
[coords(row,2) coords(col,2)],...
[coords(row,3) coords(col,3)]);... |
23079564af3e804e6e10f22ad31fc6615ffd813a38af3676abb94810d5b0353f | MATLAB | 575 | 17 | function figureS6(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(b... |
9987dffd0bc663d0f7cbd78e48466ba8cc8d429bf25431cb6a1a33d1fc179ea1 | MATLAB | 575 | 17 | function figure8(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
9e9c6ab33b869e2081156585caa9d34e5965f0d1db76872a636f7035ad398d9f | MATLAB | 575 | 18 | function figure3(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
aca4ce0f50093684916327c6df856eb12ecc466e04e1a8a2a0addde3865203e3 | MATLAB | 575 | 17 | function figure9(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
231b7db8d87398d62685b8380d805e7b848248423dfc2d3b0103e7dedd638063 | MATLAB | 576 | 19 | function r = corr2_new(a,b)
%CORR2 2-D correlation coefficient.
% R = CORR2(A,B) computes the correlation coefficient between A
% and B, where A and B are matrices or vectors of the same size.
% Class Support
% -------------
% A and B can be numeric or logical.
% R is a scalar double.
% Example
... |
90fef036fe4557887a9da77e738630f41fe33c8c88f694973782452d92304b34 | MATLAB | 577 | 15 | function MRSIStruct = removeDimension(MRSIStruct, dimLabel)
dimNumber = getDimension(MRSIStruct, dimLabel);
dimLabels = fieldnames(MRSIStruct.dims);
%updating MRSI parameters
for iName = 1:length(dimLabels)
curDimLabel = dimLabels{iName};
curDimNumber = getDimension(MRSIStruct, curDimLa... |
fe649f3dd618bd2ef116a0366e5ef7ec5e8c738740c68f83ad63587c4c913827 | MATLAB | 579 | 25 | function isReady = isReadyToStim(obj)
% Return true if Zapit is ready to stimulate
%
% zapit.pointer.isReadyToStim()
%
% Purpose
% Returns true if the scanners are calibrated, and the the
% sample is calibrated, and a stimConfig file has been loaded.
%
% Inputs
% none
%
%... |
ffae0146e4c241e0c97ddebf0ef8d9a6d454d599e72d3b21e42d38aa5e29d426 | MATLAB | 579 | 21 | function F = root_lambda_omega(x)
% LS equations for solving instability growth rate and oscillation frequency
%
% Input: 2 unknowns
% x(1) - instability growth rate
% x(2) - oscillation frequency
%
% Output: l.h.s. of 2 equations
% F(1) - LS eq 1
% F(2) - LS eq 2
global ... |
630e7a82a9296b1ffc9951fd632dbaf0529703269eaeff4f3a7672c59952b922 | MATLAB | 580 | 28 | function Y = FuncWoNGaussianCirc1D(P,X)
%% function Y = FuncWoNGaussianCirc1D(P,X)
%
% 1-D circular Gausian function WithOut Normalization for orientation tuning
%
% P = [Amp,X0,Base,Sigma] --- parameters
% Y = Amp*exp(-(X-X0)^2/2/Sigma^2)+Base;
%
% Note: X-X0 must be circularly ranged within -90~90 degree
%... |
01124a028ceec92165936ec6f0d4671f81c6f44a30122363e31dad020e958514 | MATLAB | 582 | 12 | %example code for comparing CC1 decoding to optimal decoding
% here 'cxdat' and 'lgdat' would be (num trials)x(num neurons) matrices. Each matrix entry
% is one spike count response to one trial of stimulus. And 'stimtype' should be
% (num trials)x1 matrix. Each matrix entry should be +1 or -1, which are labels
... |
b23468d3000295657774ae9771faf5661e9fcb95fdcfbc5b1291ef0fe412ba0f | MATLAB | 584 | 27 | function [filtered_data] = filter_pass(data, fs, fl, fh, order)
% operates on columns
fv = [];
if ~isempty(fh)
fv = [fh];
filt_str = 'low';
if ~isempty(fl)
fv = [fl, fh];
filt_str = 'bandpass';
end
else
if ~isem... |
e54ca66965aca32801cb17eff2434e87aae15ba9a06cc0093293cdcecc5b0edf | MATLAB | 584 | 32 | function B = BinND(A,BinSizeVector)
%% Bin A in N dimentions
% BinSizeVector must be a vector with positive integers.
%
%
% YC at ES lab
% Created on Apr. 17, 2008
% Last modified on Apr. 17, 2008
%% Parameters
nBinSizeVector = length(BinSizeVector);
SizeA = size(A);
nSizeA = length(SizeA);
N = min(... |
dbcd75009e5e834ba1eadc1b757d298ed06ee280a27c2b95a98ca698acbc67d1 | MATLAB | 587 | 18 | function figureS4(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(... |
ad287e1e868ce884bf11a3f8443bef99ed25760e13593b2de70fc06e724ba3d7 | MATLAB | 588 | 28 | function ExpDesign = mkExpDesign(nSpace,nTemporal)
% counterBalance spatial and temporal conditions.
% Tries to minimize presentation order bias
% nSpace = 36; nTemporal = 9;
% output
% ExpDesign: temporal sequence of [Run X Spatial Loc]
%
%
[space, time] = BalanceFactors(1, 1, 1:nSpace,1:nTemporal);
for steps = 1:3... |
b4b2fbbbd073c01a7d927823ad653b1df828b57024de0cd6d8982d869ce77927 | MATLAB | 588 | 25 | function setPath
% Add all subdirectories to path
%
% (c) Corey Baron
% Delete any parallel pools, because the workers won't get the new path otherwise
if(exist('gcp'))
poolobj = gcp('nocreate');
delete(poolobj);
clear poolobj
end
topPath = mfilename('fullpath');
topPath = topPath(1:end-length(m... |
bdf6a50878004da93b6d6bb000e9990c44659071ccf6588212636193a101400a | MATLAB | 589 | 11 | function allNeuronsOnOffTraces = getOnOffTracesCellArraysFromTable(StimTableNeuronStim)
allNeuronsOnOffTraces = cell(1, size(StimTableNeuronStim, 1));
for iNeuron = 1: size(StimTableNeuronStim, 1)
allOnOffTracesCell = cat(1, StimTableNeuronStim{iNeuron, 1}.paddedEpochStacks{:});
allOnOffTracesCell = cell... |
c1b514d2a58c04294c13347c752a8fc7215e73daa9beb813b22f161363ba7adc | MATLAB | 589 | 29 | % RAD2DEG Transposes from radians to degrees.
% (scheme package)
%
% result = rad2deg (x)
% --------------------
%
% Simple equation: result = mod ((x / (2 * pi)) * 360, 360)
%
% Input
% -----
% - x ::vector: vector of values in radian
%
% Output
% ------
% - result ::vector: vector of values in degrees
%
% ... |
df3b7d70e6ce3dddcb1a6bd72c146d45bbfcb39e8a2daddde95085420460057b | MATLAB | 590 | 21 | function Hd = LFP_bandpass_filter
%LFP_BANDPASS_FILTER Returns a discrete-time filter object.
% MATLAB Code
% Generated by MATLAB(R) 9.8 and Signal Processing Toolbox 8.4.
% Generated on: 23-Oct-2021 15:27:22
% Butterworth Bandpass filter designed using FDESIGN.BANDPASS.
% All frequency values are in Hz.
Fs = 30000;... |
a95eb9b754f91f7039767f7db61df01face408810b1eec7f4a70175f03ed9b9a | MATLAB | 591 | 17 | function figureS7(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(b... |
a6453dfb4691b649013aebdc892e135bb50c49cc891946d6be5a3dcac57b01b0 | MATLAB | 592 | 26 | %% CHIPS: Cellular and Hemodynamic Image Processing Suite
% Welcome to CHIPS!
%%
%
% <html><a href="./getting_started.html"><b>Getting Started</b></a>
% <br>
% Introduction to the basics of CHIPS</html>
%%
%
% <html><a href="./id.html"><b>Image Data</b></a>
% <br>
% Documentation and examples related to image data</h... |
ed5b719d163f69e0a83c459692e98b12c71987c0c5d291a47323f0fb5dc3db8c | MATLAB | 592 | 23 | function[Matten]=M_atten_tree(tree,thres)
if (nargin < 2)||isempty(thres)
thres = 0.13995;
end
N=length(tree.X);
sse = sse_tree (tree);
sseC = sse > thres * max (max (sse));
sseCM = sseC * 0;
for counter = 1 : N
sseCM (find (sseC (:, counter), 1, 'first') : ...
find (sseC (... |
5fcdf7ec67804a4cd59fd0882f0d8cd2abbeacdcbd400f489e463bea27104445 | MATLAB | 593 | 29 | % DEG2RAD Transposes from degrees to radians.
% (scheme package)
%
% result = deg2rad (x)
% --------------------
%
% Simple equation: result = mod ((x / 360) * 2 * pi, 2 * pi);
%
% Input
% -----
% - x ::vector: vector of values in radian
%
% Output
% ------
% - result ::vector: vector of values in degrees
%
... |
a8f57c4def0502c49695bba42c7d9ae62ece9e4d887179b96f053c259ccac1c4 | MATLAB | 593 | 17 | function figureS8(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(b... |
f9b0fa02c828dd8eca826a87e800868094e44bf8ab5e81044b318b51074e595b | MATLAB | 593 | 22 | function logVec = LK_idx2log(idx, num)
%
% LK_idx2log converts an n x 2 matrix with indices that denote the start
% and end samples of true values into a logical vector of length num.
%
% Use as: logVec = LK_idx2log(idx, num);
%
% Lukas Kunz, 2021
% create a logical vector of length num
logVec = false(1, num);
% if ... |
b0ec003115500bcce8f6b2c1b4356776da97730724e0e9d5480095f6acacf516 | MATLAB | 594 | 24 | function outMatrix = LK_resizem(inMatrix, augFac)
%
% LK_resizem resizes matrix "inMatrix" using the augmentation factor
% augFac. inMatrix is an n x m matrix.
%
% Output is the resized matrix "outMatrix".
%
% Lukas Kunz, 2021
% size of input matrix
[n, m] = size(inMatrix);
% initialize output matrix
outMatrix ... |
d18c5a73326ba316d5d38d90a62461fe194b0264c33c2ad557eccefa737b7dfc | MATLAB | 595 | 21 | function [ avgs ] = applyMasks(masks, img )
%APPLYMASKS Extract mask-wise averages from an image
% masks an MxNxD matrix where D is the number of masks
% img the MxN image to apply the masks to
[M, N, D] = size(masks);
avgs = zeros(1, D);
if D == 1
avgs = mean(mean(img(masks)));
else
for i = 1:D
... |
76836cc57e082b287b0e9718b3a6cd113cfe0274c16e40340f71c90a68974e5f | MATLAB | 598 | 21 | function oct = draw_oct(x, y, w, h, fill_col, line_col)
% Plots an octogon centered at (x, y) of width 2w and height 2h
% INPUTS
% 1) x: x-axis value of octogon origin
% 2) y: y-axis value of octogon origin
% 3) w: width from origin to horizontal extremes
% 4) h: height from origin to vertical extremes
%... |
bca7a212e51fe0749398c8764f5bb1e3cdf1504d6edf7ec495d90eb25620dc49 | MATLAB | 598 | 23 | function [ Pnew ] = makepi( P, trans_prob)
%makepi - Calculate probability matrix
%
% This function serves as basis for the MEX-file makepi_mex. Use codegen
% makepi.m to compile the mex file.
%
% See also utils.hmm
% Checks for P
assert ( isa ( P, 'double') )
assert(all(size(P)<=[1 1681]));
% Checks for trans... |
4c7ec9b1391780c9f3bc3f909506625423d53894cc6d78459f2f4b347ac7979e | MATLAB | 600 | 27 | classdef Mock_RawImg < RawImg & IMock
%MOCK_RAWIMG Summary of this class goes here
% Detailed explanation goes here
properties
end
properties (Dependent, Access = protected)
fileFilterSpec
end
methods
function Mock_RawImgObj = Mock_RawImg(varargin)
... |
628a2f0d1a6a518ec9609b6765071e3a455eb3f9664ddf89300684be28c1408b | MATLAB | 600 | 17 | function [predictedClass,probability] = mdmDecoder(decoder,eegCovariance)
distanceClass1=distance_riemann(decoder.classification.model.parameters{1},eegCovariance);
distanceClass2=distance_riemann(decoder.classification.model.parameters{2},eegCovariance);
%% Prediction of the classLabel and probabilities
... |
58cc7db946281522b973a32b48cefdcdb830f67a1b2b494df76449eaf4219395 | MATLAB | 601 | 18 | function figure4(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
e0042fd64565d2ac351af79a43280bfcc189f078f0c5e9732eeb8de6cea5d1ad | MATLAB | 604 | 21 | function [W_NBS, Clist_NBS, CID] = NBS(Wp, threshhold_NBS)
% a simple implementation of the network-based statistics
% Chuan
Wp_NBS = Wp;
Wp_NBS(Wp_NBS<threshhold_NBS) = 0;
% Wp_NBS(Wp_NBS>=threshhold_NBS) = 1;
% find Connected graph components
[Cindx,comp_sizes] = conncomp(graph(Wp_NBS));
[CID, C_size] = s... |
b414f6a7ddaeeb12e76b501551211f2dc183e56778ea852deec67761b343912c | MATLAB | 609 | 26 | % rf_timeReverse.m
% Jamie Near, Sunnybrook Research Institute 2022.
%
% USAGE:
% RF_out=rf_timeReverse(RF_in);
%
% DESCRIPTION:
% Time-reverse the RF pulse.
%
% INPUTS:
% RF_in = Input RF pulse definition structure.
%
% OUTPUTS:
% RF_out = Time-reversed version of the input RF pulse.
function RF_out=rf_... |
c1533ae1eef5b6f1ed4b011ff4a4fd6d0c203d5f546c7a07ae2dad3221eb7eb2 | MATLAB | 610 | 23 | % convolution and plotting
% Last modification:02/16/2023
%%
addpath('files')
figure(1)
% montage(final_I)
Con_final = imgaussfilt3(final_I,1);
% xz MIP
xzMIP_F = squeeze(max(E_measure,[],1));
figure(2)
subplot(1,2,1);imshow(flip(xzMIP_F,1),[]);xlim([0 15])
xzMIP_J = squeeze(max(final_I,[],1));
% subplo... |
624b714429c7cfddc6fcf38742185b6b6937ec29e409c7bbff0ce231bca8179a | MATLAB | 611 | 21 | function [pred,beta,R2]=stReFit(params,stim,data,t)
%%
fracAlpha = params.analysis.optim.ridgeAlpha;
nChan = getChanNumber(params);
predictions = stPredictBOLDFromStim(params, stim);
predBOLD = predictions.predBOLD;
if size(stim,3) ==1
predBOLD = squeeze((predBOLD));
else
p... |
635bc45910f4960809c4447a16d2f78824a30120195a50844eef3104a24bda81 | MATLAB | 615 | 18 | function figure5(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
c6d582f678a642b77736ec077e06fb13355ba2196d6b4507d79d9a6baf3625ae | MATLAB | 615 | 24 | function res = listExchBetweenCT(model, sol, lowerLimit)
if nargin < 3
lowerLimit = 0;
end
%just list all communication with the [s] compartment
sComp = find(strcmp(model.comps,'s'));%1
sMets = model.metComps == sComp;
rxnsWithsMets = sum(model.S(sMets,:) ~= 0, 1) > 0;
sum(rxnsWithsMets)%11529
fluxSel = sol.x >... |
22cfc9954302a24af0de6ace20c82c914ae30dc0073ba10b3fbfb9d7ebb52407 | MATLAB | 618 | 23 | % Spk = LoadSpk(FileName, nChannels, SpkSampls, SpikesToLoad)
%
% Loads a .spk file
%
% returns a 3d array Spk(Channel, Sample, Spike Number)
%
% nChannels will default to 4
% SpkSampls will default to 32
% Spikes2Load will default to [] - i.e. load them all,except noise
function Spk = LoadSpk(FileName, nChannels, Spk... |
261b0a69e7b9bdefca3b8698e08538765e0c519fe1e6d061977bbe8b22d2fafe | MATLAB | 619 | 24 | function rotMat = rotationMatrix(theta)
% Return the affine rotation matrix corresponding to the angle theta
%
% function rotMat = zapit.utils.rotationMatrix(theta)
%
% Purpose
% Return the affine rotation matrix corresponding to the angle theta
%
% Inputs
% Theta - (in radians)
... |
ec5c1c81dfbf819de176dce0f13bbdb2dd9fb24659e0715059c8161f212b0cf5 | MATLAB | 621 | 18 | function filterOrder = LK_FIRFilterOrderEstimation_20220319(cfg)
%
% LK_FIRFilterOrderEstimation_20220319 computes the filter order for an FIR
% filter using the Fred Harris rule, given some settings in the input
% structure:
% - Fs = sampling rate of the filter
% - deltaF = transition band, in the same units as Fs
% -... |
e5d1ae97a357ccf2fc4f8234bde9731e72b6c1b79aa3fd9a573ec28366d64d0a | MATLAB | 622 | 29 | function [t1, C1, preloaded] = man_fit_v4(filename, peak_guess1, ran1, span1, preloaded)
start = datetime;
tic;
%% Data reading
if ~preloaded{1}
[t1, ~, wl, spectra1, ~] = InsRead2DT_v6(strcat('..\Data\43rd experiment SSPv12\Data\',filename,'.ins'));
else
t1 = preloaded{2};
wl = preloaded{3};
spectra1 =... |
041936431deafff31442974e46908579f247e7b992021bc0967ba207ea80a298 | MATLAB | 623 | 18 |
function selected_images = mkStImages(image_dir,nstim)
image_list = imageDatastore(image_dir,'IncludeSubfolders',true); % get db of images
fileNames = image_list.Files;
randomlySelectedFiles = {}; % Initialize an empty cell array to store selected files
for i = 1:length(nstim)
pattern = sprintf('loc_%d_img', ... |
eee918d36964fad17c92a2f46587f017e6caa49eeaa7a10969d15e8f2458c8ac | MATLAB | 623 | 19 | function resultant = AngularResultant( Theta, Radius, varargin )
% Given a polar data set, calculate angle and magnitude, as well as normalized magnitude, of the resultant.
if nargin > 2, show = varargin{1}; else, show = false; end
[xTemp, yTemp] = pol2cart( Theta, Radius );
[resAngle, resMag] = cart2pol( sum... |
53005f2de736fc882afc097c6eda790f3eebf38be5413103c163253caf02ac19 | MATLAB | 624 | 22 | function [hLine, hErrorPatch] = plotErrorPatch(hAx, x, y, error, lineColor, patchColor, varargin)
if nargin >= 7
faceAlpha = varargin{1};
else
faceAlpha = 0.5;
end
x=x(:)';
y=y(:)';
error = error(:)';
yUpper = y + error;
yLower = y - error;
yLower = yLower(end:-1:1); % Flip lower bound coordin... |
73744bad49752d3f5c4284af40f3d4a177404ce54f9e93f242e97660e64d1628 | MATLAB | 624 | 33 | clear;clc;close all
T = readtable('XXX.csv');
X = T{:, 1:22};
Y= T(:,23);
y = table2cell(Y);
insket = strcmp(y,'Sal');
SVMket = fitcsvm(X, y, "KernelFunction","linear");
Wket = SVMket.Beta;
Sigmax=cov(X);
Sigmass=Wket'*Sigmax*Wket;
Aket=Sigmax*Wket*inv(Sigmass)
T1 = readtable('YYY.csv');
X1 = T1{:... |
a24e8202a973ddca00ce8ea25fba9faf2e16109360365708b7f029f5b857fc5d | MATLAB | 624 | 33 | function storeLastFrame(obj,~,~)
% This callback is run every time a frame has been acquired
%
% function zapit.pointer.storeLastFrame()
%
% Purpose
% Stores the last acquired frame in an observable property
%
%
if obj.cam.vid.FramesAvailable==0
return
end
tmp = ... |
cba7f81bc6835f960295ddc660451b81dc0d92a7d511c4ccdeeadd5fef85d276 | MATLAB | 624 | 16 | classdef test_harmonics < matlab.unittest.TestCase
methods (Test)
function designMatrixHasExpectedOrder3Columns(testCase)
mask = true(4, 5, 3);
basis = fmriPhase.harmonics.designMatrix(mask, [1 1 1], 3);
testCase.verifySize(basis, [numel(mask), 16]);
end
... |
698513a90929a15c9824baf71037ad0420d88fd71eae799a5c5d09e9381d8b11 | MATLAB | 625 | 18 | function figure8(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
ae6f8c3b8f2496f360140702d0da7c8a470e4da4f1631e94777b272b444e0501 | MATLAB | 625 | 48 | %% Sigmoid Calculation
%
% Y=Bottom + (Top-Bottom)/(1+(IC50/X)^HillSlope)
%
clear
% manually input parameters
params = [];
%% Calculate y values
bottom = params(1,:);
top = params(2,:);
IC50 = params(3,:);
slope = params(4,:);
N = size(params,2);
x = 1:0.1:20;
y = zeros(N,length(x));
for... |
ad828e20b8cd1fa694bcca1e089c80784ef6ff79dcaf67accb7c3ec6c7bc44d5 | MATLAB | 626 | 17 | function figure7(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
ee4b3dd82c3a74cede0beb81ede320fa2e0ec341a611f5280e4deb1da8d99526 | MATLAB | 626 | 20 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [input_spiketimes] = independent_poisson(max_time,n_trial,rate)
%INDEPENDENT_POISSON Generates an uncorrelated set of spike times.
input_spiketimes=cell(n_trial,1);
for trial_ind=1:n_trial
these... |
60a724694ee21b55a7aed610a2878bb8f4cddfd60ba92c94d205e73521c40e4e | MATLAB | 627 | 18 | function figureS6(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(b... |
e34702dbd7bdd660ec0aa8d88215deb764b97431a8f878b82ffcad0d78309544 | MATLAB | 627 | 19 | function figure3(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
20bf0e32868fc287e923f40febb23593127e8de64c5000b74b76c7811086c0ea | MATLAB | 628 | 28 | function fix_lighting(fig_handle,~)
% Set the light source of the selected figure (default: current figure) to
% originate from the viewing direction ("headlight"). If there is no light
% source, a new one is created.
% Get figure handle
if nargin<1
fig_handle = gcf;
end
% Find the light object
l_handle = findob... |
526d462b4c27d99fa44078942ec71070be5aa8f73c73ca839167113e42595d39 | MATLAB | 629 | 12 | function [ reduced_data ] = create_reduced_data( neuron_firing, p_neightbors_vec, number_of_reduced_dimensions_vec )
reduced_data = {};
reduced_data{1} = neuron_firing;
for iteration_index = 1:length(number_of_reduced_dimensions_vec)
reduced_data{iteration_index + 1} = reduce_data_by_lapla... |
d2ddff2c4e4b4d57164de44ceccf354d6771d6a1a3e41d408156cb014d585cd3 | MATLAB | 632 | 29 | function nifti = io_CSIload_nifti(niftiFileName)
arguments
niftiFileName (1, :) char {mustBeFile}
end
matlabError = [];
try
fileID = fopen(niftiFileName, 'r');
size = fread(fileID, 1, '*int32')';
catch matlabError
end
if(~isempty(matlabError))
... |
e0ca73dbc688de0453540b8e0c2b59188eae16827e20e6423752ed41f4a06060 | MATLAB | 632 | 24 |
function newDT = tableOutlier(DT,targetParam,outMethod)
if notDefined('outMethod')
outMethod = 'median';
end
for jj=1:width(DT)
paramName = DT.Properties.VariableNames{jj};
if strcmp(targetParam,paramName)%%|| isempty(params.(paramName))
if iscell(DT.(paramName))
rows = ~is... |
0aae557e1da1f9464b6ea372fae2a2c7c4eb2b2acaaa1c4e16c26706eb154eba | MATLAB | 635 | 26 | %% check_flip_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 10
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
flip_tree (tree);
end
end
%% test 2
flip_tree (sample_tree, 1, '-s');
tprint ('./panels/flip_tree1', ...
... |
43af425c59a76c3501204c430fec238d37e8fcbdb30703332070924f2d8da495 | MATLAB | 639 | 24 | function res = listExchBetweenCT(model, sol, lowerLimit)
if nargin < 3
lowerLimit = 0;
end
%just list all communication with the [s] compartment
sComp = find(strcmp(model.comps,'s'));%1
sMets = model.metComps == sComp;
rxnsWithsMets = sum(model.S(sMets,:) ~= 0, 1) > 0;
sum(rxnsWithsMets)%11529
flux... |
90d44db6468ed17abbcf8ae811e808c200cb1ff39242a15f693ff260a45d9b79 | MATLAB | 639 | 25 | %% check_sse_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 100
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
tree.Ri = 100;
tree.Gm = 1 / 2500;
tree.Cm = 1;
sse_tree (tree, [], 'no... |
f9f6b9daed07bac8e11bd9d7fc1e8561cd91cb37ee55c61aba587db32e181f6b | MATLAB | 639 | 19 | function figureS4(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(... |
abd3918035c12159ecf9bc07ad613b1e121b423284eb5069616a7e7f2232ea31 | MATLAB | 642 | 26 | % DEMOs reference
%% pov1_tree
pov_tree (sample2_tree, 'pov1.pov', [], '-b -s1 -w ->');
%% pov1_tree
pov_tree (sample2_tree, 'pov2.pov', [], '-b -s2 -w ->');
%% pov1_tree
pov_tree (sample2_tree, 'pov3.pov', [], '-b -s3 -w ->');
%% pov1_tree
pov_tree (sample2_tree, 'pov4.pov', [], '-b -s4 -w ->');
%% pov1_tree
pov_... |
0aa690bd13f00bdb9e56575eae97a59b316c74b5718db9b11a866849de95b5ff | MATLAB | 644 | 12 | function [triangle_normals]=mesh_get_triangle_normals_new(m)
% Calcuates the normals for each triangles. If the orientation of the
% triangle edges is ccw to a viewer, then the normal points to the viewer.
% USAGE: triangle_normals=MESH_GET_TRIANGLE_NORMALS(m)
% Mirko Windhoff, 2009
% $Id: mesh_get_triangle_n... |
33baf16904d945a28a9a1694c9bb09a2c169e6de07a6449762ddab5f8e4f2957 | MATLAB | 644 | 16 | function [saveFolder, figDir, stimSetCellStr] = parseDatasetVars(datasetInd)
switch datasetInd
case 1
saveFolder = 'D:\Data_LGRTL\Tm9GCaMP6f_2016-2017\';
figDir = 'P:\Documents\Figures\Paper\Tm9\fffOld\';
stimSetCellStr = getStimSetCellStr(1);
case 2
saveFolder = 'D:\Dat... |
11d938aa5e4bdc1383ae09ee899639044fc4b244cb483ab91c62aff19f989b80 | MATLAB | 645 | 21 | %% check_load_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
spread_tree (dLPTCs{1}, [], [], '-s');
tprint ('./panels/load_tree1', ...
'-jpg -HR', [10 10]);
%% test 2
clf;
hss = load_tree ('25HSS.swc');
plot_tree (hss, [], [], [], [], '-b');
tprint ... |
ffbd575bf149995e3768dde11dca4856348c576ac8fcbe68e07b066c6dfecafc | MATLAB | 645 | 20 | function combine_unitary_spectra
baseFolder = '/lustre04/scratch/nbrake/data/simulations/parameter_sensitivity_analysis2';
addpath('/lustre04/scratch/nbrake/code/simulation_code');
pars = zeros(9,2e4);
m = 1e3;
for iChunk = 1:20
filename = fullfile(baseFolder,['analyzed_results_' int2str(iChunk) '.mat']);
lo... |
a269b37829b379ba9c3aaf8a89067dc305c8cf20bbdd2af3491aea74a6fc0c04 | MATLAB | 648 | 26 | %% READ ME:
%
% Written by Zachary Sanger, M.S.
% University of Minnesota
% Biomedical Engineering Department
% May 16th, 2023.
% IF YOU FEEL THERE ARE ERRORS, please reach out at sange019@umn.edu!
% please cite if you use the code
%
% For informal use only, please double check your code for validity and proper imp... |
ee929cce7b088411118fc0b13ea209807472707ccb2f63a89456e00fd1ee2e69 | MATLAB | 648 | 19 | function [mouseDescriptor,mouseIdUnique] = GetAvgPerMouse(DataMatrix,LabelVec,mouseIDVec)
mouseIdUnique = unique(mouseIDVec);
mouseDescriptor = zeros(size(DataMatrix,1),length(mouseIdUnique));
labelUnique = unique(LabelVec);
for m=1:length(mouseIdUnique)
cnt = 0;
avgPerMouse = 0;
for k=1:leng... |
17fd67426380f819c65c675fb4bef14f0434591b7826fd6cffb2c36a2652d2da | MATLAB | 649 | 22 | function [All, outVars] = calcTuningCircular(All, outVars)
% settings
numExps = numel(All);
if ~isfield(All(1).out.anal, 'oriCurve')
error("No ori curve, can't calculate OSI.")
end
for ind = 1:numExps
[tune_result, var_result, curves_result] = tuningByCircular(All(ind).out.anal.oriCurve);
All(ind).out.an... |
6b0297beb3fcaf8f492ba7275972c25428470343f39e629ee0792e05206c102e | MATLAB | 653 | 19 | function figure4(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
% Add paths for function execution
myPath = mfilename('fullpath');
basePath = fileparts(fileparts(myPath));
addpath(fullfile(basePath,'auxiliary'));
addpath(fullfile(ba... |
163f06feb438bf8680a728ec73173eb680f4b507abb0e3d2b1192efa16965b15 | MATLAB | 658 | 24 | %% check_spines_tree
%% test 1
tree = resample_tree (sample_tree, 1, 'none');
spines_tree (tree, [], [], [], [], [],[], '-s');
tprint ('./panels/spines_tree1', ...
'-jpg -HR', [10 10]);
%% test 2
tree = resample_tree (sample2_tree, 0.2, '-d');
clf;
HP = plot_tree ( ... |
2fa8e697ebdd0ebff8171a9da1b3f2559b735c6c760ae7fe69b5fd59b3c0bfd9 | MATLAB | 658 | 18 | % STACKS
%
% functions to deal with image stacks
%
% Files
% fitD_stack - get cylinder diameter values from image stack.
% imload_stack - load image into a 3D matrix.
% load_stack - load stack file into a stack structure.
% loaddir_stack - load images from a folder into a stack structure.
% loadtif... |
3ed34601ac7805961aa89d9af6a69e4493d99efff266361a6c6377fd0519f37c | MATLAB | 658 | 22 | %% check_elimt_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 100
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
iB = find (B_tree (tree), 1);
dtree = redirect_tree (tree, iB);
elimt_tree (dtree, '... |
e5951d79b8785312d325e9a94bddd479f830815188e575c8e788d3424c28b4a5 | MATLAB | 660 | 29 | function [outVars] = detectShotRedCells(All,outVars)
numExps = numel(All);
c=0;
for ind = 1:numExps
us = unique(All(ind).out.exp.stimID);
for i = 1:numel(us)
% s = us(i);
h = All(ind).out.exp.stimParams.roi{i};
if h==0
htg=[];
else
... |
69d141175ece23dabbb5805d1326dcc052fe1b7e316c0657c922133430841a78 | MATLAB | 661 | 28 | function stage_base_calling()
loadParameters;
[ret,messages] = check_files_in_base_calling();
if ret
fprintf('already processed puncta extraction\n');
fprintf('[DONE]\n');
return
end
%TODO: include base calling confidence etc. into this function
% currently this min... |
7652b0bfaa17403c3bcb5a3f7f7b3e572a09a75700a8cdf121112fbc9c535c88 | MATLAB | 662 | 20 | function [blank_field,new_x,new_y] = draw_2(Image, Cores_Stats,radii)
%create a blank image
[row, col] = size(Image);
blank_field = zeros(row, col);
new_x = Cores_Stats(:,2);
new_y = Cores_Stats(:,3);
new_centers = [new_x, new_y];
% centers = Cores_Stats(:,[2,1]);
% testing the location of the two aper... |
e54aed184de7c0cf82685b12146749727a9161659c15a427d40ea6a757040220 | MATLAB | 663 | 23 | %% check_elim0_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 100
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
tree.X (5) = tree.X (4); % setting coordinates same means
tree.Y (5) = tree.Y (4); % making a zero length segment
... |
4147b46274cec0023918313bfa27e1962f2932683f319dbdbe2b8e8db4a6d82c | MATLAB | 666 | 24 | %% check_MST_tree
%% test 1
X = rand (100, 1) * 100;
Y = rand (100, 1) * 100;
Z = zeros (100, 1);
tree = MST_tree (1, ...
[50; X], [50; Y], [0; Z], 0.5, 50, 1000, [], 'none');
clf; hold on;
axis off
HP = plot_tree (tree, [0.75 0.75 0.75], [], [], [], '-b... |
548e8137dba0eeba00170f16a9c74c4e67daaad18babbb5e3d0917449fd5de2b | MATLAB | 666 | 23 | %% check_syn_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 100
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
tree.Ri = 100;
tree.Gm = 1 / 2500;
tree.Cm = 1;
syn_tree (tree, 100, 9... |
3a32e0db0874d09ccca2d8eed55b58d0f1d47ffb54bb9bb63d2d678bb2462077 | MATLAB | 667 | 31 | function devExists = deviceExists(devID)
% Return true if an NI device of a given name is connected
%
% function devExists = nidaqmx.deviceExists(devID)
%
% Purpose
% Returns true if DAQmx reports that a device called devID is attached to the PC.
% If the device is not present, false is returned.
%
% Inputs
% devID - S... |
896655120d7a6187839f33c5e6f8090f99f661ae054663521896d37eafbb32dc | MATLAB | 670 | 15 | % Sample callback function for real-time processing of signal data.
% data - double. new single data point
% channel - string. channel corresponding to the data point. a value of
% "test" is used to ensure the callback works.
function sample_callback(data, channel)
figure(5);
if strcmp(channel,'signal')
sub... |
57553f3fe09f30a9d40c4dc3dccfdf7e3f99ec1e00a860db772a3054eae303cc | MATLAB | 671 | 37 | function E=error_pred(X,Y)
E{9,2}=[];
R=X-Y; T=length(Y);
E{1,2}=sum(abs(R))/T; % MAE
E{1,1}='MAE';
Y2=find(Y==1);
R2=sum(X(Y2)==1)/length(Y2); % TP: true positive
E{2,2}=R2; % MAE
E{2,1}='TP';
R3=sum(X(Y2)==0)/length(Y2); % FP: false positive
E{3,2}=R3;
E{3,1}='FP';
Y3=find(Y==0);
E{4,2}=sum(X(Y... |
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