sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
268e09a44c9d857fb42b0198e446555df7cdd96f7cca967c3d2bebc4e163a8ae | MATLAB | 1,199 | 37 | % Last modification:01/22/2023
% by Peisheng Ding (peisheng.ding@mpi-halle.mpg.de, peisheng.ding@mail.utoronto.ca)
function [filtered_image,radii,radii2] = cores_locations(image_input)
% this function detect the cores loaction by regionprops
% The the outlier data are removed by defining an reasnable range of the... |
c751e897e61cdb923a459bfe988e36b4f4735a3f1621f790e7cebe1c320e62f0 | MATLAB | 1,199 | 35 | function cPointsVolts = calibratedPointsInVolts(obj)
% Convert the calibrated points (sample space) into voltage values for the scanners
%
% zapit.stimConfig.calibratedPointsInVolts()
%
% Purpose
% This method returns voltage values that can be sent to the scanners in order
% to point the be... |
2f8ad035c881d01d653b2b50bb51098f3eb1801d477cb3d09bdca59cd11d09ed | MATLAB | 1,204 | 31 | % op_CSIZeroBaseline
%
% Takes mean of ppm baseline and substracts spectra by this baseline. This makes
% the ppm baseline zero.
%
% INPUT
% MRSIStruct = MRSI structure used in FID-A
% ppmBaselineRange = ppm range of the baseline
%
% OUTPUT
% MRSIStruct = MRSI ouput
function MRSIStruct = op_... |
39e0a363ac17350fdd0cc300240f26d8a96f08d718e5ea9b5a10fdc5472aa430 | MATLAB | 1,205 | 1 | function dispStringInCenter(display,dispString,vLoc,textSize,colorRgb)
% dispStringInCenter(display,dispString,[vLoc],[textSize],[colorRgb]);
%
% 06/2005 SOD ported to OSX
if ~exist('vLoc')
vLoc = 0.5;
end
if ~exist('textSize') | isempty(textSize),
textSize = 20;
end
if ~exist('colorRgb')
colorRgb = display.textCo... |
dd2178201718ae29059de7e361f122c6f207117a9fdae798201099509cb2e546 | MATLAB | 1,206 | 23 | function [m, chunk_points_logical]=mesh_extract_triangle_regions(m, triangle_regions, varargin)
% Removes all points, triangles and data that are not contained in that
% triangle_region. Also all tetrahedra are removed. You can use absolute
% region numbers by disabling the relative_numbers flag.
% relative_n... |
e3daa49d268e43d30dca62d010c5a14b3f40937c2be9e2e705d75766fc7f3d5b | MATLAB | 1,206 | 41 | classdef Live2pWS < WebSocketClient
properties
end
methods
function obj = Live2pWS(ip, port)
% constructor
uri = ['ws://' ip ':' num2str(port)];
obj@WebSocketClient(uri)
end
end
methods (Access = protected)
function onOpen(obj,message)
... |
f8b743c0da9fbaff6e602a577df8a84846b0c6c0b9beb5d1e5a0ab9f2bf11a40 | MATLAB | 1,207 | 44 | function [trialmat trialmatmod] = sim_trials(lf, hf, num_trials, Fs, num_sec)
%function trialmat = sim_trials(lf, hf, num_trials, Fs, num_sec)
%
%This function creates a matrix of simulated trial data (trials stored as columns)
%which contain 'lf' modulating 'hf' PAC. Each trial is 'num_sec' seconds in length
%and the ... |
3305a916f7a853d036d0c5541cf031ba11fe8df3f8dca9948496f44a71d6eac1 | MATLAB | 1,208 | 59 | function analogInput_Continuous
% Example showing how to record data continuously through an analog input channel
%
% function out = daqtoolbox.AI.analogInput_Continuous
%
% Purpose
% Records data continuously and plots to screen.
% Displays positive values only.
%
% Rob Campbell - Basel 2016
%Create a session using... |
34c35a8ac05292356f0a6dee68014feee3eda337de88def2776fa7b42a5fbef3 | MATLAB | 1,208 | 34 | %DUSK Black-blue-green-gray-red-yellow-white colormap
%
% Examples:
% map = dusk;
% map = dusk(len);
% B = dusk(A);
% B = dusk(A, lims);
%
% A black to white colormap with several distinct pastel shades reminiscent
% of colors at dusk. This colormap converts linearly to grayscale when
% printed in black & whit... |
de26e93d38b8edae9397a3eec8a0d9bfe696708acc8a682f5d9a1bbfedbc53dc | MATLAB | 1,209 | 35 | function DataMatrix = SubstractMouseMean(DataMatrix, StimuliLabels, MouseIDs,Days,sessionNames)
uniqueSLabels = unique(StimuliLabels);
uniqueMouseID = unique(MouseIDs);
meanPerMouse = zeros(size(DataMatrix,1),length(uniqueMouseID));
for m=1:length(uniqueMouseID)
meanCurMouse = 0;
cnt = 0;
cntVec... |
d12ba3fb3b926b42038f2cb3a7d28d4a1f7e5e8220dd681935752281528eccb7 | MATLAB | 1,211 | 34 | function [R,C,reg] = RectifyStackDFT(vol, start, upscale)
[~,~,Nz] = size(vol); % Nx,Ny
R = zeros(Nz,1);
C = zeros(Nz,1);
reg = zeros(size(vol));
%figure('WindowState','maximized');
target = vol(:,:,start); %imgaussfilt(vol(:,:,start), 3); %
%forward
for i = start:Nz
source = vol(:,:,i); %imgaussf... |
1318d8470d99775a24a77fb809fa347bc4c153ef1f8c46b558e4a6e7bbe8d260 | MATLAB | 1,213 | 33 | function MRSIStruct = op_CSIZeroFillTime(MRSIStruct, numPointsToZeroFill)
arguments
MRSIStruct (1, 1) struct
numPointsToZeroFill (1, 1) double {mustBePositive}
end
checkArguments(MRSIStruct)
[MRSIStruct, prevPermute, prevSize] = reshapeDimensions(MRSIStruct, {'t'});
data = getData(MR... |
0714c310c0ad28595d4607fb66611f739b058bff13c0738cbf3ec7bddbceffb8 | MATLAB | 1,219 | 31 | function mask = choose_mask_rows(self, strBoundary)
%choose_mask_rows - Protected class method to choose an individual mask
% based on the image rows
% 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 term... |
6d7866ad2133f8782f3086c6b5e170011535fdefa0fd65d629085f397e20977c | MATLAB | 1,219 | 32 | function tf = is_deeper_than(strFun, varargin)
%is_deeper_than - Check if the level of recursion is deeper than a limit
%
% 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 m... |
f664c89f371c89f6b8e3de7855880db6baeaf37aca619891f67171a05738f339 | MATLAB | 1,219 | 34 | function trace = measure_ROI(imgSeq, xIdx, yIdx, propagateNaNs)
% 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, ei... |
b66f38bf3e8c8949257019b7c91d5cd875ede912704ce1dfcb62eefbf8b7a0e1 | MATLAB | 1,220 | 38 | function plot_frame(self, 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 3 of the Licens... |
e33877d7f33d6ad944d98e049ea104a427cf03b2419e42afa8573e3af959b557 | MATLAB | 1,221 | 25 | function [metabolitePlotArray, lcModelYIndexRange, lcModelXIndexRange] = makeLcModelHeatMap(lcModelTable, selectedMetaboliteIndex)
lcModelYIndexRange(1) = min(lcModelTable.Row);
lcModelYIndexRange(2) = max(lcModelTable.Row);
lcModelXIndexRange(1) = min(lcModelTable.Col);
lcModelXIndexRange(2) = max(lcMo... |
961b3433c7e065b1751370b3550ed81f413131f76ef225acd8be4ea377b306af | MATLAB | 1,222 | 47 | %% check_dist_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 100
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
dist_tree (tree, [50 100]);
end
end
%% test 2
dist_tree (sample_tree, [50 100], '-s')
tprint ('./pane... |
bc79fff84cf515d187d7c381bff197806dc4f650e7fc5c9e4f9bf6d21aca698f | MATLAB | 1,222 | 35 | function analyze_simulations(i)
addpath('/lustre04/scratch/nbrake/code/simulation_code');
folder = '/lustre04/scratch/nbrake/data/simulations/mixed_input';
[sa,X] = network_simulation_beluga.getHeadModel;
compute_spectrum(sa,fullfile(folder,'baseline'))
compute_spectrum(sa,fullfile(folder,'high_aperiodic'))
compute_s... |
4fba120777e45dd73a8c7675b0f1fe1e247efb2b5bfce0794eb3343e6af12c4b | MATLAB | 1,224 | 41 | function [outVars] = missedTargetDetector(All,outVars,opts)
numExps = numel(All);
c=0;
ensMissedTargetF = [];
ensMissedTarget =[];
for ind = 1:numExps
us = unique(All(ind).out.exp.stimID);
for k=1:numel(us)
s = us(k);
sidx = find(us==s);
% h is the hologram ID
h = All(i... |
3f44f7571969214ab8ee0089ae76f8dc2ad473d62622b177b1e2599de2a1d66a | MATLAB | 1,227 | 31 | function mask = choose_mask_columns(self, strBoundary)
%choose_mask_columns - Protected class method to choose an individual mask
% based on the image columns
% 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... |
580383bb0fe069ce909b86e78b990322ca9f7f8b296da6e1f09244c0b79b91cf | MATLAB | 1,227 | 38 | %decc_plotFigS1
% Related to Viswanathan, Stein, Nieder, PLOS Biol, 2024
% PV 2024
load('DECCdataFigS1.mat')
% PLOTS
for m = 1:2 %for monkey
% Scatter plots (Figure S1B)
figure1 = figure('Color',[1 1 1]);
pos = [100, 100, 80, 120];
set(gcf,'Position',pos)
set(gca,'XLim',[1-0.5 2+0.5],'XTick',1:... |
d4110f11d6c6a02411a6868bcd5473b996b93a96b89525469a3a6c170b215183 | MATLAB | 1,228 | 47 | classdef Mock_Data < Data & IMock
%MOCK_DATA Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
properties
time
raw1
raw2
processed1
processed2
mask1
m... |
df561b07642445ee20585314c0de21ec782668bfc9b591037fda84458ddba990 | MATLAB | 1,228 | 27 | function [ PCuse ] = defaultPCs(~, mixedfilters, FOV)
%defaultPCs - Select PCs to analyze automatically
% defaultPCs selects range of PCs to be used for further analysis
% automatically. The bounds of cropped interval are determined by amount
% of structural information in the PCs and expected number of relevant
... |
00daa0ef9a1a20227d6ef8d6429af77a9547c35afade5fd4a5e85a375ed7811a | MATLAB | 1,229 | 33 | function f = LK_PlotAvFRForPrefAndUnprefObjects_20231008(dt)
%
% LK_PlotAvFRForPrefAndUnprefObjects_20231008 plots the average firing rate
% for preferred and unpreferred objects.
%
% Input is a structure with multiple fields.
%
% Output is a figure handle.
%
% Lukas Kunz, 2023
% create figure
f = figure('units', 'cen... |
60058d7265270e1ff53f34a2951c91eca50bde5243382250945fe20176de6768 | MATLAB | 1,229 | 35 | folder = fullfile(pwd,'example_embedding');
% Initialize network
network = network_simulation_beluga(folder);
% Initialize post network
network = network.initialize_postsynaptic_network(2,[1,2]);
network.spikingFile = fullfile(network.preNetwork,'spikeTimesLong.csv');
% Presyanptic network parameters
nPreNeurons = 3... |
a3113735b2dddfd6d7244c48a34028deae7918c98e8d649a8ffde46a755c3e51 | MATLAB | 1,230 | 32 | function crop_and_move_files(round_num)
%interpolateDataVolumeSummary Load data and upsample the data
FILEROOT_NAME_INPUT = 'exseqautoframe7i';
FILEROOT_NAME_OUTPUT = 'exseqautoframe7icrop';
%Taken from Fiji so the XY might be measured from the wrong origin
YRANGE = 451:950;
XRANGE = 1001:1500;
ZRANGE = round(43*(.5/... |
765f0ce21ecb6fe0758cd33d80fae367ce0f6aa13123dec7f36aa635ae9ef505 | MATLAB | 1,236 | 43 | function [Rair,Rarg,Rh1,Rh2,Rw,Kair,Karg,Kh1,Kh2,xh1,xh2] = mfc_param_read_v2(fileID)
% Reads MFC parameters from LabVIEW log file header
% reads ranges, k values and hydrogen concentration
% skip the header
header = 5;
for k=1:header
fgetl(fileID);
end
fscanf(fileID,'%s',2); % reads the words before the numeric... |
dddcb2199c8af6642333d28a4e4efbe065aff39825ab143132c0e79a34abcd89 | MATLAB | 1,236 | 42 | % normalization
function success_code = normalization_cuda()
loadParameters;
if length(params.SHIFT_CHAN_STRS) ~= 4
disp('# of channels is not 4.')
return
end
arg_list = {};
postfix_list = {};
run_num_list = 1:params.NUM_ROUNDS;
for run_num = run_num_list
arg_list... |
ee5ad563ed66caeb19f8c726e0a09bc219572e5c608a8ad9e7c511653f5690d9 | MATLAB | 1,237 | 33 | function checkaddpath(dirPath)
%checkaddpath - Check a directory is on the path, and add it if needed
%
% checkaddpath(DIR) checks that the directory DIR, a subdirectory of the
% CHIPS root directory, is on the matlab path and, if it is not, adds it.
%
% See also utils.CHIPS_rootdir, path, addpath
% Copyright ... |
02149d27de272f08aaac76c79d405f9f173deabab35247931bc7b79d73777b0b | MATLAB | 1,238 | 53 | function [img_sequence, nimg, img_durations]= mkTemporal(ExpDesign,temporal)
% counterBalance spatial and temporal conditions.
% Tries to minimize presentation order bias
% nSpace = 36; nTemporal = 9;
% output
% ExpDesign: temporal sequence of [Run X Spatial Loc]
%
%
%%
% nFrames
ifi = 1/temporal.fs;
if ifi ==60
... |
c37a0c1dd2ba95d65ab3a0017b6fddf2cf41509865dfa0173209ceb7dec92f59 | MATLAB | 1,239 | 36 | function tf = is_on_worker()
%is_on_worker - Is the current execution occurring on a parallel worker
%
% TF = is_on_worker() returns a binary flag specifying whether the
% current execution is taking place on a parallel pool worker.
%
% See also getCurrentTask, gcp, parpool
% Copyright (C) 2017 Matthew J.P. B... |
109617f31eff44c66c6d1c22a38b1ee39c045d9721b36779fbd46bde7fbff4c7 | MATLAB | 1,240 | 34 | function DataMatrix = SubstractMouseMeanWithNans(DataMatrix, StimuliLabels, MouseIDs,Days,sessionNames)
uniqueSLabels = unique(StimuliLabels);
uniqueMouseID = unique(MouseIDs);
meanPerMouse = zeros(size(DataMatrix,1),length(uniqueMouseID));
for m=1:length(uniqueMouseID)
meanCurMouse = 0;
cnt = 0;
... |
3194333629e262d8a067a4c11ad8266d9fd0d4df8184ee5543d97963c0ec69a9 | MATLAB | 1,241 | 34 | % getTemporalPts.m
% Jamie Near, Sunnybrook Research Institute 2024.
%
% USAGE:
% NPtemporal = getTemporalPts(kTable,MRSIStruct)
%
% DESCRIPTION:
%This function accepts as input a "kTable" (the output of the function
%'readkFile.m' for a rapid MRSI seuqence and the corresponding MRSI
%structure 'MRSIStruct' and retu... |
8f281736c0c54ab81b33ee3e5a0eab765fe9e395c175a1d3b7ceefcebc8776d2 | MATLAB | 1,242 | 29 | function [genotypeStimArray, nFlies, varargout] = getGenotypeStimArray(validTimeSeriesCollection, ...
genotypeStr, stimStr)
genotypeInds = arrayfun(@(x) ~isempty(strfind(FindSessionPrefix(...
x.dataPath{1}, x.dataPath{2}, x.dataPath{3}... |
27428f85783c3cea5e151cb417d1879f5813b67ec3aa9ee01b7f8a9fbc1e8325 | MATLAB | 1,246 | 48 | % INTERPD_TREE Interpolates the diameter of the nodes between two node indices
% (trees package)
%
% tree = interpd_tree(tree,ind)
% ---------------------------------------------
%
% Linearly interpolates the node diameters between two node indices
%
% Input
% -----
% - tree ::structure: structured tree
% - ind... |
27d4778040b2b18203248c7817bbbcb74737cd271860caa8418c4c7cdb0d9fe4 | MATLAB | 1,246 | 36 |
function plotONOFFTracesFromCell(allNeuronsOnOffTraces, cellTypeStr, figDir, colors)
cLims = ZeroCenteredBounds(cat(1, allNeuronsOnOffTraces{:}), [0 100]);
hFig = createPrintFig(13 * [1 1]);
hSubAx = plotLasagnaTracesFromCell(hFig, allNeuronsOnOffTraces, colors);
nNeurons = numel(allNeuronsOnOffTraces);
ylabel... |
78b19cf083f06521a98e05f73c140b3a5754fa829c55ed6b0cb75b48e844594e | MATLAB | 1,246 | 39 | function [data_bin, ts_dig, dig_Fs, dig_file_ver, dig_num]= PhotometryLoadDigitalInputs(filename)
%% Load file
% filename = 'Test_20190719.dig';
fid = fopen(filename, 'rb');
file_data = fread(fid, 'uint32');
fclose(fid);
%% Process data
dig_file_ver = file_data(1);
if dig_file_ver == 1
dig_num = file_data(2);
... |
bd46ae0304fc0b523f3c11521bd477d41d6ded06dedb0710cbe59631801c7ecb | MATLAB | 1,247 | 68 |
clear
close all force
warning on
imSize = [733, 977];
load('a0_0_bhv2trialStrct.mat');
NIm = 1:62;
tic
UMuscimol = [0, 12,9 ,4,1];
nMuscimol = numel(UMuscimol);
UMonkey = [1,3];
nMonkey = numel(UMonkey);
NIm = [7
11
25
27
38
39
40
47
49
53
56
60... |
bf859e0055b150710900e31a97f938a9c8d6bc2fc69ff2405ec7197130bf37a6 | MATLAB | 1,249 | 54 | function [h,F] =plotwitherror(x,y,isstdrr,varargin)
if(strcmp(isstdrr,'CI') | isstdrr == true)
ymu = nanmean(y,2);
% ymu = nanmedian(y,2);
z = icdf('norm',0.975,0,1);
ylo = ymu-z*stderror(y')';
yhi = ymu+z*stderror(y')';
elseif(strcmp(isstdrr,'SE') | isstdrr == false)
ymu = nanmean(y,2);
ylo = ymu-stde... |
ed46ef69b28876286571d164a2169a11b9e8c5eebcd478d38095e28b75de6d55 | MATLAB | 1,249 | 54 | function stage_registration()
loadParameters;
% sub-stage 1: calculate descriptors
ret = make_links_in_normalization_dir();
if ~ret
return
end
[ret,messages] = check_files_in_calculateDescriptors();
if ~ret
calculateDescriptorsInParallel();
[ret,messages] = check_... |
2fcdb9ad92309fc1907482fa162b3ca7c1ee2b78c66c007a33c1571a47819409 | MATLAB | 1,252 | 40 | function [Power2D, SF2D, Power1D, SF1D] = CalculateSpNoiseSpectrum(RespTrial, SizePxl)
%%
% [Power2D, SF2D, Power1D, SF1D] = CalculateSpNoiseSpectrum(RespTrial, SizePxl)
%
% Calculate the noise power spectrum of the signal (mean subtrated power
% sprctrum), given RespTrial (HxWxT) and pixel size SizePxl. Retur... |
4d422ddf3010fad34d6f17823d332c842817bb2e0ed546fe9634a0447a28f316 | MATLAB | 1,252 | 49 | function clickPosReporter
% clickReporter
%
% Brings up a figure window which places a marker on the
% axes where the user clicks. Each time the user clicks,
% marker moves and the position is reported to the title.
%
%
% Make an empty figure window
fig = figure(7824);
fig.Num... |
b53a85e8ab64d3b6b00aa0ddf1757ddc9c435dc01ce418ffe0ef848696979b4d | MATLAB | 1,252 | 51 | function f = LK_HistogramFigure_20220321(dt)
%
% LK_HistogramFigure_20220321 creates a histogram figure.
%
% Input is a structure with multiple fields:
% figPosition
% axPosition
% data
% binEdges (optional)
% normalization (optional)
% xline (optional)
% xlabel
% ylabel
% title (optional)
% fontSiz... |
67d5eef4b125c45017d9efebec12eae74b0fc16e625f54938635cf38d5c9c26b | MATLAB | 1,254 | 51 | function y = nansem(x,dim)
% FORMAT: Y = NANSEM(X,DIM)
%
% Standard error of the mean ignoring NaNs
%
% NANSTD(X,DIM) calculates the standard error of the mean along any
% dimension of the N-D array X ignoring NaNs.
%
% If DIM is omitted NANSTD calculates the standard deviation along first
% non-singl... |
0d83ba0175148bd6fae87352804b8c9ba7746447d8c3a52cf6d7f94e29b91b4b | MATLAB | 1,255 | 58 | function [uF,uA] = testPointPlace
% Test adding points to a figure window by clicking on the plot
uF = uifigure;
uA = uiaxes('Parent',uF);
uA.DataAspectRatio = [1,1,1]; % Make axis aspect ratio square
pan(uA,'off')
zoom(uA,'off')
grid(uA,'on')
uA.XLim = [0,1];
uA.YLim = [0,1];
... |
4570074f646974e60d7f3a8261b031e0706e85c99ba248a72e423a0179986cbd | MATLAB | 1,255 | 48 | function r = LK_PearsonCorrelation_20220816(v1, v2)
%
% LK_PearsonCorrelation_20220816 estimates a Pearson correlation between
% the two vectors v1 and v2. This implementation is faster than Matlab's
% corr function.
%
% Use as: r = LK_PearsonCorrelation_20220816(v1, v2);
%
% Input:
% v1 --> n x 1 vector;
% v2 --... |
5800c0421cdd5db2007cba8622d6f5d4f3e9ccb3fe70d58a545c2cef50698c0b | MATLAB | 1,255 | 47 | function bool = checkfields(s,varargin)
% Check for the presence of a field, possibly nested, in a structure
%
% bool = checkfields(s,varargin)
%
% We often check for a field that is nested within other fields within a
% structure. We have been doing this with a series of nested or grouped
% isfield statements. This... |
cf16fbec95bc79a304432fc0d17c91339c396c4c3bb6d0ad694902e1f3d473bb | MATLAB | 1,255 | 33 | function [sagital_voxels, coronal_voxels, transverse_voxels] = findIntersectingVoxels(voxels, center)
numSagitalVoxels = 1;
numCoronalVoxels = 1;
numTransverseVoxels = 1;
sagital_voxels(numel(voxels)) = Voxel();
coronal_voxels(numel(voxels)) = Voxel();
transverse_voxels(numel(voxels)) = Voxel();... |
633c73111d43d8be76f7462d68e15916a23b755a0bef74831416cdff5afc0968 | MATLAB | 1,257 | 51 | function [U D,n_eig] = gen_eig(A,B,option,n_eig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Extracts generalized eigenvalues for problem A * U = B * U * Landa
% n_eig -- Number of eigenvalues to compute (optional)
% option = 'LM' or 'SM'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
2ae779ae31be969864c033d83a06d653c618e4e82683d1aee873bc07af162cfa | MATLAB | 1,260 | 37 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [output_spiketimes] = spike_thinner_temporal(input_spiketimes,n_rep,filt_len)
%SPIKE_THINNER_TEMPORAL Removes spikes from input trains if they are within
%'filt_len' of the previous spike.
if nargin<2 ... |
3c1d0a0e158a9350d8670f48810ea258308b3583894b7da434a34398a2d0a5a3 | MATLAB | 1,261 | 28 | function [amplitudeArray, positionArray, widthArray, responseIndArray, ...
categoryLabel] = getParamsArrayFromStimTable(StimTable, qualityMeasure)
[fitParams, gof] = getFitParamsStructArrayFromTable(StimTable);
% domain = StimTable.nonParamTuning{1}(1).domain;
switch qualityMeasure
... |
14c813ca5fbbd2a878ec0d9830c49008a606be218bbd1e45c292d228aea1a589 | MATLAB | 1,264 | 28 | function [ firing_rate ] = create_firing_rate_matrix( full_firing_rate, angles )
% 'angle' should be between 0 and 2 * pi
global NUMBER_OF_ESTIMATED_ANGLE_BINS BEHAVIORAL_SAMPLE_RATE BEHAVIORAL_SAMPLES_PER_TEMPORAL_BIN;
CENTER_OF_ESTIMATED_ANGLE_BINS = [0.5 * (2 * pi) / NUMBER_OF_ESTIMATED_ANGLE_BINS:... |
60d496b3e14607ab4b18f4af491532addc9331216153931b5e4731c64b858916 | MATLAB | 1,264 | 41 | classdef Test_Config_params < matlab.unittest.TestCase
%Test_Config_params Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
properties (TestParameter)
classConf = utils.find_subclasses('Config');
... |
ab2f5a13317688f01c1e946d45df5a70b522f636fc274c88caa28a5ddaf4ae0c | MATLAB | 1,264 | 57 | % SAVE_STACK save images into a file.
% (trees package)
%
% name = save_stack (stack, name, options)
% ----------------------------------------
%
% save images from a stack into a matlab type file
% data has to be in the following form:
% stack.M::cell-array of 3D-matrices: n tiled image stacks containing
% fluore... |
2d14d652116bf56b40540261a1a9a664b24cf48e8a809e11e36bc3a9cb2ea29e | MATLAB | 1,265 | 49 | function outliers = removeOutliers(X,obsdim,prc)
%flip so observations are on first axis
if obsdim ~= 1
X = X';
end
Report = zeros(size(X));
n = size(X,2); %variables
outliers = [];
for i = 1:n
x = X(:,i);
finf = find(isinf(x));
fnan = find(... |
f22dcf44eeccfe1068abf1880f7041753d57e9866db014c9b40e0b7dce8ba773 | MATLAB | 1,265 | 49 | function f = plot_distributions(data, colors)
width = 0.5; % mammals
base = 1-width/2; % mammals
% figure;
for idx=1:length(data)
curr_data = data{idx};
nObs = size(curr_data, 1);
jit = (rand(nObs,1))*width;
jit = jit + base + idx-1;
f{1,idx} = scatter(jit, cur... |
841b3357c2e8fbd31ada8725450c8aed995f5830c98b1485e311ab4c64b89af3 | MATLAB | 1,267 | 42 | function [correctimage, countimage]=applyOffset(imagedata, iFrame, ...
offsets_pf, edgebuffer, correctimage, countimage)
%pick out the number of frames and size of images
[~, Sy, Sx]=size(imagedata);
%loop over the lines we are considering placing
for jLine = 1:Sy-2*edgebuffer
%pick out the line of the data ... |
1761c2c6e30e4fcf9bc4864863def0e0a8d72bdb286c4b95545d2347367d70dd | MATLAB | 1,268 | 36 | function update_rawImg_props(self)
%update_rawImg_props - Class method to ensure that all appropriate
% properties are updated when the rawImg property changes (e.g. when
% constructing an ImgGroup).
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can... |
f26681b047e35561a78399e9206bfad02774a5137050bf4582e3a8867ba70413 | MATLAB | 1,268 | 29 | function citation()
%citation - Output the citation where this software was first published
% 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 ... |
4cf23f06df1918442e63e45992dcdd9e60cec4c8a60e878c41181189ac2b94d3 | MATLAB | 1,274 | 32 | function [maskFilters, maskSegments] = ROIsToMask(self)
%ROIsToMask - Create mask from ROI pixel data
%
% [maskFilters, maskSegments] = ROIsToMask(OBJ) requires a
% CalcFindROIsCellSort object and returns second stage of ROI
% masks produced by the CellSort algorithm. The third stage is yet to be
% exploited (i... |
1a9ea916029f93c5ffb9c129ef06aee27fd9d2532fad49df601be84795b61f1c | MATLAB | 1,276 | 36 | function f = LK_PlotCoactivityAdditionalInformation_20231015(dt)
%
% LK_PlotCoactivityAdditionalInformation_20231015 plots additional
% information related to the coactivity maps.
%
% Lukas Kunz, 2023
% create figure
f = figure('units', 'centimeters', 'position', [2, 2, 7.5, 6]);
% plot data
axes('units', 'centimeter... |
8c201e2dea8f8883f4579c22c352dc22c71a58f702765bedae4dd2febb8fa424 | MATLAB | 1,276 | 30 | function out = getONOFFParamsFromTable(StimTableNeuronStim, varargin)
if nargin > 1
nToExcludeFromEnd = varargin{1};
else
nToExcludeFromEnd = 1;
end
for iNeuron = 1: size(StimTableNeuronStim, 1)
responseInd{iNeuron} = [StimTableNeuronStim{iNeuron, 1}.responseIndex{:}];
params = [StimTableNeu... |
39289d286930c9818c19fedd557e8daa6a7c2e0cf37d52075789ab781ef6a804 | MATLAB | 1,277 | 42 | function [x,a]=data_prep(data)
% Preprocessing Data: change strings with numbers
[m,n]=size(data);
x=zeros(m,n);k=0;
for j=1:n
if isreal(data{1,j})
x(:,j)=data{:,j};
elseif isdatetime(data{1,j})
x(:,j)=datenum(data{:,j});
else
b=str2double(data{1,j});
if ~isnan(b)
... |
f63c38497707166c43757416aa0ace13f35e21126fb4d156b57cae4c2b3e8acc | MATLAB | 1,277 | 39 | classdef Test_CalcDetectSigsClsfy < matlab.unittest.TestCase
%Test_CalcDetectSigsClsfy Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
properties (Constant)
end
% ================================... |
763310187362887635aa745516a136879092def21fe22e2d451306c3012649c1 | MATLAB | 1,278 | 34 | function [ merge_flags ] = calculateMergeFlags( puncta_centroids,MERGE_DISTANCE)
%calculateMergeFlags For a cell array of centroids per round and a distance
%for which it's likely that two (or more) puncta could get merged if the
%colors were the same, give each puncta a number for the possible merge
%errors around it
... |
b3d4443e5674ed3b544f9c32752ff72fcf0c5f8ea2e31c5fbca4e62b5237eb8f | MATLAB | 1,280 | 68 | %mice are in this order:
clear; close all; clc
% % Slowing
% ylab = 'Predictive Slowing (%)';
% A = [78.15801024
% 62.52792071
% 60.00126751
% 79.71455351
% 85.03011564
% 74.70156268
% 72.00241561
% ];
% B = [81.85264945
% 74.96015417
% 75.06798356
% 68.97577327
% 56.49964455
% 65.69598949
% 71.69... |
28ac93d12530ff3346ff4dd7ee26df4a9d8b6908d537735c578706590b61c3df | MATLAB | 1,281 | 45 | %% check_angleB_tree
%% test 1
angleB_tree (sample_tree, '-m');
%% test 2
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 100
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
angleB_tree (tree);
end
end
%% test 3
angleB_tree (sample_tree, '-s... |
d0b6aea8ef23444069762cbcc73cc967d72966b690fdcd8d32729e3377bb46d4 | MATLAB | 1,282 | 40 | function [xVolts, yVolts] = pixelToVolt(obj, pixelColumn, pixelRow)
% Converts pixel position to voltage value to send to scanners
%
% function [xVolts, yVolts] = zapit.pointer.pixelToVolt(obj, pixelColumn, pixelRow)
%
%
% Purpose
% Converts pixel coordinates to volt values for scanner mirro... |
54061fd1e326eec22c104d2891f93d079a7125bec60981c899872b0a1d2344e2 | MATLAB | 1,286 | 56 | %% Stream Example
%
% <html>
% Read a streaming data store into Matlab from Tank server during a recording <br>
% </html>
%% Housekeeping
% Clear workspace and close existing figures. Add SDK directories to Matlab
% path.
close all; clc;
[MAINEXAMPLEPATH,name,ext] = fileparts(cd); % \TDTMatlabSDK\Examples
[... |
99e729f7fcec6aaadbbf9c34236519a3822716d3955d98ac7e0b3ab1cd7d4464 | MATLAB | 1,286 | 43 | function varargout = plot_trajs(self, 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 3 o... |
0c18e9565750ae35720161251540c09216a02501bc9916805089cd77bdd9fe57 | MATLAB | 1,287 | 27 | %function [rSpk, Res, Clu] = GetRawSpk(DatFileName,Res,Clu,nSpkSamples,Channels,Par)
%loads from .dat file the waveshapes of spikes corresponding to Res/Clu from given Channels
% nSpkSamples is either number, then the waveshape will contain equal number of samples left/right or a 2 element vector [left right] # of ... |
36b4ce53e97be563689af4556cc0785e8072ef7f3132f1ac564e83d344374888 | MATLAB | 1,289 | 41 | svrobj = svr({'C=1', 'optimizer="andre"', kernel('linear')});
dataobj = data('spider data', double(discovery.dat)', discovery.Y);
% clear rating
[~, svrobj] = train(svrobj, dataobj, loss);
weights = get_w(svrobj)';
bias = svrobj.b0;
% save('VIFS', 'weights', 'bias', '-v7.3');
% load('Discovery_dataset.mat');
... |
1a8f5bdcf71e545c43e6da1d47f701a0cfcb49cf4e32f4029b5c9516f1263a00 | MATLAB | 1,290 | 56 | %% Stream Example
%
% <html>
% Read a streaming data store into Matlab from Tank server during a recording <br>
% </html>
%% Housekeeping
% Clear workspace and close existing figures. Add SDK directories to Matlab
% path.
close all; clc;
[MAINEXAMPLEPATH,name,ext] = fileparts(cd); % \TDTMatlabSDK\Examples
[... |
cbe5bbca48b632c64bab5fc16a81bc80977ffdd4b0d017a2e280c233c4e1f8a8 | MATLAB | 1,292 | 43 | % op_CSIPlotVoxelfids.m
% Brenden Kadota, SunnyBrook Hosptial 2021.
%
% USAGE:
% [out]=op_CSIPlotVoxelfids(in, x, y, ppmmin, ppmmax, xlab, ylab, title);
%
% DESCRIPTION:
% Plots the fids of one voxel in the CSI FID-A structure. Additional
% arguments augments the output plot. Uses the op_plotfid function.
%
% INPUTS:... |
53d0ec7e5a8c69dbdf64317824d3194e11c3134499ee7c63eb2cd00554f16b93 | MATLAB | 1,293 | 37 | function generate_images()
addpath(genpath('TOOLBOX_DIR/BrainNetViewer_20191031/'))
addpath(genpath('TOOLBOX_DIR/vistasoft/'))
niis_dir='PROJECT_DIR/results/restfmri/dnn/niis/indiv_niis/';
output_dir='PROJECT_DIR/results/restfmri/dnn/brain_plots/indiv_plots/';
file_list=dir(niis_dir);
for nii_... |
29616414d84d86acf9614c8f02f726078114104241d95b9f4424e14a898c075b | MATLAB | 1,294 | 25 | %Swapping the target directory
%MUST be ran in root repo directory!
%Eggplant directory:
%target_dir = '/mp/nas0/ExSeq/AutoSeq2/xy10HP'; %No trailing slash!
%target_dir = '/mp/nas0/SplintR/09deconv'; %No trailing slash!
%target_dir = '/mp/nas0/SplintR/09deconv'; %No trailing slash!
target_dir = '/mp/nas0/SplintR/09dec... |
744a1129782b1b7f11ee395479bc730b43c15d879af559e9db7d67d70e8ba2e4 | MATLAB | 1,295 | 29 | function [spikeMat, tVec] = t2n_poissonSpikeGen(freq, par, nTrials)
% This function creates Poisson spike trains at a frequency 'freq' the
% output is a spike matrix and a time vector, both which can be used to
% define a artificial NEURON VecStim that follows such a spike train.
%
% INPUTS
% freq desired freq... |
e657e74e0a6e6a663e7c6afe2240b64127b5258b2115bdf3ebdab49867c7628f | MATLAB | 1,295 | 27 | % CONSTRUCT
%
% functions to generate synthetic trees
%
% Files
% allBCTs_tree - Outputs all possible trees with N nodes.
% BCT_tree - Creates a tree from a BCT string.
% clean_tree - Cleans a tree from nodes inside of main branches.
% clone_tree - Cloning a tree type using the MST c... |
2fde131c883d4b3c7d6930427f0dbab46eb9ac570df9f3407fa7d6c9d70c6c38 | MATLAB | 1,296 | 35 | function [ roiTcs ] = ApplyROIsToStack_TimeCourse( I, roiStruct )
% takes a 3D stack and roiStruct and extracts time courses from the stack
% for the ROIs. adapted from matlab file exchange 26482. this approach is
% ~3x faster than my original approach, which obtained a ROI's timecourse
% by repmat'ing the mask to the ... |
110df5d14788a115f134d182c9ac71ffd5e6e11a1355383afc1e5abb7b6e4132 | MATLAB | 1,298 | 43 | function bfunc = basisFuncSphHarm(obj,n)
% Outputs basis function for index n of spherical harmonics
% n = index of phs_spha in sampHighOrder.m
x = obj.phs_grid.x;
y = obj.phs_grid.y;
z = obj.phs_grid.z;
switch n
case 1
bfunc = ones(size(x));
case 2
bfunc = x;
... |
dc8bce759fe36e13e47570573b12768497503fd61ef606ef08feb01664b6f9c0 | MATLAB | 1,298 | 40 | function varargout = plot_average(self, 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 3... |
a878aac49ba78717b5bc423c577d21e908ac14c997037807fd584acdb861317e | MATLAB | 1,299 | 48 | function [h,p] = my_sig_test_fdr(pacval, pac_shf_values, alpha, measure)
% function [h,p] = my_sig_test_fdr(pacval, pac_shf_values, alpha, measure)
%
% Returns a binary value for significance 'h' and a p-value 'p', given a
% value under analysis 'pacval', a distribution of values for comparison
% 'pac_shf_values' and a... |
84ee251582db36b84e9beaa3e3d2f60e8932e3cb53ac9a3d7aa95fa6bcf18725 | MATLAB | 1,300 | 45 | %% Trigger Input
%
% <html>
% This examples shows how to start a Synapse recording using an external
% trigger into your processor <br>
% Matlab monitors the bit input and controls Synapse state <br>
% </html>
%% Housekeeping
% Clear workspace and close existing figures. Add SDK directories to Matlab
close a... |
8d37535f9edbd832d34019e7c3a5ea0efd7263c5fdfe0201f7894940cfc0e49f | MATLAB | 1,300 | 48 | function [bp_sig1, bp_sig2] = filt_signalsWAV_bp(sig1,sig2,...
Fs, freq_vec, width)
% function [bp_sig1, bp_sig2] = filt_signalsWAV_bp(sig1,sig2,...
% Fs, freq_vec, width)
%
% This function band-pass filters sig1 and sig2 using a wavelet filter.
% Bandwidth of filter assumed equal to the difference between max(f... |
0678e6dec7b857ddefc8b6d34e64af04284e7a8e93d017ddf6aaed03142227ef | MATLAB | 1,301 | 33 | function MakeSbxZ(sbxPath, sbxInfo, shiftPath, varargin)
% Load interpolation results
load(shiftPath,'-mat');
RS = RS1 + RS2 + RS3 + RS_chunk;
CS = CS1 + CS2 + CS3 + CS_chunk;
ZS = ZS1 + ZS_chunk;
tic
fprintf('\nLoading %s', sbxPath); tic;
sbx_data = readSBX(sbxPath, sbxInfo, 1, sbxInfo.Nscan, -1, []); toc
... |
88e4bcd4af9e2b6369e609dd42e9a5ab920a1cbb03ed4f209b5d6d9b9574e97b | MATLAB | 1,303 | 38 | function c = redblue(m)
%REDBLUE Shades of red and blue color map
% REDBLUE(M), is an M-by-3 matrix that defines a colormap.
% The colors begin with bright blue, range through shades of
% blue to white, and then through shades of red to bright red.
% REDBLUE, by itself, is the same length as the current figu... |
ff8d9c0471dad58773b00d9b615fe27da9aea18a7ead53f58c4a1b3e555ad232 | MATLAB | 1,305 | 39 | function [ b_out ] = A_pca_3d(Fpsf, weights, x, Size, BG, padding)
% [ b ] = A_pca_3d(Fpsf, weights, x, BG, pad, crop)
% Fpsf: 2D Fourier transform of PSFs, size Ny x Nx x Npc x Nz
% Ny - num pixels in y (after padding)
% Nx - num pixels in x (after padding)
% Npc - num of spatially varying PSF... |
97a0adff935d6c85e9d8e994f9de679525a13e766d5427e7974e194f238f9246 | MATLAB | 1,307 | 33 | dataFolder = 'E:\Research_Projects\004_Propofol\manuscript\Version3\Data';
load('E:\Research_Projects\004_Propofol\data\experiments\scalp_EEG\raw\time_series_all_channels.mat')
load(fullfile(dataFolder,'data_time_information.mat'));
t0 = timeInfo.infusion_onset-timeInfo.object_drop;
elName = {'Fz', 'Cz', 'Pz', 'C3', ... |
c4561230855eb1753276c62b9e5b34a02c7cefa65cab315198a3969bb82be6e9 | MATLAB | 1,309 | 43 | function [shuffled_output_spiketimes] = spike_expansion_random(input_spiketimes,n_exp,n_rep,p_del)
%SPIKE_EXPANSION_RANDOM Expands input spike trains into random numbers of output units
if nargin<2 || isempty(n_exp)
n_exp=5;
end
if nargin<3 || isempty(n_rep)
n_rep=8;
end
if nargin<4 || isempty(p_del)
p_del=... |
f368d881aaaadc719a6e82c88d95438a7098575f5d9788eab7521877c39892c1 | MATLAB | 1,309 | 46 | function [xVolts, yVolts] = mmToVolt(obj, pixelColumnInMM, pixelRowInMM)
% Converts position in the image in mm to scanner voltage value to send to scanners
%
% function [xVolts, yVolts] = zapit.pointer.mmToVolt(pixelColumnInMM, pixelRowInMM)
%
%
% Purpose
% Converts mm coordinates to volt v... |
8721673f95b49c77b38915acb93a53decb8013126a702af7c4ae3c2c2239aad1 | MATLAB | 1,313 | 33 |
load('figure_2_data.mat');
% The variables "all_wake_thal_to_cort" and "all_wake_cort_to_thal" contain
% the average normalized patterns of spectral information transfer between
% the thalamus and cortex, estimated on a sub-sample of our data, for 9
% human ET patients, 8 Long-Evans Rats, 7 GAERS rats, and 5 C57/BL6 m... |
291a50db752fa87bc24e150ac9e22bbaba8bb45d548103c8cc4708f64afc0385 | MATLAB | 1,314 | 40 | function initialize_network(masterFolder,branchNo,arrayID)
addpath('/lustre04/scratch/nbrake/code/simulation_code');
fid = fopen('dyad_morphologies.txt');
txt = textscan(fid,'%s%s','Delimiter',',');
mTypes = cat(2,txt{:,1},txt{:,2});
for j = 1:10
i = 10*(arrayID-1)+j;
m_ID(1) = mNa... |
d2811e320ee3ff9c60bac439e02e7da86261db0143847e62baa4fed2e4ac9320 | MATLAB | 1,315 | 45 | %% check_dissect_tree
%% test 1
dLPTCs = load_tree ('dLPTCs.mtr');
for counterN = 1 : 100
for counter = 1 : length (dLPTCs{1})
tree = dLPTCs{1}{counter};
dissect_tree (tree);
end
end
%% test 2
dissect_tree (sample_tree, '-s');
tprint ('./panels/dissect_tree1', ... |
1af744a96a3422a0ff4e0e7bf71f810fa35f947496fd62a3109cfc4c1024f75c | MATLAB | 1,316 | 35 | function pac_plot_fun_tf(pacmat, time_vec, amp_freq_vec, measure,...
structure1, structure2, dataset, ph_freq)
% function pac_plot_fun_tf(pacmat, time_vec, amp_freq_vec, measure,...
% structure1, structure2, dataset, ph_freq)
%
% This function plots a PACgram with time along the x-axis and modulated
% (higher) f... |
3e48241acb8043dcd622a9b92a7248114f864450072fbf2441904de97fc538ca | MATLAB | 1,316 | 38 | function goi = goi_gradients(ts,maxorder,biascorrect)
% Compute low order O-infomation descriptor of data
% INPUT
% ts input (observations x variables), time series or static/behavioral data
% maxorder maximum order for the gradients
% biascorrect apply or not bias correction for en... |
94a5a1fd61418ed8997dcf6d7f6c3bb6e6b46161d26b1d85a44f18f0222e27b4 | MATLAB | 1,316 | 57 | raw_data = '/Users/gustavo/git/ahof_vocalmat/vocalmat_classifier/training/.rawdata';
model_name = 'alexnet_pretrained';
dataset_name = '18-october-dirty';
load(fullfile(raw_data, model_name, dataset_name, 'table_performance.mat'));
scores = table2array(T(:,5:16));
sorted_scores = sort(scores,2);
ratio = sorted_sc... |
cd2b48381ba36f2f1094c6e6b368608b4bf3afd07cd76d07db995fc12ac2509b | MATLAB | 1,316 | 59 | % op_leftshift.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_leftshift(in,ls);
%
% DESCRIPTION:
% Remove leading datapoints from the fid to get rid of 1st order phase
% errors.
%
% INPUTS:
% in = input data in matlab strucure format.
% ls = number of points to remove from the beginning of the f... |
f507da3acdc1aecfe142cf4c548376a9a793ec3481ed4a0d13eac81287d93f5b | MATLAB | 1,316 | 50 | function varargout = DAQmxVersion
% List DAQmx version via the .NET assembly
%
% function [versionAsString, versionAsStructure] = nidaqmx.DAQmxVersion
%
% Purpose
% Query the NI DAQmx version using the .NET assembly. If no outputs are
% requested, the results are printed in screen. If outputs are requested,
% the user ... |
a0b74932096effa31af5b7f67ad35197820041d97398764faebee087b700d63d | MATLAB | 1,319 | 35 | function [t, a] = computelorenz(sigma, beta, rho,tspan, h, x0, y0, z0)
% sigma, beta, rho: Lorenz attractor parameters
% tspan: a 2-element vector [t0, tf] specifying the initial and final time
% h: the time step size
% x0, y0, z0: the initial values of x, y, z at t0
% t: a column vector containing the time steps
% x, ... |
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