sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5737f54939002fceeeed240bbed9becc48082e75d7208636e1b44c66b0909998 | MATLAB | 5,149 | 148 | function varargout = findSettingsFile
% Find the Zapit settings file and return as a string
%
% function settingsFile = zapit.settings.findSettingsFile()
%
% Purpose
% There are three places the Zapit settings file could be located. This function
% Looks through this in the following order:
... |
13620791dc4b1ef3ce2a2314fd517981253795885fd148e661d902555f26beb8 | MATLAB | 5,152 | 242 | clear
close all
%% 1) read data and prepare them
%addpath('../TOY/data')
load ellipses2D.mat
exp = '4';
options.kernelt = 'rbf';
modif = createModif(exp);
modif.additDim = 1; % number of replication of the dimensions
%% create data
N=20;
load ../TOY/data/ellipses2D.mat
r = 0.15; % noise in the multidim data
%A... |
1bbb0ce91da9e817a65707af531fb41d359d1c68094cee6b9d55831742b90dd8 | MATLAB | 5,163 | 157 | function varargout = denoise(imgSeq, varargin)
%denoise - Denoising of an image sequence
%
% This function implements a block matching 3D (BM3D) algorithm for
% improving signal-to-noise ratio in two-photon imaging data. For further
% information about BM3D, please refer to <a href="matlab:web('http://doi.org/10.... |
e4c155c29ccd9fb63e7e4847cfc4eeeff709db41824fe82ffe83b72b927e4226 | MATLAB | 5,169 | 184 | % op_alignScans.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [out,ph,frq]=op_alignScans(in,in1,tmax,mode);
%
% DESCRIPTION:
% Use spectral registration to align two separate scans (align in to in1);
%
% INPUTS:
% in = input (spectrum to be registered)
% in1 = base (spectrum that the input is to ... |
63306472c9ee1ceebb4c5d2b732a6821608fc041e806b0f7d8863dc7626412e2 | MATLAB | 5,183 | 99 | function fig = t2n_IVplot(targetfolder_data,neuron,ostruct)
% This function uses the simulation data generated by t2n_voltSteps and
% plots the IV relationship at each voltage step.
%
% INPUTS
% targetfolder_data folder which was given to t2n_voltSteps, where the
% data of the simulation lies... |
dd58d8c77e2c114c49431b03a46c616e4e98b3a55fe53061934bb701150aea0b | MATLAB | 5,185 | 115 | classdef ConfigCellScan < ConfigMultiple
%ConfigCellScan - Class containing Config objects for CellScan
%
% The ConfigCellScan class is an abstract superclass that is designed to
% contain more than one Config object to simplify construction of
% CellScan objects. This ensures that a single Config object can be
... |
809a70d084fd2487f7704a00073befcfa6abd5eb976a535cb6d9ec655cc02e51 | MATLAB | 5,201 | 147 | %%
% Reproduces Iso vs. Ortho plot for Compact vs. Diffuse
% co-tuned condition (Fig. 4B and 4C)
%
% Function inputs:
% cellTable: structure containing neuron data
% cellCondTuned: vector of 1's and 0's that denotes which cells should be
% included (e.g., only tuned cells)
% cellCondNonVis: vector of 1's a... |
72941949b589d33c42d52b1048d85de8095be48259dc515cec1939ba992123f1 | MATLAB | 5,209 | 128 | function connectClockedAO(obj, varargin)
% Set up a clocked AO task
%
% function zapit.DAQ.dotNETwrapper.connectClockedAO
%
% Purpose
% Create a clocked AO task for opto-stimulus delivery.
% The connection options are set by properties in the dotNETwrapper
% class. see: .device_ID, .AOc... |
af921e62464dfebdf5d1da9de0d3b9462e5f7181359deb51fc22d52cfc00df9b | MATLAB | 5,209 | 177 | % SSECAT_TREE Steady-state electrotonic signature of connected trees.
% (trees package)
%
% sse = ssecat_tree (intrees, inodes1, inodes2, gelsyn, I, options)
% -----------------------------------------------------------------
%
% Concatenates many trees with electrical synapses and calculates the
% steady-state matri... |
832c77a88814a451bc246c55de1b9c5b8adedfba01fe231dbdfd8f64409248be | MATLAB | 5,210 | 164 | %REAL2RGB Converts a real-valued matrix into a truecolor image
%
% Examples:
% B = real2rgb(A, cmap);
% B = real2rgb(A, cmap, lims);
% [B lims map] = real2rgb(...);
%
% This function converts a real-valued matrix into a truecolor image (i.e.
% double array with values between 0 and 1) using the colormap specifie... |
024afb888ee3c4d0b5860f578f2dca2be2ac8810e00b42e56456987dc571255b | MATLAB | 5,213 | 152 | %% 2D Fast Reconstruction code for Bio-FlatScopeNHP
% Set to working directory
protoDir = './Examples/';
psfExt ='.mat'; % '.mat', '.tiff';
capExt ='.tiff'; % '.mat', '.tiff', '.avi'; % For avi, select only one file
H = 2048; W = 3072; %Imaging SourceMos
binFlag = 0;
%% Params
gamm_l2 = 5000; % Typica... |
bba2358872d196a819891c6b95c8d6aea25d2d4cf0fc638be0b0ff53ac531d02 | MATLAB | 5,225 | 153 | function [out] = EEGfMRIPav_cbm_mod04_modSim(parameters, subj)
% Standard Q-learning model with delta learning rule and Go bias and
% Pavlovian learning bias.
% ----------------------------------------------------------------------- %
%% Retrieve parameters:
% 1) Feedback sensitivity:
nd_rho = parameters(1); % ... |
939fc05407a1199b188b3ae3beb54f26c19638027428353a47bb90fef67e4380 | MATLAB | 5,240 | 147 | function [P] = snpm_P_FDR(Z,df,STAT,n,Ps)
% Returns the corrected FDR P value
% FORMAT [P] = snpm_P_FDR(Z,df,STAT,n,Ps)
%
% Z - height (minimum of n statistics)
% If empty, find all FDR P values for Ps vector (in which case
% STAT is ignored, as Ps must be P-values already).
% df - [df{interest}... |
11831b177f0e1b5a8cdc682ae398047fc692802ade640f7602f244e20873911a | MATLAB | 5,249 | 157 | % op_peakFit.m
% Jamie Near, McGill University 2017.
%
% USAGE:
% [fit,parsFit,residual]=op_peakFit(in,ppmmin,ppmmax,parsGuess);
%
% DESCRIPTION:
% Perform a Voigt lineshape fit to a prominent singlet resonance within the
% provided ppm window of a proton MRS dataset.
%
% INPUTS:
% in = input data in matlab stuc... |
1f28956e4227d1d9fdd352da551ab47e4f823851a5d2b7f19410b33650f4c7cd | MATLAB | 5,252 | 153 | function varargout = plot(self, varargin)
%plot - Plot CalibrationPixelSize objects
%
% plot(OBJ) produces a plot of the CalibrationPixelSize object OBJ.
%
% plot(OBJ, DOSAVE) specifies whether to save the plot to a file. DOSAVE
% must be a scalar value convertible to a logical. The function will
%
% plot(OB... |
34022585926a67e4ac0615ce2e92fab4d5775ffeaeebbc932f23276c2cf51b46 | MATLAB | 5,256 | 174 | function [offsets, refImgs, doPar] = calculate_offset(chSeq, ...
refImg, maxShift, frameRate, varargin)
%calculate_offset - Calculate line-by-line offsets
%
% [offsets, refImgs] = calculate_offset(CHSEQ, REFIMG, MAXSHIFT, FRAMERATE)
% calculates the offsets for each line in an image stack based on the
% maxim... |
bd8cd7aa48c0de387403a8226d6ddaa6b591ac6e91c2b98354062d2e838ad519 | MATLAB | 5,262 | 165 | function varargout = hardwareContinuousVoltageRampDown(devID,nonInteractive)
% Example showing how to ramp down a regenerative signal
%
% function nidaqmx.AO.hardwareContinuousVoltageBasic(devID)
%
% Purpose
% Shows how to do hardware-timed analog output using the DAQmx .NET interface.
% Thi... |
73bff7f8c385665eb965b8476ca8eca63ca6627a20922886399ff3bdd79020b0 | MATLAB | 5,264 | 122 | %Used to copy all data from the complete CA-1 morphology round into h5
%files in an organized folder structure. Specifically, this script must
%also create a common field of view numbering structure, which is important
%because a microscope glitch created a varying number of tiles per
%sequencing round
% Written by Dan... |
57cbd1891c77d04d7382e810e542880f4b9db5e9c23a8e8d502d578e7bd6a95b | MATLAB | 5,283 | 194 | addpath './Tools';
load M28D20220720R11TS.mat
fnTS = 'M28D20220720R11TS.mat';
load 'M28D20220720R11FFTAmpS026E100PF0400.mat';
Condition = TS.Header.Conditions;
Num_valid = TS.Header.Index.iValidBLKCond;
%% Parameters
DefaultValues;
iCondBlank = 1:TS.Header.NumBlankCond;
nCond = TS.Header.NumValidCond;
... |
34270c9497b6ee6087fd5a4c5c3eae3d3ec7d2f7a5bca554616b32e3478c4324 | MATLAB | 5,285 | 160 | function tests(obj)
N0 = 128;
%% Check adjoint for basic case
imN = [N0 N0];
b0 = randn(imN) + rand;
imk = [N0 1];
sampTimes = randn(imk)/sqrt(prod(imk));
phs_spha = randn([16, size(sampTimes)]);
phs_coco = randn([4, size(sampTimes)]);
phs_grid.x = randn(size(b0));
phs_grid.y = randn(size(b0));
phs_grid.z = randn(siz... |
b1fd213dab0fd335d8bbefd9a7a08e1bb66a915a4c74556728eddf66d9682742 | MATLAB | 5,286 | 129 | classdef (Abstract) CalcDiameterXSect < CalcDiameter
%CalcDiameterXSect - Superclass for CalcDiameterXSect classes
%
% CalcDiameterXSect is an abstract superclass that implements (or
% requires implementation in its subclasses via abstract methods or
% properties) most functionality related to CalcDiameterXSect o... |
992e351092a2305e0a789abe73b1c4ad91cf68200ba6956a6134f0d503b2d9d1 | MATLAB | 5,289 | 133 | classdef CalcDiameterFWHM < CalcDiameterLong
%CalcDiameterFWHM - Class to calculate diameter using the FWHM approach
%
% The CalcDiameterFWHM class is Calc class that implements all basic
% functionality related to calculating the diameter of images using the
% full width at half maximum (FWHM) approach.
%
% Ca... |
889d051393f2891c0f6a659f72e5ce6bd14e67c43f8c76525a2c57eeaa5303cd | MATLAB | 5,292 | 134 | % run_simSteamShaped.m
% Jamie Near, Sunnybrook Research Institute 2022.
%
% USAGE:
% [out,out_posxy]=run_simSteamShaped(spinSys);
%
% DESCRIPTION:
% This script simulates a STEAM experiment with fully shaped RF
% pulses. Coherence order filtering is employed to remove unwanted
% coherences. Simulations are run at ... |
95e46029fae4c6930e05cd8116c56a5a166249ff9f4d189c758c012b7625843f | MATLAB | 5,304 | 138 | classdef Test_ZZZ_Make < matlab.unittest.TestCase
%Test_ZZZ_Make Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
methods (Test)
% function testMakeTlbx(self)
%
% ... |
2981c4a1cba65167e02ba63d99715e6beab6c93001e1a7df11f57ea78777b254 | MATLAB | 5,309 | 141 | function varargout=shadedErrorBar(x,y,errBar,varargin)
% generate continuous error bar area around a line plot
% function H=shadedErrorBar(x,y,errBar, ...)
% Purpose
% Makes a 2-d line plot with a pretty shaded error bar made
% using patch. Error bar color is chosen automatically.
% Inputs (required)
% x - vect... |
3a09ba8d09b403b10444309840e7d4e757bb33ef07c99a2901fe2f9b6e1506fd | MATLAB | 5,312 | 142 | % 2021 EDIT: This function is now deprecated. The current version of the
% shaped PRESS simulation is sim_press_shaped.m, which employs
% coherence selection rather than phase cycling to null undesired signal.
% sim_press_shaped_phCyc.m
% Robin Simpson and Jamie Near, 2014.
%
% USAGE:
% out = sim_press_shape... |
bc1269c0b68dd5e85d465a3a262a89e241727ec70f36d6db65b6e255bf722394 | MATLAB | 5,313 | 127 | function [maxdv,fig] = t2n_plotdV(targetfolder_data,neuron,ostruct,targetfolder_results)
% This function creates a phase plot (dV/dt) of the current steps that were
% simulated with t2n_currSteps.
%
% INPUTS
% targetfolder_data folder which was given to t2n_currSteps, where the data
% of the ... |
aadedfda3003036427765c1351532de5d5b3d20db9f5f2cde80fb48399669912 | MATLAB | 5,320 | 131 | % run_simSemiLASERShaped_phCyc.m
% Dana Goerzen (McGill University, 2019).
%
% USAGE:
% This script runs a spatially resolved, shaped simulation of the sLASER
% experiment, using the sim_sLASER_shaped_phCyc.m function.
% Adjust all parameters as desired and click "Run"
%
% DESCRIPTION:
% Simulates CMRR semi-LASER ex... |
66601408b15507cd5219949ac18cd752510de593269c8155db6407ce49b3f960 | MATLAB | 5,324 | 162 | % FigureS09.m
% Plots for Supplementary Figure S09.
% Will call taft_save_PEs() to load PEs for selected subject (sub 07).
%
% EEG/fMRI STUDY, DONDERS INSTITUTE, NIJMEGEN.
% J. Algermissen, 2018-2023.
% Should work in Matlab 2018b.
% we are here:
% cd /project/3017042.02/Analyses/FiguresOutcomeLocked
% clear all; cl... |
62f239256671974bea9991d88de83fb340dfc00f94a6be52d31035070e7f0618 | MATLAB | 5,325 | 176 | function tree = myelinate_axon(tree)
%Adds simple myelin to an existing axon, with nodes at every axon
%bifurcation as well as between internodal myelin segments.
%Terminal branches below 20um are left unmyelinated; diameters are set to
%uniform 1um for myelin segments, 0.8um for unmyelinated.
%Note: Regions must... |
c19a3cf39215a4ea42b11bbfd9faa5039fb7a49996cc23872e303cc9ef42515b | MATLAB | 5,327 | 136 | function [sortBetas, Tvalues] = taft_postprocess_time_selectData(job, betas, iROI)
% Extracts time-domain data for selected ROI,
% sort channels across subjects, selects valid subjects,
% combine subjects into 3D data, perform one-sample t-test for each
% time-channel bin across subjects.
%
% Use as
% [sortBetas, ... |
4a0d531ef2772669553d253268ccbaee6f32c1cd42c7c8b9e550e45a4f584e99 | MATLAB | 5,331 | 145 | function [par] = set_par()
% Set parameters for EEG pre-processing and analyses.
%
% INPUT:
% None
%
% OUTPUT:
% par - structure with settings for pre-processing
%
% EEG/fMRI STUDY, DONDERS INSTITUTE, NIJMEGEN.
% J. Algermissen, 2018-2023.
% Should work in Matlab 2018b.
% ---------------------------------------... |
3a80db803820c5cdf4d9c25e930e6ff99ed2efc607d712e665375a4e15907a8d | MATLAB | 5,343 | 125 | function [neuron] = t2n_blockchannel(neuron,channels,amount,regions,specify)
% This function manipulates the neuron structure to reduce specific channel
% conductances defined by "channels" in specific regions of the cell(s)
% defined by "regions" by a certain amount defined by "amount"
%
% INPUTS
% neuron ... |
6a6c352be37bc05ad6d9978b886c449dbea918607b2c4e042c7f62de6ed6f484 | MATLAB | 5,357 | 156 | function [out] = EEGfMRIPav_cbm_mod05_modSim(parameters, subj)
% Standard Q-learning model with delta learning rule and Go bias and
% Pavlovian response bias and Pavlovian learning bias.
% ----------------------------------------------------------------------- %
%% Retrieve parameters:
% 1) Feedback sensitivity:
nd_... |
cb32bcc6bae1b458cbc3e5f1a0379741f1b4db5a4e7b0eb0f72bc43c1ffe90b8 | MATLAB | 5,359 | 161 | % QUADDIAMETER_TREE Map quadratic diameter tapering to tree.
% (trees package)
%
% tree = quaddiameter_tree (intree, scale, offset, options, P, ldend)
% -------------------------------------------------------------------
%
% Applies a quadratic decaying diameter on a given tree structure. P
% and ldend are derived pr... |
1de69bebc1af1411b2ec6f2955b53e80c888a0bafcd266022eddcecc540a978b | MATLAB | 5,365 | 171 | % SMOOTH_TREE Smoothes a tree along its longest paths.
% (trees package)
%
% tree = smooth_tree (intree, pwchild, p, n, options)
% ---------------------------------------------------
%
% Smoothns a tree along its longest paths. This changes (shortens) the
% total length of the branch significantly. First finds the he... |
0d924b124da85708b193fdad864399b430d9b4250fe767432dc25c49a889b812 | MATLAB | 5,367 | 175 | % POINTER_TREE Draws pointers (electrodes) to nodes on a tree.
% (trees package)
%
% HP = pointer_tree (intree, inodes, llen, color, DD, options)
% ------------------------------------------------------------
%
% Draws pointers to nodes inodes. Several options exist, some look a bit
% like electrodes.
%
% Input
% -----... |
66f25656b707c86d243b7382ea17d23160be82f50ea9cc8dca41cc5b37fc906d | MATLAB | 5,377 | 137 | %% Ripple detection
clearvars -except subnum sub Summary
addpath \\mycloudpr4100\ivan\Ivan_analysis\Ivan\human-20190516T170723Z-001\human\FMAToolbox\Helpers
addpath \\mycloudpr4100\ivan\Ivan_analysis\Ivan\human-20190516T170723Z-001\human\FMAToolbox\Analyses
addpath \\mycloudpr4100\ivan\single_unit\human\wcst\awak... |
67fb0d67ff58d2841778ea4b02752d4301e481e4f2e3f0a584669e3d9f5d25d2 | MATLAB | 5,377 | 132 | % run_simPressShaped.m
% Dana Goerzen and Jamie Near, McGill University 2021.
%
% USAGE:
% This script is run simply by editing the input parameters and then
% clicking "Run".
%
% DESCRIPTION:
% This script simulates a PRESS experiment with fully shaped refocusing
% pulses. Coherence order filtering is employed to o... |
8b76aeecdc47702f8c9666b74876941455eda2f10fab2129d185523022208280 | MATLAB | 5,378 | 245 |
close all force
%
clear
load('a0_0_bhv2trialStrct.mat');
load('a19_2_distWithinAndBetweenEachTrial.mat', 'distToMeanSameCondition', 'distToGrandMean')
load("a22_1_NewVarDistance.mat",'distT','distW')
distToMeanSameCondition = distW'.^2;
distToGrandMean = distT'.^2;
%load("a22_2_NewVarDistancePermute.mat", "distT",... |
e92c25b1a8c86c3f47c3987f5e108bf75f90749a029eba9a166f8df7400337ec | MATLAB | 5,379 | 312 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
e983bca3a64b2d7ab68247a561d3dd2bf0b479ccad7ef360851a11697204f3f1 | MATLAB | 5,382 | 197 | % FigureS10.m
% Plots for Supplementary Figure S10.
% Will call taft_save_PEs() to load PEs for selected subject (sub 07).
%
% EEG/fMRI STUDY, DONDERS INSTITUTE, NIJMEGEN.
% J. Algermissen, 2018-2023.
% Should work in Matlab 2018b.
% we are here:
% cd /project/3017042.02/Analyses/FiguresOutcomeLocked
% clear all; cl... |
c17f21fd84f202fc3229a4bc52d6a747c9c38de6954979836f853515c500ed32 | MATLAB | 5,383 | 172 | clear
close all
%save(mfilename);
imSize = [733, 977];
%hmSize = [210, 280];
hmSize = [733, 977];
hmScale = mean(hmSize./imSize);
pix2deg = 34.910;
filesAll = dir('../../Images_Movies_Functions/analyze1/data0_Image/image_*');
I = arrayfun(@(x) x.isdir, filesAll);
filesAll = filesAll(I);
nFile = numel(filesAll);
i... |
0d7255f2d7044ef0c4c84bea840a1210969615dd1d3d84ca5e3faa47bec87585 | MATLAB | 5,385 | 112 | function ViewROI3D(expt, ROI, fluor, loco, varargin)
%
IP = inputParser;
addRequired( IP, 'expt', @isstruct )
addRequired( IP, 'ROI', @isstruct )
addRequired( IP, 'fluor', @isstruct )
addRequired( IP, 'loco', @isstruct )
addParameter( IP, 'minInt', 2000, @isnumeric ) %
addParameter( IP, 'setROI', 1:expt.Nroi, @... |
e8333711538584520e47f6774e4390b057f498e4587dcf9e46e8f73a2f243909 | MATLAB | 5,386 | 188 | % CHULL_TREE Convex hull around whole or part of a tree.
% (trees package)
%
% [HP hull] = chull_tree (intree, ipart, color, DD, alpha, options)
% -----------------------------------------------------------------
%
% Plots a convex hull around indexed nodes (ipart) of a tree. If tree is
% 100% flat 3D convex hull doe... |
3fe4985ed8376650977e861a50c99a60d6af5778d6018009a11a9838dec2d153 | MATLAB | 5,388 | 161 | function [theta, estSNR, flux, thetaRangeMid, linearDensity, rbcSpacingT] = ...
calc_angles_radon(self, windows, isDarkStreaks, pixelSize, ...
lineTime, pixelTime, isOldToolbox)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute ... |
f1852743e3857fcdb342a506d9180457e1b55cc8a0b220054eeac41729a338e9 | MATLAB | 5,388 | 166 | function [rphase, fh] = tapas_physio_get_respiratory_phase(pulset, rsampint,...
verbose, thresh)
% get_respiratory_phase is a function for creating respiratory phase regressor.
% from physiological monitoring files acquired using spike, that
% can be included in SPM5 design matrices.
%
% FORMAT [rphase] = tapas_ph... |
8ae6b0c4e83bb9300ffbf632514cbc77de5ad4055b18277c70602bf4525eab94 | MATLAB | 5,390 | 141 | %%
% Reproduces Compact vs. Diffuse co-tuned plots (Fig. 4A)
%
% Function inputs:
% cellTable: structure containing neuron data
% cellConn: vector of 1's and 0's that denotes which cells should be
% included (e.g., only non-offTarget cells)
%
%%
function Fig4A(cellTable,cellCond)
%% We must average the resul... |
9694164f5c10f7db8fb785e21702e6a9ec52250075e9eed5f33101d83236bab8 | MATLAB | 5,394 | 98 | Ntop = 5;
minDur = 10;
minIso = 10;
fitWindow = [10,10];
waveType = 'spont';
modelStep = @(b,x)( b(1)./(1+exp(-(x-b(3))/b(2))) + b(4)./(1+exp((x-b(6))/b(5))) + b(7)); %
betaInit(1) = 1; % Saturation response
betaInit(2) = 0.1; % onset time constant
betaInit(3) = 0; % Onset time
betaInit(4) = 1; % offset sa... |
308566709ac0f5e8649a781ae24949fd3781299f683be3bdf1ac3dd6049ac47b | MATLAB | 5,396 | 312 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
d20bd00edd4c2703355ffbd82f66aa2e46967d75e92877ab5a3bfd5667162d9f | MATLAB | 5,399 | 312 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
e0b38d0780f5ddebd051baad9bb95dc2e88ca7de05c2005b2d6b3934940c1bd9 | MATLAB | 5,408 | 155 | %decc_plotFig7
% Related to Viswanathan, Stein, Nieder, PLOS Biol, 2024
% PV 2024
load('DECCdataFig7.mat')
% Figure parameters
lcolor = [0.0 0.4 0.5; 0.6 0.3 0.0; 0.1 0 0.5; 0.0 0.6 0.0];
dotcolor = [0 0.3 0; 0 0.5 0; 0 0.7 0];
dur = 3700;
kern = 50;
alpct = 99;
x1 = kern:kern:dur;
lpos = [500 1000 2000 2500 3500]./... |
259d88acca80ab68fc676c27610a4293415f066080bef6ca05ef9fef2b059961 | MATLAB | 5,409 | 139 | function hardwareContinuousVoltageWithCallBack
% A simple example showing hardware-timed continuous analog input using the Vidrio dabs.ni.daqmx wrapper
%
% function vidrio.AI.hardwareContinuousVoltageWithCallBack
%
% Purpose
% Demonstrates how to do hardware-timed continuous analog input using V... |
d912fa8c31060bc27c39e28cb14d3098bee155c2d7ff1669ac9467dfff2fb189 | MATLAB | 5,413 | 127 | %Split up a directory of registered images into _1, _2, etc.
loadParameters;
params.registeredImagesDir = '/mp/nas0/ExSeq/AutoSeqHippocampus_results/20170904/4_registration';
params.FILE_BASENAME= 'exseqautoframe7';
%how many subsections to calculate the descriptors?
params.ROWS_DESC = 3;
params.COLS_DESC = 3;
params.... |
65038a2358088f1f227b83d170e1d21abda92f646a79f3fc126fe76eea14c010 | MATLAB | 5,421 | 128 | % sim_megapress_shapedRefoc.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% sim_megapress_shapedRefoc(n,sw,Bfield,linewidth,taus,sys,editFlip,refPulse,refTp,Gx,Gy,dx,dy,refPh1,refPh2)
%
% DESCRIPTION:
% This function simulates the MEGA-PRESS sequence with shaped
% localization pulses and instantaneous editing pu... |
1f927d73fc1e0a068e9fef5885a733b6a26507630a198914314a54ef7a6917f1 | MATLAB | 5,429 | 125 | function hardwareFiniteVoltage
% Example showing hardware-timed analog output of a finite number of samples using the Vidrio dabs.ni.daqmx wrapper
%
% function vidrio.AO.hardwareFiniteVoltage
%
% Purpose
% Shows how to do hardware-timed analog output using Vidrio's dabs.ni.daqmx wrapper.
% ... |
937180563565b3b6d25199d8d33bf6ce20c927a4af39a02db17e7d241c6ae034 | MATLAB | 5,442 | 119 | % ----------------------------------------------------------------------------------------------
% -- Title : VocalMat
% -- Project : VocalMat - A Tool for Automated Mouse Vocalization Detection and Classification
% ----------------------------------------------------------------------------------------------... |
e2f57895f6916932d936c57eba49aa0d1a44e2f65afb40802e84d74352179945 | MATLAB | 5,453 | 148 |
loadParameters;
for roundnum = 1:params.NUM_ROUNDS
try
summed_norm = load3DImage_uint16(fullfile(params.registeredImagesDir,sprintf('%s_round%.03i_%s_%s.%s',params.FILE_BASENAME,roundnum,'summedNorm',regparams.REGISTRATION_TYPE,params.IMAGE_EXT)));
catch
fprintf('Failed to load round %i\n',roundnum)
... |
7e13da13213510b15394b171da52d3629222b5f4858417acd055848aa52d3aed | MATLAB | 5,458 | 136 | function taft_runonce_select_trials()
% taft_runonce_select_trials()
%
% Load behavior, retrieves indices of trials on which certain relevant
% behaviors/ conditions happen (Go/ NoGo, Win/ Avoid, congruent/
% incongruent), save indices as separate files under TAfT_Betas/selTrials.
% Mind setting the root directory in ... |
aa0aa9ff7b76bb40b3cfd2a08de58f4e6c2d3e7dc34ab33ce8afd279d6c82b9d | MATLAB | 5,460 | 185 | function [traces, tracesExist] = measure_ROIs(self, objPI)
%measure_ROIs - Measure the ROIs and return the traces
%
% [TRACES, TRACES_EXIST] = measure_ROIs(OBJ, OBJ_PI) measure the ROIS
% contained in the CalcFindROIs object OBJ using the CellScan object
% OBJ_PI and returns an array of TRACES, as well as a mask ... |
3803d3e8bdea13ab6be798a24dcb2939da89cbbee213cbe9ce7894cfe8c78a93 | MATLAB | 5,464 | 199 | function [tStats] = ttestEffectSize(data1,data2,testName,nUnits,pair,MC,limitP,testType)
% Performs two-tailed Student's t-test. Outputs all statistics in a cell
% array. Can be used to manually generate correlation information for
% compliance with journal manuscript requirements. Can perform paired or
% unparied ... |
70a984e049ffda3090857399b68f7e6daefff5e3d438decd8a2db4e0c5809066 | MATLAB | 5,464 | 156 | classdef Test_RawImgComposite < matlab.unittest.TestCase
%TEST_RawImgComposite Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
methods (Test)
function testConstructor(self)
... |
55554abcc6a6575b4c2a71f89023e8d5b9615888279a6d7fc310e68258419ad9 | MATLAB | 5,469 | 136 | classdef DataFindROIsFLIKA_2D < DataFindROIsFLIKA
%DataFindROIsFLIKA - Data from FLIKA-based ROI identification
%
% The DataFindROIsFLIKA class contains the data generated by
% CalcFindROIsFLIKA.
%
% DataFindROIsFLIKA_2D public properties inherited from Data:
% mask - A mask combining all of the other ... |
72c60dda121067470fea29a3603d35e264fec58a4c82b3c85ae5c5c05916eb43 | MATLAB | 5,480 | 123 | %loadSimParams;
%% Generate number of puncta, positions and the transcripts
load('groundtruth_dictionary.mat')
volume_microns = (simparams.IMAGE_FOVSIZE_XY*simparams.IMAGE_RESOLUTION_XY)^2 *...
(simparams.IMAGE_FOVSIZE_Z*simparams.IMAGE_RESOLUTION_Z);
if strcmp(simparams.puncta_placement_method,'random')
n... |
ba8df047036cb9d1fc571a4ca4ce53a25d71b8403fb84250cd4c15aa84cf97ae | MATLAB | 5,486 | 190 | %op_removeWater.m
%Jay Hennessy, McGill University 2017.
%
% USAGE:
% [out, K, wppm, amp, alpha, ph, model]=op_removeWater(in,wlim,Kinit,M,plot_bool);
%
% DESCRIPTION:
% This function removes the water signal from MRS data using HSVD method
% described by H. BARKHUIJSEN et al. 1987.
%
% INPUTS:
% in = MRS dat... |
e1dd151640bfc7eb57d5b5f927e45a3c4a26ad1b47dc868f415b02fa715f4498 | MATLAB | 5,486 | 178 | % mv_classify_timextime unit test
%
rng(42)
tol = 10e-10;
mf = mfilename;
%% Create a dataset where classes can be perfectly discriminated for only some time points [two-class]
nsamples = 100;
ntime = 300;
nfeatures = 10;
nclasses = 2;
prop = [];
scale = 0.0001;
do_plot = 0;
can_discriminate = 50:100;
cannot_discrimi... |
75ceaa78cd9bc6b9690fd47e8fc8e5bd38b80cd0b6d9b0fdaa2ab28e1af0aca9 | MATLAB | 5,490 | 169 | function make_tlbx(varargin)
%make_tlbx - Create a MATLAB toolbox
%
% make_tlbx() creates a MATLAB toolbox file, in the root directory, based
% on the current master branch of the repository.
%
% make_tlbx('branch', BRANCHNAME) creates the toolbox file based on the
% BRANCHNAME branch in the repository.
%
% m... |
2b4e724c3b1402da838f064095689ece5668645fb9e91361093286bbc8d7ba3b | MATLAB | 5,499 | 139 | function varargout = plot(self, objPI, varargin)
%plot - Plot a figure
%
% plot(OBJ, OBJ_PI) plots the default figure for the CalcDetectSigs
% 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 speci... |
f0cebd357ac1850b1d37bdb5da86550b800b41dd68f409b1d4dac6b88a23cf85 | MATLAB | 5,505 | 123 | function CorrectData3D(sbxPath, sbxInfo, shiftPath, varargin) % , tforms_optotune , Nchunks
IP = inputParser;
addRequired(IP, 'sbxPath', @ischar )
addRequired(IP, 'sbxInfo', @isstruct )
addRequired(IP, 'shiftPath', @ischar )
addOptional(IP, 'refChan', 'green', @ischar ) % for scanbox, PMT1 = green, 2 = red. -1 = b... |
01eade5bf24df0f9ef0f26673a9e52d8d4e59993cd08fc9da879665e8496ed50 | MATLAB | 5,509 | 310 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
ed7fa9c443af4f858511f01f833f83442a61c1cfe010fd657aa8e4af3ac9afee | MATLAB | 5,509 | 251 | close all force
%
clear
load('a0_0_bhv2trialStrct.mat');
load('a19_2_distWithinAndBetweenEachTrial.mat', 'distToMeanSameCondition', 'distToGrandMean')
%load("a22_3_NewVarDistanceBootStrp.mat",'distT','distW')
%distToMeanSameConditionBt = distW.^2;
%distToGrandMeanBt = distT.^2;
%load("a22_2_NewVarDistancePermute.ma... |
9f266906365ccea07c2c8ef082309db81ffdd7ff7488f8ac8e9065e55f68d71f | MATLAB | 5,511 | 147 | function ridObj = downsample(self, dsamp, varargin)
%downsample - Downsample the images in space and/or time
%
% OBJ_DS = downsample(OBJ, DSAMP) downsamples the raw image data of the
% RawImg object OBJ, in space and/or time, using the utility function.
%
% DSAMP, the downsampling factor, can be a numeric scalar ... |
d439c0eee4273ad7cac05cbe4adf40f3ec6fdcc21ee0752c90e3f437427ed575 | MATLAB | 5,511 | 149 | function varargout = process(self, useParallel, varargin)
%process - Process the elements of the ProcessedImg object
%
% process(OBJ) processes the relevant ProcessedImg concrete subclass
% according to its specific requirements.
%
% process(OBJ, USEPARALLEL) explicitly specifies whether to process the
% Proces... |
a8ec3acd2e05f49ab52d2fcd7da95f4dfcecfe16ef2ffd4b33788620fe1d6b47 | MATLAB | 5,512 | 310 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
b1c16130a4a64db684eccfab9a0acb452a22721041c83812bdadf3612281f52c | MATLAB | 5,521 | 175 | function [pacmat, freqvec_ph, freqvec_amp] = find_pac_nofilt (sig_pac, Fs,...
measure, sig_mod, ph_freq_vec, amp_freq_vec, plt, waitbar, width, nfft,...
dataname, sig_pac_name, sig_mod_name)
%function [pacmat, freqvec_ph, freqvec_amp] = find_pac_nofilt (sig_pac, Fs,...
% measure, sig_mod, ph_freq_vec, amp... |
7e839371711e50de9067e6402d1be063c5b4b912e25b84d15717d05af8e11fcb | MATLAB | 5,523 | 122 | function [job, data, data_ups, i_ons] = taft_preprocess_filter_upsample_epoch(job, iROI, iBlock)
% [job, data, data_ups, i_ons] = taft_preprocess_filter_upsample_epoch(job, iROI, iBlock)
%
% For given ROI, for given block, upsample volume-by-volume time series,
% epoch it into trials.
%
% INPUTS:
% job = ... |
286803be7c88fb8d45e92fac466757f8f4137ffbc4a37081468e5ec17788ec1e | MATLAB | 5,526 | 157 | close all;
path = fileparts(mfilename('fullpath'));
addpath(sprintf('%s/common', path));
[filenames, path] = uigetfile({'*.abf'}, 'Select file(s)', 'MultiSelect', 'on');
if ~iscell(filenames) % if filenames is not an array
filenames = {filenames};%make it into one element array
end
number_of_files = length(filen... |
6f1b85751c4dff1f0e6a98ce37f4cf6c02562967787aab908aae0b41dd1e1264 | MATLAB | 5,536 | 196 | function data = st_plot_EccTemporal(df,binsize)
% rmPlotEccSigma - plot sigma versus eccentricity in selected ROI
%
% data = rmPlotEccSigma(v, lr, [fwhm=0], [plot_position_variance], [plotFlag=1]);
%
% INPUT
% v: view
% lr: left (1) or right (2) if FLAT view is used
% fwhm: plot sigma (0) or fwhm (1)
% plot_pv... |
90f46ed0334529a0bc1500c8319c7a1184489092d248d2356a2cc73bf23eda45 | MATLAB | 5,543 | 163 | function [type1,type2,typem,types,types_pvals] = abcd_statisticalerrors(Corrs,Pvals,fscorrs,fspvals,iter)
% Generate Fig 2 of MP
% Calculates error rates for a given brain-phenotype correlation
% type1 = 0;
% type2 = 0;
% iter;
%% Type 1 error rate % Should in theory be whatever your pvalue is
thr = [.0000001];
type... |
88356c997ea98768658e10187eaf70ab9e34b2719c094a24386a9d87ae78b087 | MATLAB | 5,545 | 155 | function [traj, otherChs] = calc_traj(refImg, trajImg, varargin)
%calc_traj - Calculate a single trajectory
% 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 publi... |
c4c740ac0f8c6bf18a7f84d9a153d723bf09e58657f2cc37364b734d36c714ba | MATLAB | 5,545 | 177 | function EEGfMRIPav_OutcomeLocked_5_TR(rootDir, iSub)
% EEGfMRIPav_OutcomeLocked_5_TR(rootDir, iSub)
%
% Interactive script.
% Visualize trials with EEGlab, identify trials to reject via visual
% inspection.
% Mind setting your own EEGlab directory!
%
% INPUTS:
% rootDir = string, root directory of projec... |
a362defdb324bfae82829949c6b6758be4a588eceda0744847e827781038f768 | MATLAB | 5,546 | 168 | load(fullfile(dataFolder,'EEG_data','data_time_information.mat'));
t0 = timeInfo.infusion_onset-timeInfo.object_drop;
load(fullfile(dataFolder,'EEG_data','electrode2_Cz.mat'),'psd','freq','time');
% Compute Baseline spectrum
for i = 1:14
preInfusion(:,i) = nanmedian(psd(:,and(time>=t0(i)-10,time<t0(i)),i),2);
... |
d012faadfa9b9b98cd0ea6587ec31200951c5f7064b5bc3d97275dd955a7e256 | MATLAB | 5,552 | 115 | function prepareWindow(obj)
% Prepare the window
%
% zapit.gui.main.controller.prepareWindow
%
% Purpose
% Set up the figure window, attach callbacks and listeners, etc.
%
%
% Rob Campbell - SWC 2023
% Insert and empty image into axes.
obj.refreshImage
% Set the image c... |
ff691d47e209a61be58bb76809bd17907ccf00c786d24d8ad9eb024ef3cf2166 | MATLAB | 5,554 | 110 | function refShift = CorrectData2D(sbxPath, sbxInfo, regParams, shiftPath, sbxDftPath, varargin)
IP = inputParser;
addRequired(IP, 'sbxPath', @ischar )
addRequired(IP, 'sbxInfo', @isstruct )
addRequired(IP, 'regParams', @isstruct )
addRequired(IP, 'shiftPath', @ischar )
addRequired(IP, 'sbxDftPath', @ischar )
add... |
a37919b7fdc151c43db7ef5090f2df44700e8e480360dec2d4d2d312e3915052 | MATLAB | 5,565 | 142 | function [sortBetas, Tvalues] = taft_postprocess_TF_selectData(job, betas, iROI)
% Extracts time-frequency data for selected ROI,
% sort channels across subjects, selects valid subjects,
% combine subjects into 4D data, perform one-sample t-test for each
% time-frequency-channel bin across subjects.
%
% Use as
% [s... |
ae9d09de42b423159235d61ab8a8b5aed4f2226aa062dc41605c312a7e6511dd | MATLAB | 5,565 | 176 | function [pacmat, freqvec_ph, freqvec_amp] = find_pac_nofilt_win(sig_pac, Fs,...
measure, win_length, overlap, sig_mod, ph_freq_vec, amp_freq_vec, plt, waitbar, width, nfft,...
dataname, sig_pac_name, sig_mod_name)
%function [pacmat, freqvec_ph, freqvec_amp] = find_pac_nofilt_win(sig_pac, Fs,...
% measure... |
123c6a3cd4c508a5a66fde196e12c0b67447b41db06ba53d4dbace9b936937b3 | MATLAB | 5,572 | 168 | % ELIMT_TREE Replace multifurcations by multiple bifurcations in a tree.
% (trees package)
%
% [tree, ntrif] = elimt_tree (intree, options)
% --------------------------------------------
%
% Eliminates the trifurcations/multifurcations present in the tree's
% adjacency matrix by adding tiny (x-deflected) compartments... |
098a7eaa552de59e22b0438c6bd60e09826deca2058abd8ec681a1ea37f04338 | MATLAB | 5,575 | 145 | function performAffineTransforms(moving_run,do_downsample)
loadParameters;
if do_downsample
filename_root = sprintf('%s-downsample',params.FILE_BASENAME);
image_type = 'DOWNSAMPLE';
else
filename_root = sprintf('%s',params.FILE_BASENAME);
image_type = 'ORIGIMAL';
end
%params.MOVING_RUN = moving_run;
... |
3b9bae5a8e9d644114fecfba69e01b138b1908a14a6f89adfcd8d8d42a2e4efa | MATLAB | 5,577 | 174 | function self = calc_diameter(self, imgSeq, frameRate, doInvert, t0)
% 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 Foundatio... |
7effe3437d8f6787d9a367c628f59cf1f98cd4dc8058896a16bda2fcfd235689 | MATLAB | 5,583 | 149 | function Combine_Confound_EVs_Subject(iGLM)
% Combine_Confound_EVs_Subject(iGLM).
%
% Will take
% - 6 realignment parameters
% - cerebrospinal fluid (CSF) signal
% - out-of-brain (OOB) signal
% - spikes in relative displacement
% and combine those into a single matrix.
% Will concatenate blocks to yield single matri... |
40b3ea3a6cc7ed327d5db7c1bfa78fdd2c15466d773c51ac593f369bca3b59c0 | MATLAB | 5,589 | 128 | function minterf = t2n_makeNseg(tree,minterf,par,mech)
% This function calculates at which position of each cell there will be a
% segment node in NEURON. This is necessary for T2N to correctly translate
% TREES toolbox node information into NEURON section and segment information.
%
% INPUTS
% tree single TREES t... |
a88f91abf2a677c532964627335772c4f579bef8e4cbcd06d4a930539911f950 | MATLAB | 5,594 | 229 | function result = WriteYaml(filename, data, flowstyle)
import zapit.yaml.*
if ~exist('flowstyle','var')
flowstyle = 0;
end
if ~ismember(flowstyle, [0,1])
error('Flowstyle must be 0,1 or empty.');
end
result = [];
[pth,~,~] = fileparts(mfilename('fullpath'));
... |
f4368f18260d2325935f7d03f0cb94f06ef707cce79798f3df8b3d89aa5de03a | MATLAB | 5,594 | 195 | function varargout = import_image(self, channels, calibration, downsamp)
%import_image - Class method to import/create the BioFormats
% 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 Gener... |
6682e2026442e3afab1d5079c56886e2cf7a9d3f20c1f3bbaebd1ebd21811c54 | MATLAB | 5,601 | 131 | function [bandwidth,density,xmesh,cdf]=kde(data,n,MIN,MAX)
% Reliable and extremely fast kernel density estimator for one-dimensional data;
% Gaussian kernel is assumed and the bandwidth is chosen automatically;
% Unlike many other implementations, this one is immune to problems
% caused by mul... |
48a0b45f977ccda5fdd67973414235fae34c610b5a3103a03d00efed9d269160 | MATLAB | 5,612 | 111 | function loco = GetLocoState(expt, loco, varargin)
% Determine locomotive state using a Hidden Markov Model
IP = inputParser;
addRequired( IP, 'expt', @isstruct )
addRequired( IP, 'loco', @isstruct )
addParameter( IP, 'var', 'velocity', @ischar )
addParameter( IP, 'Nstate', 2, @isnumeric ) % Nstate = 2; % still/m... |
f202b1d50a9249f13db9359a3a0d00fc39102b6b61f85e0e123ecf0458642fd2 | MATLAB | 5,612 | 186 | % op_alignScans_fd.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [out,ph,frq]=op_alignScans_fd(in,in1,fmin,fmax,tmax,mode);
%
% DESCRIPTION:
% Use spectral registration on a limited frequnecy range to align two
% separate MRS datasets (align in to in1);
%
% INPUTS:
% in = input (spectrum to be registered to ... |
1b63e508965d08ba9654e76f55dc7f2e93085d48d4ce794111002514e151a064 | MATLAB | 5,614 | 173 | [full_model,synFun] = fittingmodel('eq1');
load(fullfile(dataFolder,'simulations','trend_peak_interactions','mixed_dynamics'));
psd_baseline = mean(psd_baseline,2);
psd_high_oscillation = mean(psd_high_oscillation,2);
psd_high_aperiodic = mean(psd_high_aperiodic,2);
psd_high_both = mean(psd_high_both,2);
psd_asynch =... |
960d913dabd3fb9829489920854ab61133b057c898222eb73430ddd790ea63d0 | MATLAB | 5,622 | 133 | function laserFit = fitLaserPowerCurve(controlValues, sensorValues, doPlot)
% Fit the measured laser power curve and (optionally) plot it
%
% function laserFit = zapit.utils.fitLaserPowerCurve(controlValues, sensorValues, doPlot)
%
% Purpose
% Fit the relationship between laser control voltage a... |
5b4046621c3b211ee9a60972f7d3abfd61828dcbb99f01b933d4e8336a911ac0 | MATLAB | 5,627 | 174 | %use aligned common cells to register all FOVS
load('E:\learningAnalysis\summaryManyMice_includingOldEnvBadMoreMice\foldersAll.mat');
% foldersAll{3}='E:\ID20210206\findCells\loc2\subsetFOVsWithOldNo11\analyzeCells';
%above: fix one mismatch between fodlersAll and foldersAllN
load('E:\learningAnalysis\summaryManyMi... |
3db0c12e0ba5a169b63409e374396f829f7754ccf959ccf8bbfcd08c099b598d | MATLAB | 5,630 | 141 | classdef (Abstract) CalcDiameterLong < CalcDiameter
%CalcDiameterLong - Superclass for CalcDiameterLong classes
%
% CalcDiameterLong is an abstract superclass that implements (or requires
% implementation in its subclasses via abstract methods or properties)
% most functionality related to CalcDiameterLong object... |
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