sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6cb18bb9721a7b0c229fa6d0531793e7109ee146534b92a41fa96ecc7396ea9d | MATLAB | 224 | 10 | function [ y ] = modelfun_dHC( beta, x )
%UNTITLED7 Summary of this function goes here
% Detailed explanation goes here
beta_aux = beta([1 2 3 4 4 5 6 6]);
beta_aux(5) = 0;
y = modelfun_dHEC(beta_aux, x);
end
|
7b24e6d1d253016f2864e51605f3c564bae1a2f585f105080eff20bf4dce5bbe | MATLAB | 224 | 13 | function regtanks = GetRegTanks(TTX)
% regtanks = GetRegTanks(TTX)
%
% DJS 2013
for idx = 1:100
regtanks{idx} = TTX.GetEnumTank(idx-1);
if isempty(regtanks{idx}), break; end
end
regtanks(end) = [];
end |
0c49b0579d0aa97ba5ab919cdfc3705edb30b67054aa521dfcb285c218571ad1 | MATLAB | 225 | 7 | % TWOPHOTON PROCESSING PACKAGE
%
% This directory contains code for processing data collected from
% a GENERIC device, where directories are a list of TIFF files.
%
% Does NOT include support for linescans at this time.
|
cd667282ed0d932e076e04d1471be27874da791b2a59799054dbe242fea03f4e | MATLAB | 226 | 11 | function esc=Esc()
% Set escape character separating folders
machine=computer;
if strcmp(machine(1:3),'MAC')
esc='/';
elseif strcmp(machine(1:3),'GLN') % unix cluster GLNXA64
esc='/';
else % windows
esc='\';
end
|
d5ddee7b3e43d963f6006f2e47acc0a9a0087847a738277eadc820cd14ba8517 | MATLAB | 226 | 11 | function c = getCov(y,ypred)
idxnan_y = any(isnan(y),2);
idxnan_ypred = any(isnan(ypred),2);
idxnan = idxnan_y | idxnan_ypred;
y(idxnan,:) = [];
ypred(idxnan,:) = [];
c = sum((y-mean(y)).*(ypred-mean(y)))/(numel(y)-1);
end
|
a173bfb9769c64b6b87d9945d37bad9a418ee653b02a1196ea1c449e2f577d48 | MATLAB | 227 | 11 | function c = getCov(y,ypred)
idxnan_y = any(isnan(y),2);
idxnan_ypred = any(isnan(ypred),2);
idxnan = idxnan_y | idxnan_ypred;
y(idxnan,:) = [];
ypred(idxnan,:) = [];
c = sum((y-mean(y)).*(ypred-mean(y)))/(size(y,1)-1);
end
|
815aae0f77c9525b617d49a3f4d44cf1d2fa70d269cf72a5717521f8cc6a23f2 | MATLAB | 228 | 13 | function [f,g,nh_2] = poissExpLL(x, y, dt)
x = x + log(dt);
rate = kgmlm.utils.boundedExp(x);
f = -rate + y.*x;
if(nargout > 1)
g = -rate + y;
if(nargout > 2)
nh_2 = kgmlm.utils.boundedExp(0.5*x);
end
end |
3230312cd5e2cde49fd2448f2048183082dd9d277f6fecb9b4df058e5d84fc9c | MATLAB | 229 | 8 |
function project = MarkClipsAsIncomplete(project, numberToMark)
nRows = size(project.ClipTable,1);
randIdxs = randperm(nRows);
selRowNums = randIdxs(1:numberToMark);
project.ClipTable.Type(selRowNums) = categorical({'UR'});
end |
204fe115cee115890d4bf232db554130c1f39a74793dab17054c3484f99d3087 | MATLAB | 230 | 11 | up = SpherePatch(8, 10, [0 0 1], true, false)
down = SpherePatch(8, 10, [0 0 -1], true, false)
CreateRenderingFigure()
DrawVertStructure(up, [0 0 0], [1 0 0])
CreateRenderingFigure()
DrawVertStructure(down, [0 0 0], [0 0 1])
|
247c3e1e6ba66fb5ca028045dbbb4a8e84fb389a3459216da35d706f3e9f5cfc | MATLAB | 230 | 7 | function solTag = find_sol(FEM, studyTag)
solTags = FEM.sol().tags;
solsStudy = arrayfun(@(s) char(FEM.sol(s).study()), solTags, 'uni', false);
solIndex = strcmp(solsStudy, studyTag);
solTag = char(solTags(solIndex));
end
|
442cf73a3db18942d15e8f57f5f681513ef90e35651bb252780f570159fa22c5 | MATLAB | 231 | 12 | function imgData = readTiff(filename)
info = imfinfo(filename);
numFrames = numel(info);
imgData = zeros(info(1).Height, info(1).Width, numFrames, 'uint16');
for n = 1:numFrames
imgData(:,:,n) = imread(filename, n);
end
end |
7733167537c606f1c34428258adcc5d8036d5903b7325e9a975e3cdad2d1f111 | MATLAB | 231 | 7 | function [names, fullpaths] = list_csv(folder)
files = dir(fullfile(folder, '*.csv'));
names = {files.name};
names = cellfun(@(n) n(1:end-4), names, 'UniformOutput', false);
fullpaths = fullfile({files.folder}, {files.name});
end
|
e4b69497372672dfc7c58f37eba22f41996b39bdc84548e25215cfb617ea9643 | MATLAB | 232 | 10 | function [cells,cellnames] = analyzegeneric2pdata(dirname, saveit)
ds = dirstruct(dirname);
[cells,cellnames] = tpdoresponseanalysis(ds);
if saveit,
disp(['Saving results back to file']);
saveexpvar(ds,cells,cellnames,0);
end;
|
7c86c49840d3b8775a59dc258b2de4c43f655bf4c926f796ae448da943b6024c | MATLAB | 233 | 14 | function annotT = GetAnnotations(self, varargin)
self = Load(self);
if ~isempty(self.AnnotationTable)
return
end
annotT = self.AnnotationTable;
if nargin == 2
indices = varargin{1};
annotT = annotT(indices, :);
end
end |
cd0cda80bf14cbbf1b0ca182760cc2c7db32b2a7ab13acbead82ea783500dc5a | MATLAB | 234 | 9 | function [ Verts, iVertsA, iVertsB, Normals, Faces ] = CreateConnector( Pos, Radius)
%CREATECONNECTOR Given a 3x3 matrix with points on rows return a set of
%verticies and faces which can connect cylinders between the points
end
|
14b7446469127b076dfc051c6add7a53ef6b6d704f2b239440187166d09115a7 | MATLAB | 235 | 7 | function [T] = remove_dup_ROIs(T)
%REMOVE_DUP_ROIS remove two duplicated ROIs from beta tables
duplicated_ROIs = {'L_agranularIns_bin_dAICtrim_roi.mat',...
'filtered_L_dAIC_custom_bin_new_roi.mat'};
T(duplicated_ROIs,:) = [];
end
|
2ef527b2365c7ef7a1d0c7cf0305ae79c2a90b26aa0ab4d17b63f0cd23398201 | MATLAB | 235 | 8 | function [im,fname]=tpreadframe(dirname,tpfileparams,cycle,channel,frame)
%TPREADFRAME
% read frame from single tiff
%
% 2008, Alexander Heimel
%
fname=fullfile(dirname,tpfilename(tpfileparams,cycle,channel,frame));
im=imread(fname);
|
3f1ae446de39b3c4d0877e240f3f96ebacd69bf39bf42e082d1fa470fa8e3811 | MATLAB | 235 | 12 | function out = convert_1x6_to_3x3(in)
if size(in,1) == 6
in = in';
end
f = 1/sqrt(2);
out = [ in(1) f * in(4) f * in(5); ...
f * in(4) in(2) f * in(6);...
f * in(5) f * in(6) in(3) ];
end |
55ad69876f9b0c5a6f9ce52c82ec929bd98bc780bb8061eccef4d8715d3ca0b8 | MATLAB | 235 | 7 | function [averages] = mean_by_module(betas)
%MEAN_BY_MODULE mean by module
[t_groups, t_ids] = findgroups(round(betas(:,2)));
assert(isequal(t_ids,[0,1,2]'));
averages = splitapply(@(x) mean(x, 'omitnan'), betas(:,1), t_groups)';
end
|
bbd0afb7f9c5b7c9294a2943c41dd2b7354f1ff433ef06fc3e3dee7b10b56bec | MATLAB | 235 | 8 | function [LFpsf,height,width,depth,Nnum,CAindex] = read_psf(file)
psf = load(file);
psf5d = psf.H;
Nnum = psf.Nnum;
CAindex = psf.CAindex;
[height, width, Nx, Ny, depth] = size(psf5d);
LFpsf = double(psf5d);
end |
b9b1d46c0811cd16abb8b30a86932c97c28f285e4137c746a9ae21802ed8d7f4 | MATLAB | 236 | 8 | % test
Liley_params;
fhz1 = 19.965*4; % main timstep
tcut = 5000; % apply for transients
TDatend = 20000; % length of model simulation ms
T1=0:1/fhz1:TDatend+tcut;
params1 = [paramsvec, zeros(1, 10)];
y = em_Liley(T1, params1);
|
f1418b03f1e093554b50a27ffabe3910e1ebe703735639dc19d9e8379a859dcc | MATLAB | 236 | 9 | function clear_model(model)
sol_tags = model.sol().tags;
for i = 1:size(sol_tags)
model.sol(sol_tags(i)).clearSolutionData();
end
model.mesh().clearMeshes(); % Might not work
% model.resetHist(); % might reduce size
end
|
72a90639d9b1d5c0e1ea28987324eb6a527a0ab902a74e705793accbf1dfd279 | MATLAB | 237 | 9 | function clear_models_folder(folder)
modelFiles = dir(fullfile(folder,'**', '*.mph'));
for modelFile = modelFiles'
f = fullfile(modelFile.folder, modelFile.name);
disp(['Clearing ' f]);
clear_model_file(f);
end
end
|
d801bede624b927e8e9c085fb7cfac5cc88b95e0de92e24a76454196dc30a749 | MATLAB | 237 | 8 | function [im,fname]=tpreadframe(dirname,fnameprefix,cycle,channel,frame)
%TPREADFRAME
% read frame from multitiff
%
% 2008, Alexander Heimel
%
fname=fullfile(dirname,tpfilename(fnameprefix,cycle,channel,frame));
im=imread(fname,frame);
|
bf4648453ade6f4b227e4028c8adbe1750fb34a74660e96790145a4b22103f56 | MATLAB | 238 | 7 | function [noise_raster] = generate_noise_raster(raster)
[n,t] = size(raster);
noise_raster = zeros(n,t);
num_spikes_raster= sum(sum(sum(raster)));
noise_raster(randperm(numel(noise_raster),num_spikes_raster)) = 1;
end |
c013f2a01785fa88fe9c63b1ba852d24f6fd2d92c4f8d963609a44a67130fa76 | MATLAB | 239 | 7 | function [name, fullpath] = get_subfolders(folder)
folders = dir(folder);
folders = folders(~ismember({folders.name},{'.','..'}) & [folders.isdir]);
name = {folders.name};
fullpath = fullfile({folders.folder}, {folders.name});
end
|
77b7bf002ec66c642d25c9e4c5b6015a12fa8e49e59dff2c59d89eb471cf152b | MATLAB | 240 | 7 | function [g_surf] = get_surface_from_gifti(f_name)
%GET_SURFACE_FROM_GIFTI read gifti file and convert it to a mesh structure
% Note: requires gifti package
g = gifti(f_name);
g_surf = struct('faces', g.faces, 'vertices', g.vertices);
end
|
798bf4fe5822ec8fcf902631378f287402427859313db4184a70a350cb8cec6f | MATLAB | 240 | 10 | function p1 = compute_p1(p_1from2,p_2from1)
% Compute p(I1) for the input values of p(I_1|I_2) and p(I_2|I_1) given in
% arguments.
% p_1from2 and p_2from1 must have the same size.
p1 = p_1from2./(p_1from2 + p_2from1) ;
end
|
e5318e1627e8fdd699df368afd9c2e115f177b1386fb20a74a76d65c0f8a87ff | MATLAB | 240 | 7 | % TWOPHOTON PROCESSING PACKAGE
%
% This directory contains code for processing data collected from
% the CellVoyager device, where data is represented in a stack of TIFF images.
%
% Does NOT include support for linescans at this time.
|
8ed8310c0909ec9aaba7a6425a529a76343b7ca7b49da46588a7c6fe79d39119 | MATLAB | 241 | 7 | box off
set(gca,'FontSize',14,'TickDir','in','XAxisLocation','bottom',...
'YAxisLocation','left','LineWidth',1.5,...
'XMinorTick','off','YMinorTick','off'...
,'TickLength',[.015 .015],'Layer','bottom')
set(gcf,'Color','w') |
99262080365631563d6efe9f08ad336c1dcacc321f3595e32aa1ea9d7cbd078e | MATLAB | 241 | 13 | function muscle = select_muscle_dlg()
med = 'Medial gastrocnemius';
lat = 'Lateral gastrocnemius';
answer = questdlg('Select muscle', 'Muscle selection', med, lat, med);
if strcmp(answer, med)
muscle = 1;
else
muscle = 2;
end
end
|
23bfbaab9eb36264c637d77783cf207bd939804ef11e7f23ff9dca77115b5521 | MATLAB | 242 | 8 | m2html('mfiles','MichalDataAna',...
'htmldir','doc', ...
'recursive','off', ...
'global','on',...
'globalHypertextLinks','on',...
'template','blue',...
'index','menu', ...
'graph','on'); |
3c395af4ba8d97862e791b209df6b4222c8f8eaa496c8c703b9005f97d6d9e71 | MATLAB | 243 | 10 | function [pow_parcel,rois] = do_sourceparcell_surface(atlas,ImageGridAmp)
rois = [];
pow_parcel = [];
for i=1:length(atlas.Scouts)
pow_parcel(i) = mean(ImageGridAmp(atlas.Scouts(i).Vertices));
rois{i} = atlas.Scouts(i).Label;
end
end |
8b83166d1129e5f5aa335a67c7c6eb2b5350641f89a3693a08a77ed5266c5fd1 | MATLAB | 243 | 12 | function prepare_plot_cross_section(ax)
hold(ax, 'on');
axis(ax, 'equal');
title(ax, 'Cross-section');
xlabel(ax, 'x [um]');
ylabel(ax, 'y [um]');
colormap(ax, flipud(parula));
c = colorbar(ax);
c.Label.String = 'Charge threshold [nC]';
end
|
e15b7cac8233b34cab2f03ba1f8c2014e689428c34213bd454dea5c89abd8faf | MATLAB | 243 | 11 | % Run simulations
Le_values = [5, 10, 30];
wNa_values = [2, 6, 14, 30];
for i=1:length(Le_values)
run_simulation_Part1(Le_values(i))
for j=1:length(wNa_values)
run_simulation_Part2(wNa_values(i), Le_values(i))
end
end |
edb235738666e17b83b667896ce895315c5cb137ff16716ddc5d7d3e442f0370 | MATLAB | 244 | 6 | function fname = save_temp_FEM(FEM)
fname = fullfile(get_base_paths().solutions, 'Temp', [erase(char(java.util.UUID.randomUUID), '-') '.mph']);
% '-' are removed because COMSOL does not like them in the filename
mphsave(FEM, fname);
end
|
8d8aa65a48203ce5aa2380c5826499419c5cfc3250d504283083ef10841e4628 | MATLAB | 245 | 8 | function fibers = ungroup_fibers(fibersPerFascicle)
fibers = vertcat(fibersPerFascicle{:});
if ~isempty(fibers)
fascId = repelem(1:numel(fibersPerFascicle), cellfun(@height, fibersPerFascicle))';
fibers.fascId = fascId;
end
end
|
65b30f9a0cf7c4523b447f38712aa72d4837352f795ec022cfa86093f75120e9 | MATLAB | 247 | 12 | function out = cholesky_factorization(in)
% function cholesky_factorization()
try
out = chol(in,'upper');
catch
[L,Di] = mchol(in);
try
out = chol(L*Di*L','upper');
catch
out = (L*sqrtm(Di))';
end
end |
f9884798f493ac754f256b5a3c9652e19bbffcc4b25af53b0d068e62ebf51e49 | MATLAB | 247 | 9 | function [e,h] = cat_entropy(ci)
if ~all(floor(ci) == ci)
error('need category data')
end
ele = unique(ci)' ;
countcount = @(AA,BB) arrayfun(@(x)sum(AA == x), BB) ;
h = countcount(ci,ele) ;
p = h ./ sum(h,2);
e = -sum(p.*log2(p),2,'omitnan');
|
fe4d14e09dd95018e8adcee23b2d88f860792ee6af4bcc655ea6060b5f3159a7 | MATLAB | 248 | 11 | function c = getCorr(y,ypred)
idxnan_y = any(isnan(y),2);
idxnan_ypred = any(isnan(ypred),2);
idxnan = idxnan_y | idxnan_ypred;
y(idxnan,:) = [];
ypred(idxnan,:) = [];
c = sum((y-mean(y)).*(ypred-mean(y)))/(numel(y)-1)./(std(y).*std(ypred));
end |
0505cb02ec8781a3034e8b7593bad3c0502c45a44b5dabd8de51d8cdebe11dfb | MATLAB | 249 | 11 | function c = getCorr(y,ypred)
idxnan_y = any(isnan(y),2);
idxnan_ypred = any(isnan(ypred),2);
idxnan = idxnan_y | idxnan_ypred;
y(idxnan,:) = [];
ypred(idxnan,:) = [];
c = sum((y-mean(y)).*(ypred-mean(y)))/(size(y,1)-1)./(std(y).*std(ypred));
end |
21b28d804ec6409bdb57e248649d6e8ce74f4208a862d314d398324f2092c07c | MATLAB | 249 | 15 | classdef LinkGraph
%LinkGraph: A graph with locations as nodes and location links as edges
properties
Valid = 0;
end
methods
end
function obj = LinkGraph( Loc_data, LocLink_data)
end
end
|
52bab43fa24788bf3d18afde551da46efad5498e933943e559c72498caca2a61 | MATLAB | 249 | 10 | function save_parfor(fname, data)
% Permits saving by functions whilst operating within a parfor loop
var_name=genvarname(inputname(2));
eval([var_name '=data;']);
try
save(fname,var_name,'-append');
catch
save(fname,var_name);
end |
7bf3ff710c008d81dbe71614bdca49ebb0fb69f6693878c73154f060d9dce57b | MATLAB | 249 | 14 | function q = q_for_n_activations(act, n)
if isempty(act)
q = Inf;
return;
end
assert(numel(act)>=n, 'Fascicle has not enough fibers');
sorted = sort(act(act>0));
if numel(sorted)<n
q = NaN;
else
q = sorted(n);
end
end
|
bcfad716dd8e3966262832bd9767b2647f0f8c105c5e259295e474cccbbaf5ce | MATLAB | 251 | 8 | function [out] = isRightC(im_str, c_request)
%ISRIGHTC helper function, is the requested channel in the image string?
c_request = uint16(c_request);
[~, c_current, ~] = load.czi.getInfo.channel(im_str);
out = c_current == c_request;
end
|
ed74d9653b5383cb9af47920459dfe92064e97a7c3473ec2c2c22543ca12131e | MATLAB | 252 | 8 | function [out] = isRightZ(im_str, z_request)
%ISRIGHTZ helper function, is the requested z-plane in the image string?
z_request = uint16(z_request);
[~, z_current, ~] = load.czi.getInfo.zpos(im_str);
out = z_current == z_request;
end |
7d1a677bc49e1b48a195673b6a35296704dde1faf61aa1953945e18bfe677907 | MATLAB | 253 | 13 | function str_TP = get_str_TP(p_vec)
% Str describing the TP in inputs.
%
% Input
% p_vec length-2 vector of TPs
%
% used in run_all_laser_stim
str_TP = ['_TP', num2str(round(100*p_vec(1))), '_', num2str(round(100*p_vec(2)))] ;
end
|
c8752ead2251142af5627c6da9bdf447ad49eb8b3b6e5b881f77999bdc290ef6 | MATLAB | 253 | 15 | function print_to_serial(serial_dev, st, use_fprintf)
disp(st) ;
if use_fprintf
%\r = enter
st = [st, '\r'] ;
fprintf(serial_dev,st);
else
for i=1:length(st)
fwrite(serial_dev,st(i),'uchar') ;
end
end
end
|
e0ef9a72f1c6b904fa5fa11924ab701dc488718b532483c32b6f060f7cf283c7 | MATLAB | 253 | 18 |
%% Generates mex file of the model function
cd('Generate_mex_functions')
mex_path = pwd;
addpath(mex_path)
tcut = 5000; % apply for transients
TDatend = 20000; % length of model simulation ms
makeCoderEm(TDatend,tcut);
cd ..
|
f0800db71e49a3dfad3891c7dde9e923b0f4e45cd780e06af87a54058ad8c1bd | MATLAB | 253 | 8 | function [colors_p] = get_color_gradient(c_1, c_2, length)
%GET_COLOR_GRADIENT get gradient between colors c_1 and c_2
colors_p = [linspace(c_1(1),c_2(1),length)', ...
linspace(c_1(2),c_2(2),length)', ...
linspace(c_1(3),c_2(3),length)'];
end
|
d69850a01e0fea78b2d5412f5d536df2fd571dfe0ae9cb51345a47da7e7320f5 | MATLAB | 254 | 10 | function [ Verts ] = TranslateVerts( Verts, vector )
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
Verts(:, 1) = Verts(:,1) + vector(1);
Verts(:,2) = Verts(:,2) + vector(2);
Verts(:,3) = Verts(:,3) + vector(3);
end
|
6e63fa01099d5d83f945158e4aee91dc2d4594afc9e899ae483941a5e8da958d | MATLAB | 255 | 8 | function self = GetClassifierData(self)
if self.VerboseLevel > 0
fprintf('Creating clips and loading clip data to train the classifier...\n')
end
self = self.CreateClipTable('IncludeFeatures', true);
self = self.LoadData('IncludeFeatures', true);
end |
38fdf97f17b95b62504b069b35d2b4355aa2715f472955e50db7d70616d2988c | MATLAB | 256 | 12 | clear all
close all
clc
load nets
mats = cat(3,Cij,Cij_rmvLong,Cij_rmvShort);
cn = zeros(1,3);
for i = 1:size(mats,3)
% mats(:,:,i) = mats(:,:,i)/sum(sum(mats(:,:,i)));
% cn(i) = f_CN_corr_aprox(mats(:,:,i));
cn(i) = f_CN_smp(mats(:,:,i));
end |
5c4857cce1255c6230919f3c756053dee1d460ef0d22e15e0a1d8f6d7a119b7a | MATLAB | 257 | 13 | function out = getFourierSum(a0,a,b,x)
% assert(length(a) == length(b),'a and b should be the same length')
n = length(a);
inds = 1:n;
cosSum = sum(a(:)'.*cos(inds.*x(:)),2);
sinSum = sum(b(:)'.*sin(inds.*x(:)),2);
out = a0/2 + cosSum + sinSum;
end |
822ab6a25666d1af6792ce609e05ab1c5810ec85640101f93106a5d5bc8a492a | MATLAB | 258 | 9 | % Write table of betas to CSV for further analysis in python
beta = util.load.beta_table();
%% Actual writing
f_name = fullfile(util.get_paths().data_versioned, 'betas', 'full_beta_tbl.csv');
writetable(beta, f_name)
%% Reread to see
T = readtable(f_name); |
fdfd66909bb97ba115d18fce336ac63efdf188b1bc3d0e215738bfa7c0f0de8a | MATLAB | 258 | 9 | function [ options ] = ODataWebOptions( )
%ODATAWEBOPTIONS Standard options for OData webread requests
options = weboptions('Timeout', 60, ...
'ContentType', 'json', ...
'CharacterEncoding', 'UTF-8');
end
|
0207828211f4aaab387809cfe4489f691ca36eca11555033ab5eff294962bbd4 | MATLAB | 259 | 9 | function fibersPerFascicle = group_fibers(fibers)
[G, fascIds] = findgroups(fibers.fascId);
fibersPerFascicle = cell(1, numel(fascIds));
for iG = 1:numel(fascIds)
fascId = fascIds(iG);
fibersPerFascicle{fascId} = fibers(G == iG, :);
end
end
|
02401951dac7d6f2f27cbadc3c42d8dc6814141696294bfa242d81c4e822d0e3 | MATLAB | 259 | 8 | function p_alt = compute_p_alt(p_1from2,p_2from1)
% Compute p(alt) for the input values of p(I_1|I_2) and p(I_2|I_1) given in
% arguments.
% p_1from2 and p_2from1 must have the same size.
p_alt = (2.*p_1from2.*p_2from1)./(p_1from2 + p_2from1) ;
end |
1c0bd0ca00cee4edf9d56f2deac644a9d77ada14e40cb08a60581bdc898442b0 | MATLAB | 259 | 6 | function [fiberActive, deltaQnC, qMaxnC] = load_thresholds(modelName, AS)
modelNameAS = [modelName '_AS' AS];
nrnModel = 'MRG';
load(['data\Recruitment\' modelName '\' nrnModel '\recruitment_1_' modelNameAS '.mat'], 'fiberActive', 'deltaQnC', 'qMaxnC');
end
|
9b25ccc98f1effb1cb0797b402ed0a2c1099513c849b3e5cacfe32f50854ba41 | MATLAB | 259 | 8 | function myopen(host,user,pwd)
% myopen Connect to MySQL [mym utilities]
% Example myopen('localhost','root','pwd')
try
a = mym('open',host,user,pwd); %#ok
catch
error('Could not connect to MySQL; check login parameters')
end |
7f80d7734a77c2fad0fc731ccf06e019aacb15265f66cf8acef34bd60e942db6 | MATLAB | 260 | 14 | function index = getclass(str,strs)
ind=find(ismember(strs,'KU'))
if isstring(arg)
for index=1:length(strs)
if strcmp(arg,strs{index})
return;
end
error('Internal error. Contact developers');
end
else
|
1fcde4b62749a7fecd5c97cbeb0243ae59b0dc74f588b03a1259f88339ef9611 | MATLAB | 261 | 7 | function data_out = umap_Rmatlab(data_in)
% data_in = #sample x #feature
dlmwrite('data_inR.txt',data_in,'delimiter','\t','precision',4);
unix('Rscript func_umap.R data_inR.txt > data_outR.txt');
%unix('python ./func_umap.py');
data_out=load('data_outR.txt');
|
106a9fbe1144e54afae74182191b394aedad76a13f9a529401b3190fcb466214 | MATLAB | 262 | 12 | function Save(self)
% Save annotations table to file
AnnotationTable = self.AnnotationTable;
currFolder = fullfile(self.ProjectPath, 'annotations', self.VideoName);
if ~isfolder(currFolder)
mkdir(currFolder)
end
save(self.FilePath, 'AnnotationTable');
end |
5bcf20f4145baa0d04cb8f0ab793577b9753e57ae0dad661c8c7dcbc1f8a0fc9 | MATLAB | 263 | 9 | function tri = tri_obj(model, object)
fnames = load_stl(model, object);
tri = cellfun(@tri_each, fnames, 'uni', false);
end
function tri = tri_each(fn)
tri = stlread(fn);
tri = triangulation(tri.ConnectivityList, tri.Points * 1e3); % Convert to um
end
|
3776ca75539382dd01695fab0f870f2c595c71a55fcbff78a0c542f1b9ec89e8 | MATLAB | 267 | 8 | function [cmap_interp] = interp_existing_cmap(cmap_orig,m)
% From the colormap cmap_orig (with one color in each row)
hsv = rgb2hsv(cmap_orig);
cmap_interp=interp1(linspace(0,1,size(cmap_orig,1)),hsv,linspace(0,1,m));
cmap_interp=hsv2rgb(cmap_interp);
end
|
464627b971273e6db199b994409740c9f0e2440c745244d0d0140b4aae084b12 | MATLAB | 267 | 7 | dataPath = 'D:\ephys_results\processedData\audioVis';
rawFiles = dir(fullfile(dataPath,'*raw.mat'));
for d = 1:numel(rawFiles)
dat = load(fullfile(rawFiles(d).folder,rawFiles(d).name));
expRef = rawFiles(d).name(1:end-8);
save2ONE(dataPath,expRef,dat)
end |
58475b1cf468a78a6b077a462fcd6acde805de3700eb5d7c634e797f1764137b | MATLAB | 267 | 8 | function print_beta_weights (beta, names)
neg_idx = find (beta < 0);
beta = beta (neg_idx);
names = names(neg_idx);
[sorted_beta, sort_idx] = sort (beta, 'ascend');
for i = 1:length (neg_idx)
fprintf ('%g\t%s\n', beta(sort_idx(i)), names{sort_idx(i)});
end |
92a9bc526e4ea06aa4752271b851b8bc7c5e526de5a32a0a5ac029cd4a4f7df7 | MATLAB | 267 | 9 | function [beta_table] = beta_table()
%BETA_TABLE Load beta table MAT file
% OUTPUT:
% beta_table: The loaded table of beta values
m = load(fullfile(util.get_paths().data_versioned, ...
'betas', 'full_beta_tbl.mat'));
beta_table = m.final_beta_table;
end
|
8edbb39716c185d267b5e26e27cb7f06bfba53d12f51f556f1b67695c31fcce3 | MATLAB | 268 | 13 | function [ y ] = f_wdt( x, mu, sigma, bases )
%UNTITLED5 Summary of this function goes here
% Detailed explanation goes here
den = 0;
mean_b = mean(bases);
for b=bases
den = den + normpdf(b, mean_b, sigma);
end
y = normpdf(x, mu, sigma)/den;
end
|
71676bbcdba4338ce2351d4b0e00c86a7b3703b58035bb7e67990a266c2faf3f | MATLAB | 269 | 8 | function [cor] = average_correlations(correlations)
% AVERAGE_CORRELATIONS average a group of correlations
% Averge through a tanh transformation
cor.atanh = atanh(correlations);
cor.average = tanh(mean(cor.atanh, 3, 'omitnan'));
cor.tril = tril(cor.average, -1);
end
|
9bbcef7e568134006354d7a9acc9b1f3c4717ee814afa0cc18343731b5466e4b | MATLAB | 269 | 8 | function tbprint(table)
% tbprint List a few rows of MySQL table [mym utilities]
% Example tbprint('junk')
if ~istable(table)
error('Table %s not found; use ''tblist'' to list available tables',table)
else
mym(['select * from ' table ' limit 20'])
end |
9d399a87524f81f3d1e0512e58782ef0be2faec8ed75b986c2b769d35c0d2ec6 | MATLAB | 269 | 8 | function elapsed_time = finish_time(tic_handle, log)
elapsed_time = toc(tic_handle);
if nargin > 1
log.info('Elapsed time: %g minute(s)', elapsed_time/60);
else
fprintf('\t< Elapsed time: %g minute(s)\n', elapsed_time/60);
end
end |
ce013d2025c0fd8cc57d4ef6cf787bc96563cc3746c7d4da81e70ba00bba4ef8 | MATLAB | 269 | 12 | function [logdetA, G_chol] = logdet(G)
if(~isdiag(G))
try
G_chol = chol(G);
logdetA = 2*sum(log(diag(G_chol)));
catch
logdetA = log(max(1e-20,det(G)));
end
else
logdetA = sum(log(diag(G)));
G_chol = diag(sqrt(diag(G)));
end |
71a4b51343d019b0b7fdefde8e2a62be5697b2878a7fe397881fbd9e5001e0f8 | MATLAB | 270 | 8 | function [x_labels] = label_names(taste_str,additional)
%LABEL_NAMES Get label names from taste and additional strings
[T, C] = ndgrid(taste_str, additional);
T = T'; T = T(:);
C = C'; C = C(:);
x_labels = cellfun(@(t,c)strcat(t,'-',c),T,C ,'UniformOutput',false);
end
|
8de982b6e79919238edb6bd0bcc72b754e8d9c73731b6e45b32d5fcd5dea88cf | MATLAB | 271 | 9 | function [raw_xls_data] = readFile()
%Reads selected .xlsx raw trace data file
% User selects input file
% Outputs raw_data variable
[fileName, pathName] = uigetfile('*.xlsx');
[~,~,raw] = xlsread(fullfile(pathName,fileName));
raw_xls_data = raw;
end
|
f68acfb4e88c45ffbd2453776a47d273fa452846ff451d3a21705e84280263b2 | MATLAB | 271 | 8 | function h = plot_ci(x, lo, up, color)
hold on;
h = patch([x(:); flip(x(:))], [lo(:); flip(up(:))], color, 'FaceAlpha', 0.1, 'EdgeColor', 'none');
% Borders, not nice:
%plot(x, squeeze(lo), '--', 'Color', color);
%plot(x, squeeze(up), '--', 'Color', color);
end
|
653125e35778cd403269038d3c643dd771d925339e7701e93d38d8f746fa9afb | MATLAB | 272 | 5 | function fname=tpfilename(tpfileparams,cycle,channel,frame)
error('this must be re-done for FluoView');
fname=[tpfileparams.fnameprefix '_Cycle' sprintf('%.3d',cycle) '_' tpfileparams.myconfigstr 'Ch' int2str(channel) '_' sprintf('%.6d',frame) tpfileparams.extension];
|
c09d3fd70d9d6ca5d7348dd98738c08ff42206abf72741a28a869286bdff92f9 | MATLAB | 272 | 15 | function ts = GetTimeStamps(self)
self = self.Load();
if isempty(self.AnnotationTable)
ts = [];
return
end
if self.MultiCam
ts = self.AnnotationTable.TimeStamp;
ts = ts.(self.PrimaryCamera);
else
ts = self.AnnotationTable.TimeStamp.TimeStamp;
end
end |
4e489378a01916cc6c256f4211bb0682df9a90bdf3ab4c17c93e9a8e8986e91f | MATLAB | 273 | 9 | function [ww, bb] = subGetModelWeights (model, clipping)
ww = model.sv_coef' * model.SVs; % model weights
bb = -model.rho; % model offset
if (clipping == 1)
ww (find (ww < 0)) = 0;
elseif (clipping == -1)
ww (find (ww > 0)) = 0;
end
% end subGetModelWeights |
ae9d078873916606aa31408f6046d729c4dd31c607bf17bc5ce080bdb68ab3fe | MATLAB | 273 | 18 | function h = sfigure(h)
% SFIGURE Create figure window (minus annoying focus-theft).
%
% Usage is identical to figure.
%
% Daniel Eaton, 2005
%
% See also figure
if nargin>=1
if ishandle(h)
set(0, 'CurrentFigure', h);
else
h = figure(h);
end
else
h = figure;
end |
e090f7dbad5975005e22d2bd15b3bd15b56ecd76d54ded02af063b65ef61b7af | MATLAB | 273 | 9 | function [im,fname]=tpreadframe(dirname,tpfileparams,cycle,channel,frame)
%TPREADFRAME
% read frame from multitiff
%
% 2008, Alexander Heimel
%
fname=[dirname filesep tpfileparams.fnameprefix '_t' sprintf('%.4d',frame-1) tpfileparams.extension];
im=sum(imread(fname),3);
|
fa0ca95702e64b92f148d7cde0f0fc96a3b273d4854bd9049e7343dbc81d15f3 | MATLAB | 274 | 9 | %% Save all GIFT Montage images to current directory
h = findobj('type','figure','-and','-regexp','tag','Explorer')
for i = 1:length(h)
tn = get(h(i),'tag');
tn(1:length('Explorer'))=[];
saveas(h(i),sprintf('ICA_Component_%03d.tif',str2double(tn)),'tiffn')
end |
9437d7972185e21f6946242322912c3cf0429bdf286302fe0b3e0317fc93bffb | MATLAB | 275 | 5 | function [featureMap,dScoresdMap] = gradcam(dlnet, dlImg, softmaxName, featureLayerName, classfn)
[scores,featureMap] = predict(dlnet, dlImg, 'Outputs', {softmaxName, featureLayerName});
classScore = scores(classfn);
dScoresdMap = dlgradient(classScore,featureMap);
end
|
a811056884e09b81dd45ab7e83be901632ee807e190393e82b34c461a85ab470 | MATLAB | 276 | 10 | function [p_1from2,p_2from1] = compute_TP(p_alt,p_1)
% Compute p(I_1|I_2) and p(I_2|I_1) for the input values of p(alt) and
% p(I_1)given in arguments.
% p_alt and p_1 must have the same size.
p_1from2 = p_alt./(2.*(1-p_1)) ;
p_2from1 = p_alt./(2.*p_1) ;
end
|
e12728732959a31c028bb7b0810da9367c3cff406fa742d98f7b060c848893cb | MATLAB | 276 | 13 | function [ scale ] = FetchODataScale(endpoint)
%FetchData - Collect scale from a database. Returns struct
% with XScale, XUnits, ..., ZUnits fields
options = ODataWebOptions();
endpoint = [endpoint '/Scale'];
scale = webread(endpoint, options);
end
|
019c1362c1be5509f387eaebc6c59213e816f698e01f3fb274cbe32fda837e1d | MATLAB | 277 | 7 | function [identifier] = get_table_identifier(T, row, col)
%GET_TABLE_IDENTIFIER an identifier for plot names from the variable and
%row name
identifier = strjoin([strsplit(T.Properties.RowNames{row},'_'), ...
strsplit(T.Properties.VariableNames{col}, '_')], ' ');
end
|
25861067d8a4db0928bbbf9b742ba26f7396cd90576c52595ddfda5aa1114726 | MATLAB | 277 | 12 | function [yfit,X, P] = fit_linear(X, Y)
%LINEAR_FIT linear fit to the data
% remove the nans
ind = isnan(X) | isnan(Y);
X(ind) = [];
Y(ind) = [];
% fit to the remaining data
P = polyfit(X, Y,1);
fprintf('The linear fit: Y = %f * X + %f \n',round(P,5))
yfit = P(1)*X+P(2);
end
|
30031f69dcae6c6f3e543129c109ac3e3758481ce2aab969355e063560aa44de | MATLAB | 279 | 16 | function [sgc] = my_sg_cent(W)
%inputs
% W weighted connection matrix
%
%outputs
% co subgraph centrality
%=================================================
B = sum(W,2);
C = diag(B);
D = C^(-(1/2));
E = D * W * D;
F = expm(E);
sgc = diag(F) ;
end |
58404f2ef831f1fe735fde0637911f616030c84f7b75bfcb760cae49056b5b39 | MATLAB | 279 | 17 | function [ll, p0, log_p0] = truncatedPoiss(rr, Y)
ll = zeros(size(Y));
Y1 = Y > 0;
Y0 = Y == 0;
rl = rr < -30;
ll(Y1 & rl) = rr(Y1 & rl);
ll(Y1 & ~rl) = log(1-exp(-exp(rr(Y1 & ~rl))));
ll(Y0) = -exp(rr(Y0));
if(nargout > 1)
log_p0 = -exp(rr);
p0 = exp(log_p0);
end
|
c1d47c0b7b7a62ddeab899ab6393dffd5adaba640cb9e58f944a75d604a5d2a9 | MATLAB | 279 | 19 | function [x, fixedPoint] = Left_Right_Choice(FASTRAK, tolerance)
x = 0;
fixedPoint = 0;
if abs(FASTRAK(5)) < 7
return
end
x = 1;
if abs(FASTRAK(6)) < 15
if FASTRAK(5) > 0
fixedPoint = 20;
else
fixedPoint = -20;
end
else
fixedPoint = 0;
end |
80c4b3a27fdacbf652444454d08bd4c9419cc2e0c220db644dfa131596050507 | MATLAB | 280 | 11 | function [noise_raster] = generate_whole_raster_activity_matched_noise_3D(raster)
[x,y,t] = size(raster);
noise_raster = zeros(x,y,t);
num_spikes_raster= sum(sum(sum(raster)));
noise_raster(randperm(numel(noise_raster),num_spikes_raster)) = 1;
end |
7900aa02ddc1364da9bc612537aa9d7c970a3cd00e6fc6d00d15b0d544a65f64 | MATLAB | 281 | 10 | function eps = permittivity(x, y, z, G)
%eps = permittivity(x, y, z, G)
on_membrane = (x >= G.Li-G.dx_min/2).*(x <= G.Li+G.Lm+G.dx_min/2) + ...
(x >= G.Li+G.Lm+G.Le-G.dx_min/2).*(x <= G.Li+G.Lm+G.Le+G.Lm+G.dx_min/2);
eps = G.eps*(~on_membrane) + G.eps_mem*on_membrane;
end
|
09a067c33b07b92bc01ce65aec34933dfba33cfbc9eec9cfa1e01aedae46b209 | MATLAB | 284 | 13 | function RunTtest
close all
clc
%---FLAGS---%
NH = [5.06 4.72 3.79 3.34 3.66 3.71 4.61 5.80];
CHL = [4.98 4.09 4.41 3.2 3.86 4.81 4.22];
[~,P,~,STATS] = ttest2(NH,CHL);
disp(['p = ' num2str(P)])
disp(['t = ' num2str(STATS.tstat)])
disp(['df = ' num2str(STATS.df)]) |
2ccaa0124d268348ac2f43edfceb97e4ddac793382221da23c0d4b4b36a80aae | MATLAB | 284 | 11 | function BP = lowpass(timecourse, SamplingRate, f_cut, filterOrder)
% BP = bandpass(timecourse, SamplingRate, low_cut, high_cut, filterOrder)
if (nargin < 4)
filterOrder = 2;
end
[b, a] = butter(filterOrder, [(f_cut/SamplingRate)*2],'low');
BP = filtfilt(b, a, timecourse );
|
a12138cc6d04535c58ab147983a1ac98db4fdb4c07c1cdcb7a5afc3cb9d5867f | MATLAB | 284 | 8 | Pwd=pwd;
esc=Esc();
if ~exist(strcat(Pwd,esc,'Main.m'),'file')
error('Please run program from folder with file Main.m in it');
end
addpath(strcat(Pwd,esc,'DirectFEM',Esc,'FEM'));
addpath(strcat(Pwd,esc,'DirectFEM',Esc,'Geometry'));
addpath(strcat(Pwd,esc,'DirectFEM',Esc,'VTK'));
|
61a32c7bff79201f026da71668c7a62e3a8840bb29e9337b43b75250ad236f3d | MATLAB | 286 | 9 | function fiberActiveAll = load_activation_all_AS(model)
fascIdsByAs = load_active_sites(model.paths);
nAS = height(fascIdsByAs);
fiberActiveAll = cell(nAS, width(fascIdsByAs));
for iAS = 1:nAS
fiberActiveAll(iAS, fascIdsByAs(iAS,:)) = load_activation(model, iAS);
end
end
|
92e95e64a5624c1ff11335354498830fb496a5f474ae74812bc4a9f491c1bb08 | MATLAB | 287 | 8 | function [summaryS, calClipT, revClipT] = EvaluateScorer(self, clipT)
% clipT = GenerateClipScores(self, clipT);
[summaryS, calClipT] = EvaluateCalibration(self, clipT);
[revSummaryS, revClipT] = ReviewEfficiencyMetric(self, clipT);
summaryS = MergeStructs(summaryS, revSummaryS);
end
|
9a8d00f0e785f11c3625df6f4820d9579ac2455242ebeeb7888166c1525851ff | MATLAB | 287 | 17 | function h = vec(H)
% h = vec(H)
%
% Vectorize matrix.
%
% H: Matrix
%
% $Revision: 1.2 $ $Date: 2015/01/06 17:14:57 $
% Original Author: Jorge Luis Bernal Rusiel
% CVS Revision Info:
% $Author: mreuter $
% $Date: 2015/01/06 17:14:57 $
% $Revision: 1.2 $
%
h = H(:);
|
0c962d89061636176ac706480efdd56b533a7a633b7e301a65a463c848952b50 | MATLAB | 289 | 12 | function b = VerifyTwoPhotonConfiguration
b = 1;
TwoPhotonGlobals;
if isempty(TwoPhotonPlatform)|isempty(TwoPhotonSynchronization)|isempty(tpstacklabels)|isempty(tpstacktypes), b = 0; end;
TPPreviewImageFunctionListGlobals;
if isempty(TPPreviewImageFunctionChannelList), b = 0; end;
|
1db863ff8a0a21c69596301c673d0911c9d53321f5644ae06890613dc91f1b4e | MATLAB | 289 | 14 | function [ ] = write_empty_lines(filename, nb_lines,permission)
% Add nb_lines empty lines in the file filename.
if nargin<3
permission = 'a' ;
end
file_txt = fopen(filename,permission);
for idx_line=1:nb_lines
fprintf(file_txt, '\n') ;
end
fclose(file_txt);
end
|
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