sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
8d5047e86ec5dfd2dce5ad154c06d31ee63701ae8ccfd620e573d5a881427f69 | MATLAB | 1,173 | 23 | function mscmd_branch_cluster_v2(timeseries_path,detect_path,adjacency_matrix_path,out_firings_path,opts)
% TODO: Docs
if (nargin<5) opts=struct; end;
if (~isfield(opts,'clip_size')) opts.clip_size=100; end;
if (~isfield(opts,'min_shell_size')) opts.min_shell_size=50; end;
if (~isfield(opts,'shell_increment')) opts.sh... |
b633261543e470cb49679c8c3815971d6430a4966992e068b86ef6ffc1b735c8 | MATLAB | 1,173 | 38 | function writeims(sloc,packdir)
% Currently single-view only
sdir = TrnPack.SUBDIRIM();
if exist(fullfile(packdir,sdir),'dir')==0
mkdir(packdir,sdir);
end
imovall = [sloc.imov]';
imovun = unique(imovall);
fprintf(1,'Writing training images...\n');
bufsize = 128;
for iimov = 1:numel(imovun),
... |
14a823a230aa3bfa7139e4285ab86c7b3f504937b15970e3e6a96dcc1403a641 | MATLAB | 1,174 | 1 | function out = randtest1d(a,b,paired,tail,nrand)
% function out = randtest1d(a,b,tail,nrand);
% tail = 0 (test A~=B), 1 (test A>B), -1 (test A<B)
if ~exist('b', 'var'), b = zeros(size(a)); end
if ~exist('nrand', 'var'), nrand = 100000; end
if ~exist('tail', 'var'), tail = 0; end
if ~exist('paired', 'var'), paired = ... |
1f4bd138876edbfc8326d42c87eb5165079be50cba71c609e0d2e9b605c2ac5e | MATLAB | 1,174 | 31 | function [shape] = ft_transform_headshape(transform, shape)
% FT_TRANSFORM_HEADSHAPE applies a homogenous coordinate transformation to a
% structure with headshape and fiducial information.
%
% Use as
% shape = ft_transform_headshape(transform, shape)
%
% See also FT_READ_HEADSHAPE, FT_TRANSFORM_GEOMETRY
% Copyrigh... |
b5173f1daf74540766185dd56d949d81f76f9534bc172812b3d6bad42148588e | MATLAB | 1,174 | 39 | function data = afxCsvRead(fname,delimiter)
% Import CSV-Files
% array = mycsvread(filename,delimiter)
%
% max.wawrzyniak@medizin.uniklinikum-leipzig.de
if nargin < 2, delimiter = char(9); end % Tab
data = {};
% check if file exists
if ~exist(fname,'file')
disp(['F... |
bb7ee4f031fe46627286e1f537fa4384cbdbf26b6af7cf6f1aae5d63d683bd2f | MATLAB | 1,175 | 39 | %% Illustration of central vs high posterior density intervals
%
%%
% This file is from pmtk3.googlecode.com
function postDensityIntervals
f = @(x)gaussProb(x, 0, 1) + gaussProb(x, 6, 1);
domain = -4:0.001:10;
h = plot(domain , f(domain), '-r', 'LineWidth', 2.5);
axis([-4, 10, 0, 0.5]);
shade(f, 0, -1.5, 7.5, 'b', 0.... |
be2118b0172c3412569786e21f629c12e41c17bc216b105fea356fd7b10a2133 | MATLAB | 1,175 | 44 | function [preproc, X] = preprocessorApplyToTrain(preproc, X)
% Apply Preprocessor to training data and store updated
% parameters inside pp object for use at test time
% This file is from pmtk3.googlecode.com
if isempty(preproc), return; end
% For backwards compatibility, we replicate the
% behavior of preprocessorC... |
35d423fac94ec812e792e8932647f1e285a24fffedfcfa954cc630d67b8f2deb | MATLAB | 1,176 | 41 | function MovT = NoCamp_MovieTime_Gaps(data,Sr,Nz)
%% old data (summer 2014)
% UP=[1;find(data>-1)];
% Step=find(diff(UP)>1000);
% for i=1:NFilms
% if i+1>length(Step)
% MovLim(i,:)=[UP(Step(i)+1) UP(end)];
% else
% MovLim(i,:)=[UP(Step(i)+1) UP(Step(i+1))];
% end
% dttmp=diff(MovLim(i,:... |
1797ad414da03100fc46e2f587b17cafcf1f57c072e2dae683e1dbf35efe65b3 | MATLAB | 1,177 | 49 | function [x] = comp_fisheye_distortion(xd,k)
%comp_fisheye_distortion.m
%
%[x] = comp_fisheye_distortion(xd,k)
%
%Compensates for fisheye distortions
%
%INPUT: xd: distorted (normalized) point coordinates in the image plane (2xN matrix)
% k: Fisheye distortion coefficients (5x1 vector)
%
%OUTPUT: x: undistorted... |
204d2a07e6f4442983cd8b6ebeee42f6c7f6d785333b352d3c1c3a4c8ed43e7a | MATLAB | 1,177 | 35 | function pMat = calculatePosteriorMatrix(trajExpectedSpikes, trajExponExpectedSpikes, spkPerBin)
% pMat = decode.calculatePosteriorMatrix(trajExpectedSpikes, trajExponExpectedSpikes, spkPerBin);
%
% Baye's rules: calculate posterior prob for given traj and event
%
%% Set up
nSpkPerTBin = squeeze(sum(spkPerBin, 3)); ... |
247257c7b2f64523d79d27affa52a122a25da9889302cddf71ff2925788e4c0c | MATLAB | 1,177 | 32 | function [calibModelError, reconModelError] = test_reconstruction(frame, camPts, numTrials)
nCamera = round(size(camPts,2)./2);
reconModelError = zeros(numTrials, 1);
calibModelError = zeros(numTrials, 1);
camPts_good = camPts(sum(~isnan(camPts),2)>2,:);
frame_good = frame(sum(~isnan(camPts),2)>2,:);
numPoint... |
8f04be556cc41bb0a9fabbe838fa6cbdb38bcca40ca47ce430912db8766a11c6 | MATLAB | 1,177 | 22 | function output = SOFAappendText(Obj,attribute,new)
%SOFAappendText
%
% output = SOFAappendText(input,new) appends the new text to the
% attribute using the correct SOFA separators. If the attribute is empty
% or non-existing, the output will be the new text only.
%
% SOFA API - function SOFAappendText
% Copyri... |
4667e7be072749384b0634226f4a042de5b0242d392f201bfe3fe726f1dccb88 | MATLAB | 1,178 | 51 | function S = VBA_sqrtm (C, inv)
% // VBA toolbox //////////////////////////////////////////////////////////
%
% S = VBA_sqrtm (C, inv)
% quick derivation of the square root of a matrix
%
% IN:
% - C: the entry matrix
% - inv: binary flag for inverse square root (inv = true).
% Default = false.
%
% OUT:
% -... |
55d126b8df07a9e065e6dc1eae2295ead920189d6434c5f6e610b6cd7ba4fcd2 | MATLAB | 1,178 | 52 | %% Fit a Gamma distribution to the rainfall data by MLE and moment matching
% Rice (1995) p383
%%
% This file is from pmtk3.googlecode.com
function gammaRainfallDemo()
X = loadData('rainfall');
X = X'; X = X(:); % concatenate across rows, not columns
%X = X(1:end-5); % removing trailing 0s
[a(1), b(1)] = gamMOM(X);... |
4dba1eef95d5f3f46789c88b0df87e4a65a1ce7b2739c673898dd1b39f09108a | MATLAB | 1,179 | 28 | clear all
%%
%Define default parameters
[opt] = ParameterOptions();
%%
%Create an oscillating gradient waveform (here consistent with definition in Aggarwal et al.)
opt.nOscillations=3; % Number of oscillations per TR
opt.Waveform='Sine'; % Type of Oscillating Gradient ('Sine' or 'Rect')
opt.G=674; %... |
880bac02f930f32c01a4086a5b9de05bb7400af902a0e31ecc28441547d84d69 | MATLAB | 1,179 | 35 | function ok = tt_sizecheck(siz)
%TT_SIZECHECK Checks that the size is valid.
%
% TT_SIZECHECK(S) throws an error if S is not a valid size array,
% which means that it is a row vector with strictly postitive,
% real-valued, finite integer values.
%
% X = TT_SIZECHECK(S) returns true if S is a valid and false otherwi... |
edde8f99ab9665190db02f9ab42481e6a902b199aa2d1b8f14ae8335cb068b3c | MATLAB | 1,179 | 53 | function rt_2_ev2(RT,cfg)
% v.0.0.0
% <*LAN)<|
% write ev2 file from reaction time (RT) structure
%
% cfg.filename = 'nombredearchivo.log'
% cfg.where
% cfg.srate = n ; %
% cfg.first_laten = 45, % Corregi la priemra latencia
%
if isfield(cfg,'unit')
RTunit = cfg.unit;
elseif (isfield(RT,'cfg') && isfield(... |
31a64f55d389d5b80ff784cf982c5290f4171e8819baaf2c7eaae51321c0f8a4 | MATLAB | 1,180 | 38 | function [w, loglikHist] = probitRegFitEm(X, y, lambdaVec, EMargs)
%% Find MAP estimate (under L2 prior) for binary probit regression using EM
% y(i) is +1,-1
% This file is from pmtk3.googlecode.com
% PMTKauthor Francois Caron
% PMTKmodified Kevin Murphy, Matt Dunham
if nargin < 4, EMargs = {}; end
model.w = [];... |
51e78e02ff5e3890dfd70554fa2c676775fde425cf198192b58010ac80945491 | MATLAB | 1,180 | 27 | % compile mex file
disp('Compiling perform_front_propagation_mesh, might time some time.');
files = { ...
'perform_front_propagation_mesh.cpp', ...
'gw/gw_core/GW_Config.cpp', ...
'gw/gw_core/GW_FaceIterator.cpp', ...
'gw/gw_core/GW_SmartCounter.cpp', ...
'gw/gw_core/GW_V... |
70e203d6650ba449c3c5648cb232f5ce3ba7381fde821d1c5e59cf0c58b6ed56 | MATLAB | 1,180 | 38 | function [pvalue] = mmdTestBoot(X1,X2,shufflenum,fvalue)
global sigma2
n1=size(X1,1);
n2=size(X2,1);
D1 = rbf_dot(X1,X1,sigma2);
D2 = rbf_dot(X2,X2,sigma2);
D12 = rbf_dot(X1,X2,sigma2);
Kz = [D1 D12; D12' D2];
MMDboot = zeros(shufflenum,1);
for bootnum=1:shufflenum
[~,indShuff] = sort(rand(n1+n2,1));
KzShu... |
989bc4c2b67feea3baec491185a926daf9a7c178f4919bb9559c798e0cb00f97 | MATLAB | 1,180 | 63 | % h = drawfly(trk,varargin)
% h = drawfly(x,y,theta,quartermaj,quartermin,varargin)
% draw triangle corresponding to fly position
% extra arguments will be fed to patch
function varargout = drawfly(x,y,varargin)
% draw an isosceles triangle with center (x,y)
% with rotation theta
% with height maj*4
% with base min*4
... |
d58518aa19d74be552fe0915b8b08a168aa7533d6763ab53ceef906347439cdc | MATLAB | 1,180 | 48 | %% Residuals Demo
%
%%
% This file is from pmtk3.googlecode.com
setSeed(2);
%xTrainRaw = (-10:1:10)';
n = 20;
xTrainRaw = randn(n,1);
%xTrainRaw = (-3:0.5:3)';
Ntrain = length(xTrainRaw);
xTrain = [ones(Ntrain,1) xTrainRaw(:)];
wtrue = [1 1];
sigma = 1;
yTrain = wtrue(1) + wtrue(2).*xTrainRaw + sigma*randn(Ntrain,1)... |
630058ecb8220c33b642165f541faae1596dd21c379871c74ecc46bc6691684e | MATLAB | 1,181 | 34 | function PlotFigure2_S1(vars)
% function PlotFigure2_S1()
% Figure 2 - Figure Supplement 1
% sRT vs distractor pull, per incentive*thp level
% only distractor-present trials
%% load if not given
if nargin==0
load('Figure 2 - Source Data 1.mat', 'vars')
% vars is struct with fields of [nPP, nConds, ... |
fae6494fb3dde38d7fc5bd89a18fc4e6d15ed930e72062cf69b41fc671ff212a | MATLAB | 1,181 | 41 | % CalculateSigmasWithinMice_Inverted.m
% Sarah West
% 10/24/23
% need for calculating corr of fluorescence with corrs by nodes.
% Made to be called by RunAnalysis.m
function [parameters] = CalculateSigmasWithinMice_Inverted(parameters)
MessageToUser('Calculating sigmas ', parameters);
% INVERT HERE
... |
2faf8efe788902c57485638563d567fe3aaa54c66ed0ae82f3f4a35262e9323d | MATLAB | 1,182 | 41 | function tests = mex_mergefilesTest
tests = functiontests(localfunctions);
end
function setup(testCase)
if ~exist('/mp/nvme0/tmp/testworks')
mkdir('/mp/nvme0/tmp/testworks')
end
n = 4000;
data = {};
for i = 1:4
data{i}=[rand(n,1); (1:n)'];
end
data{1}(2,1)=0.1;
data... |
64291e7762f0ed7f3497ede8d1f10c3d0241fd5729c3228dca20b117a97a0bb2 | MATLAB | 1,182 | 32 | function run_image_list = spm5_image_list(num_vols, file_list)
num_runs = length(num_vols);
if(length(file_list) == num_runs)
% EITHER cell array with full image list OR single 4-D image names
for i = 1:num_runs
if size(file_list{i}, 1) == num_vols(i)
% we have the ... |
07a6885c5da24ef4324415252babed2695c50283d74c36f57eb7c39cbe2822e3 | MATLAB | 1,183 | 35 | function model = discreteFit(X, alpha, K)
% Fit a discrete distribution, or if X is a matrix, a product of discrete distributions
%
% X(i, j) is the ith case, assumed to be from the jth distribution.
% X must be in 1:K.
%
% alpha - dirichlet alpha, i.e. pseudo counts
% (defau... |
34ec761f48a9263e7e00222966010ae54f8adb19d36f9d681e0e1d7585c693ac | MATLAB | 1,183 | 38 | % Translate an image to subpixel accuracy.
%
% Note that for subplixel accuracy cannot use nearest neighbor interp.
%
% USAGE
% IR = imtranslate( I, dx, dy, [method], [bbox] )
%
% INPUTS
% I - 2D image [converted to double]
% dx - x translation (right)
% dy - y translation (up)
% method - ['linear... |
05925d3d543928bd349680fba6527c1be63771339e6c5b9c7678ad98632dcea0 | MATLAB | 1,184 | 52 | %
% _ _
% ___ _ __ __ _| |__ ___ ___ _ __| |_
% / __| '__/ _` | '_ \/ __|/ _ \| '__| __|
% | (__| | | (_| | |_) \__ \ (_) | | | |_
% \___|_| \__,_|_.__/|___/\___/|_| \__|
%
function S = getFilesWithSortedSpikesOnChannel(self,channel)
arguments
self (1,1) crabsort
... |
12643e0959edbc38dacefc067f42ad53f984d19f9dbe3e90a2d846aa9acfb5b9 | MATLAB | 1,184 | 51 |
function model = shrunkenCentroidsFit(model, Xtrain, ytrain, lambda)
%author Robert Tseng
C = length(unique(ytrain));
[N, D] = size(Xtrain);
Nclass = zeros(1,C);
% compute pooled standard deviation
xbar = mean(Xtrain);
sse= zeros(1,D);
for c=1:C
ndx = find(ytrain==c);
Nclass(c) = length(ndx);
% if there... |
7e717545434a9eb6832a3cb5e77177b2e12411e5c27fe8a1f221564a6a20b2d9 | MATLAB | 1,184 | 47 | function [tfsucc,movfile,trxfile] = promptGetMovTrxFiles(tfMultiSelect,tfHasTrx)
% [tfsucc,movfile,trxfile] = promptGetMovTrxFiles(tfMultiSelect,tfHasTrx)
%
% tfsucc: scalar logical
% movfile: cellstr
% trxfile: cellstr same size as movfile
if nargin < 2,
tfHasTrx = true;
end
multiSelOnOff = onIff(tfMultiSelect);
... |
af5a5fd0559aea1a290d671ce7285314844d839c5bab8ec4babb558503333be7 | MATLAB | 1,184 | 32 | function source = find_source_points( evaluation_points, X, Y, dx, dy )
% *SPONTANEOUS WAVE DEMO*
%
% FIND SOURCE POINTS find "putative" source points - the most likely
% starting point for a wave on the mulichannel
% array by locating the arg max of divergence of a... |
dd7a58df633709d8038fe92073375b91f5571444c7b8caad6c7001c8e93baf8b | MATLAB | 1,184 | 36 | function [XX, XY,Yn,allstim,n,T] = MkSuffStats_BilinReg_Sims(Z,X,hk)
[n,T,N] = size(Z);
% P = cols(X);
P = size(X,2);
allstim = cell(n,1);
ntrials = sum(hk,1);
Yn = cell(n,1); % neural responses (each cell has resps for one neuron)
for ii = 1:n % loop over neurons
allstim{ii} = zeros(ntrials(ii),P); % stim vals ... |
1c36226c5585c9d1b268a6afd76a06221a15ee3933b3d18ad593a53e27d058fc | MATLAB | 1,185 | 35 | %% pro_Create: Create an empty new project structure
%
% Usage:
% pro = pro_Create()
%
% Inputs:
%
% Output:
% pro project structure
% .Inputs.pdfs: cell-array of the model inputs with the pdf handles
% .Inputs.Names: cell-array with the input names... |
b7ec3fe336da221facb75cbbd02f640a1027686793e2018a91bc648a037b397c | MATLAB | 1,185 | 46 | function clean()
% checks every files, and makes sure we can load it. if we can't,
% puts it in a folder called "corrupted"
self = crabsort(false);
% figure out what file types we can work with
allowed_file_extensions = setdiff(unique({self.installed_plugins.data_extension}),'n/a');
allowed_file_extensions = cellfun... |
be608cf1452bf6652402839b9d531aca4d90132f7c8a5c7be4eff7a6bdeefa1f | MATLAB | 1,185 | 62 | %
%
disp("This is an example matlab driver");
disp("On output the code prints the pot+grad in example1 and, pot+pottarg in example2");
disp(" ");
disp(" ");
%% source to source, charges only, pot+grad example
%
clear srcinfo ns U eps pg zk;
disp("Example 1: source to source, charge, pot+grad");
disp(" ");
disp(" ");... |
c1eec5638b31f86d977824d7c6c491d33ea81e138228a6898451ea240be513d6 | MATLAB | 1,185 | 47 | function [ conn_lengths ] = get_graph_lengths( nodes )
%GET_GRAPTH_LENGTHS Summary of this function goes here
% Detailed explanation goes here
parameters; % get dx, dy, dz % TODO: Test weather z is really z-stack dimension
n_nodes = max(size(nodes)); % todo: may fail in rare cases
%% Traverse the nodes
Adj = zero... |
1289b11c145e196830d404592db6bdb3dd0663c2b72056bf70463123619c92d2 | MATLAB | 1,186 | 41 | function FileSiteDistribution(SiteID, savepath)
% Count unique elements
[uniqueElements, ~, indices] = unique(SiteID);
counts = histcounts(indices,1:(numel(uniqueElements) + 1));
% Create figure
fig= figure('Visible', 'off');
b = bar(counts, 'FaceColor', '#007FFF', 'EdgeColor', 'w');
%... |
351d5e1be68168f8b4ec2ca88512be70eb19db9c636d49b675b1f4ae5d4d3a80 | MATLAB | 1,186 | 36 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
function [labels, elec_pos, grid_size, grid_pos] = get_gridparameters(subjects)
%% electrode positions in mm
% import electrode positions
for isubject = 1:length(subjects)
subject_id = sprintf('sub-%03i', subjects(isubject));
raw_path = [getenv('RAWDIR') subject... |
d5eaea4defe458f8916ebb05935f9564f79833d997badafc994dcb62144237a6 | MATLAB | 1,186 | 42 | function [ dataOut ] = meglegacy_fftFiltHilb( dataIn, f1, f2, srate )
%MEGLEGACY_FFTFILTHILB Filters data using an FFT and calculates hilbert transform
%
% Uses an FFT and inverse FFT to filter and calculate hilbert transform of
% the input data set in one step.
% A bandpass filter is applied to the data between the sp... |
ef3c95584dc1af68c1be6ab00aea71ad324657bb3e07120c852fddf8244dc450 | MATLAB | 1,186 | 51 | function writenodes_tetgen(fn,p,nodemap)
% writenodes_tetgen(fn,p,nodemap)
% Writes the 3D nodes in 'p' to a file called 'fn' in tetgen format
% <# of points> <dimension> <# of attributes> <boundary markers (0 or 1)>
% nnodes 3 0 0
% 1 x y z
% 2 x y z
% 3 x y z
fprintf('%s','Writing data to file...')
np=size(p,1); dim=... |
051590b303bc4c7e20f2597e51e6f4303fa2f584076c9ac02c6599bca294a063 | MATLAB | 1,187 | 52 | %% Burgers_test.m -- an executable m-file for solving a partial differential equation
% Automatically created in CHEBGUI by user Prateek Bhustali.
% Created on April 22, 2020 at 18:43.
%% Problem description.
% Solving
% u_t = -u*(u)' + (0.01/pi)*u",
% for x in [-1,1] and t in [0,1], subject to
% u = 0 at x = -1
%... |
263f7d5023dbe7e0603553956de9b6e47790ed537fa2894932883c5a6d47a8c4 | MATLAB | 1,187 | 41 | function varargout = figureResized( screenratio, varargin )
% Creates a figures that takes up certain area of screen.
%
% Almost same as figure, except get to specify what fraction of available
% screen space figure should take up. Figure appears in center of screen.
%
% USAGE
% varargout = figureResized( screenratio... |
59fbe72f0e24034543e1c21c558e4672af7d2ab8de1afff6a397a04a5427755c | MATLAB | 1,187 | 39 | function [model, logev] = logregFitVb(X, y, pp, useARD)
% Variational bayes inference for logistic regression
% This is a wrapper to Jan Drugowitsch's code.
% We use the following prior:
% p(w, alpha) = N(w | 0, diag(alpha)^{-1} ) * prod_j IG(alpha(j) | a0, b0)
% where a0, b0 are set small (vague prior)
% where alph... |
a03f370fc54ce50467b793777bdbc40343d452bb7e6e5dc6099c04e58678d567 | MATLAB | 1,187 | 58 | addpath ..
load clab_example;
load ../../surfaces/skin
sa=prepare_sourceanalysis(clab_example);
vcx=skin.vc;
trix=sa.vc{1}.tri;
vcx=sa.vc{1}.vc(:,1:3);
[np ndum]=size(vcx);
vcx=vcx-repmat(mean(vcx),np,1);
rads=sqrt(sum(vcx.^2,2));
vcx=vcx./repmat(rads,1,3);
sphere.vc=vcx;
sphere.tri=trix;
figure;showsurface(sphere);... |
74f18b72fdd6578039f02157bce6c65a1f01b6283af0293c46799aa86cf8e366 | MATLAB | 1,188 | 40 | function output = gzipdecode(input)
%GZIPDECODE Decompress input bytes using GZIP.
%
% output = gzipdecode(input)
%
% The function takes a compressed byte array INPUT and returns inflated
% bytes OUTPUT. The INPUT is a result of GZIPENCODE function. The OUTPUT
% is always an 1-by-N uint8 array. JAVA must be enabled ... |
e3d9b80d5f24b8621349a70f30d9cfbbd657ce46c0c2fc11a0b6425868c2a8c3 | MATLAB | 1,188 | 51 | function LAN = lan_autoref(LAN,tol)
% <*LAN)<] lantoolbox
% v.0.0.1
%
% Auto local references for iEEG
% tol = 0 ; how many distances of electrode tolerate for the local references
% 0 = Only the immediately adjacent electrode
% n = n electrode of distance
%
% Pablo Billeke
% 16.11.2013
if na... |
11304d5c8a343755b75aa6ed69f417548d11b38c3e0d6dc8045d5a9bed8759a6 | MATLAB | 1,189 | 27 | function linkToolName(tool_fig,target_fig,tool_name)
% LINKTOOLNAME(TOOL_FIG, TARGET_FIG, TOOL_NAME) uses the function
% createFigureName to set the name of TOOL_FIG. It then creates a listener
% that will update the TOOL_FIG name property to match changes that occur
% to the TARGET_FIG name property.
% Copyright 2... |
1c416890f126bef39cf65ddf4122d2dd109b29cd56bc56dddca55a38613446ea | MATLAB | 1,189 | 43 | function [x_comp] = comp_distortion(x_dist,k2);
% [x_comp] = comp_distortion(x_dist,k2);
%
% compensates the radial distortion of the camera
% on the image plane.
%
% x_dist : the image points got without considering the
% radial distortion.
% x : The image p... |
9b76b0e041ed9b8ed280ef0c5dede0ac641629267775ab47df58a5ff538efb8a | MATLAB | 1,189 | 36 | %% sdotype
% Utility to quickly classify an SDO matrix as 'L' (linear/ dpx) or 'M'
% (markov/transition matrix). An array of all zeros should be passed as
% 'L'.
%
% Tolerance value calculated is relative to the number of states.
% Copyright (C) 2023 Trevor S. Smith
% Drexel University College of Medicine
... |
c2a38e085ae539aa79a76f15bf235e581b42e761e92f143579a25825999f16c5 | MATLAB | 1,189 | 53 | function [hax,hfig] = get_axes(hax,hfig,varargin)
[axparams,axi0,axi_create,figi,figpos] = ...
myparse(varargin,...
'axparams',{},...
'axi0',1,'axi_create',[],'figi',1,...
'figpos',[]);
if isempty(axparams),
nax = 1;
else
nax = axparams{1}*axparams{2};
end
if isempty(axi_create),
axi_create = axi0:axi0+... |
f6224b7045962c72c15a1dbf6a016f73b8fd18676e53068519cef200898fb866 | MATLAB | 1,189 | 50 | function u = SB_ATV(g,mu)
% Split Bregman Anisotropic Total Variation Denoising
%
% u = arg min_u 1/2||u-g||_2^2 + mu*ATV(u)
%
% g : noisy image
% mu: regularisation parameter
% u : denoised image
%
% Refs:
% *Goldstein and Osher, The split Bregman method for L1 regularized problems
% SIAM Journal on Imag... |
27da8824470cddb2bcd547a944338064daf7fea6001d6141d826346bc2cc4e4c | MATLAB | 1,190 | 36 | function r = randSample( n, k, isArray )
% Generate values sampled uniformly without replacement from 1:n.
%
% If n is an integer, samples k values from 1:n without replacement. If n
% is an array, samples k values without replacement from n. This function
% implements much of the same functionality as randsample.m in ... |
8ad2771eda628cd7a74328ce7a10301f6cdffd6f98fd5304e63fbdc3bf325d05 | MATLAB | 1,190 | 45 | function [fx] = f_HRF(Xt,P,ut,in)
% Balloon (HRF) model evolution function in log-space (wo options)
% function [fx] = f_HRF(Xt,P,ut,in)
% This function evaluates the evolution function derived from the balloon
% model for the hemodynamic response function. Note that the hemodynamic
% states are in log-space, for posit... |
0d56b901fcd9bae67feb1b67765204653e3bcaa2e2f64f643aaeb4ffcb6d77df | MATLAB | 1,191 | 32 | %-----------------------------------------------------------------------------------------
% Plot spike shape of example amygdala neuron
%
% Kehl et al. 2024 (DOI:XX)
% Single-Neuron Representations of Odors in the Human Brain
% Figure 4b
% Author: Marcel Kehl
% License: MIT License
%--------------------------------... |
0d6c6cdcee977524b2652e023babc93306ecb07fade9c2fdb0465aa482ce0481 | MATLAB | 1,191 | 53 | function TF = tabularFactorMultiplyDomain(facs, dom)
% Multiply tabular factors
% T = tabularFactorMultiplyDomain({fac1, fac2, fac3}, domain)
% Same as tabularFactorMultiply, except we explicityl specify
% the domain of the resulting factor, which may not be in sorted order
% This file is from pmtk3.googlecode.com
N... |
2ec22e9a1ba5b831003e028afca926ccdb6e27c7eebbb59a68b53742f1628a70 | MATLAB | 1,191 | 50 | % HIFIE_SPDIAG_SV_H Dispatch for HIFIE_SPDIAG with DINV = 1 and F.SYMM = 'H'.
function D = hifie_spdiag_sv_h(F,spinfo)
% initialize
N = F.N;
n = length(spinfo.i);
P = zeros(N,1); % for indexing
D = zeros(N,1); % for output
% loop over all leaf blocks from top to bottom
for i = n:-1:1
% find act... |
7130d3161fa8937cda0f98b8fc48e75ce254c53292b6ce2ab8cd001c589642ef | MATLAB | 1,191 | 40 |
ind = 1;
data = dir('/DATAPOOL/ERRORMONITORING/SEM_mri_data/P*');
%%
for i = 1:size(data,1)
data_func = dir([data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/nifti/func/run*']);
for j = 1:size(data_func,1)
images = [data_func(j).folder, '/', data_func(j).name, '/wra', data_... |
a9b7387f6ff085d179f58ade7c5f6e7ebe57f5e1b31cd6c4bc87e077b31f37b7 | MATLAB | 1,191 | 31 | function flag=istfraff(method);
% flag=istfr2(method) returns true is method is an affine
% time frequency representation.
% See also istfr1, istfr2.
% F. Auger, may 98
% Copyright (c) CNRS - France 1998.
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU Genera... |
bdf1ce73f478f2f56114a0c7fb46f7be88a0394e78c50355dde786607cea38e4 | MATLAB | 1,191 | 34 | % Quick script to get a maxProjection of all images to show
% the difference between pre/post registration and color correction
function reporting_getMaxProjections(directory_images, channels)
loadParameters;
if ~exist(params.reportingDir,'dir')
mkdir(params.reportingDir);
end
for roundnum = 1:params.NUM_ROUNDS
... |
e23ef4d5799d4d30a553e625740ed3c05524a560f42df50f44cb5afc9ead2626 | MATLAB | 1,192 | 50 | % HIFIE_SPDIAG_MV_H Dispatch for HIFIE_SPDIAG with DINV = 0 and F.SYMM = 'H'.
function D = hifie_spdiag_mv_h(F,spinfo)
% initialize
N = F.N;
n = length(spinfo.i);
P = zeros(N,1); % for indexing
D = zeros(N,1); % for output
% loop over all leaf blocks from top to bottom
for i = n:-1:1
% find act... |
f579db2bf9e1a2e4040249cd50522dd35693f337736d1564e4c0aed491c6df48 | MATLAB | 1,192 | 33 | function downloadAllData(destnRoot, quiet)
%% This function downloads all pmtkData from pmtkData.googlecode.com
% By default, it stores data in pmtk3/data, but you can specify a
% diffferent destnRoot. This function does not add the folders to the
% matlab path. If the folders already exist, the contents are overwritte... |
fd10808734d1785fc4e55a9d8f8fec4fb0ac2564da079326c4ac4afeff1c5823 | MATLAB | 1,192 | 12 |
fprintf(1,'Saving the stereo calibration results in Calib_Results_stereo.mat...\n');
string_save = 'save Calib_Results_stereo om R T recompute_intrinsic_right recompute_intrinsic_left calib_name_left format_image_left type_numbering_left image_numbers_left N_slots_left calib_name_right format_image_right type_numberi... |
fe3ca718fd43395ba096dc8b9311ee85b08f6c8183595abc1b50734170404bc1 | MATLAB | 1,192 | 46 | %% MLP Classification Demo
% Based on Mark Schmidt's Demo from
%http://people.cs.ubc.ca/~schmidtm/Software/minFunc/minFunc.html#9
%%
% This file is from pmtk3.googlecode.com
H = [3, 6, 9];
H = 6;
for hi=1:length(H)
nhidden = H(hi);
setSeed(0);
nVars = 2;
nInstances = 400;
options.Display = 'final';
options.MaxIter ... |
29172df164dbdccd24bad39ee72885f673736d9d372e9287f9740fac64024a08 | MATLAB | 1,193 | 31 | % ALIGNTIMESTAMPS align signal by subtracting event timstamp from spike
% timeStamps
% alignTimeStamps.m
%
% Copyright 2008 Vanderbilt University. All rights reserved.
% John Haitas, Jeremiah Cohen, and Jeff Schall
%
% This file is part of JPSTH Toolbox.
%
% JPSTH Toolbox is free software: you can redistribute it ... |
30f02175d7a7ee864b71bcaca3e05c20d158d9bba5596eed060b8d21160afd79 | MATLAB | 1,194 | 28 | function [exFactor, iReSIGt, norm, centroid] = getonlineparameters(EMG, EMGmask, MUFilters, fsamp)
EMG(EMGmask > 0,:) = [];
nbextchan = 1000;
exFactor = round(nbextchan/size(EMG,1));
eSIG = demean(extend(EMG,exFactor));
ReSIG = eSIG*eSIG'/length(eSIG);
iReSIGt = pinv(ReSIG);
nMU=1;
for i = 1:size(MUFilters,2)
Pul... |
43211acab28509a5f6faea80ba122f49ad20c612eae85b49b6e84ce7de8fe708 | MATLAB | 1,194 | 25 | function dbURL=SOFAdbURL(dbURL)
% dbURL=SOFAdbURL
%
% dbURL=SOFAdbURL returns the internet URL to the directory containing
% HRTFs. The default URL is http://www.sofacoustics.org/data.
%
% dbURL=SOFAdbURL(newURL) sets the internet URL to the newURL for further calls
% of SOFAdbURL.
% SOFA API - function SOFA... |
49b1c881f1f7a6b827c5cc35b1d7ecba5fb6247ab872ba50e407ceded63e76e7 | MATLAB | 1,194 | 26 | function SC = state_colors(obj) %#ok<INUSD>
% Colors that the various states take when plotting
SC = struct( ...
'wait_for_cpoke', [210 105 205]/255, ... % orchid
'wait_for_cpoke_dir', (255/210)*[210 105 205]/255, ... % orchid
'wait_for_cpoke_freq', (105/255)*[210 105 205]/255, .... |
53c22b322b07be2387148d4c57f1d905739d477d8e028b8d058dcc7ae80c969d | MATLAB | 1,194 | 34 | % This code will calculate the relative displacements value for the 2d glass.
function out = Compute_StrainCumulative_2D(small_x,big_x,small_y,big_y)
%tracks the particle between two subsequent stacks and calculates the strain
filename = ['d2_af=73_10neibs_squared_'];
savepath = '/media/hdd2/softness/review/final/... |
5d8e30d210300c542d8f01ab299ce9379a5c25a883ff94dd60b9c304c68e1b77 | MATLAB | 1,194 | 27 | % MESH_SUPPORT Calculates total area (2D) or volume (3D) of elements
% connected to each node. (how much support is around a node).
%
% SYNTAX:
% [SUPPORT] = MESH_SUPPORT(NODES,ELEMENTS,ELEMENTS_AREA)
%
% [SUPPORT] = MESH_SUPPORT(NODES,ELEMENTS,ELEMENTS_AREA) Sums all element
% areas/volumes around a node.
% ... |
a9bab339d95a25786b8492f4ffd0719c06f36bae2cf459c2f4d0d599aba5b607 | MATLAB | 1,194 | 34 | function result = fillInCustomStage2(rawTCI3, stage2Spec)
% Used to fill in the type of stage 2 in a custom two-stage tracker.
% This is a pure function.
if ~isempty(stage2Spec)
if iscell(stage2Spec) ,
stage2ConstructorArgs = stage2Spec ;
result = stage2ConstructorArgs ;
elseif isa(stage2Spec... |
b710d815a03ff4eb021bc30caa00132db424d52bcd629f90aa3082af36af8604 | MATLAB | 1,194 | 35 | function dataArray = splitPSTH(PSTH,waveforms,inputCat)
uniqueCat = unique(inputCat);
PSTHCell = cell(1,length(uniqueCat));
waveFormCell = cell(1,length(uniqueCat));
uniqueWhere = cell(1,length(uniqueCat));
[~,numBins] = size(PSTH);
for ck = 1:length(uniqueCat)
curVal = uniqueCat(ck);
curLoc = find(curV... |
c71808a4dc73b2bbec4c2ebb6f275f525dc1f20dcf6d8e60025f8d4b8b7a6fa2 | MATLAB | 1,194 | 42 | % mtrax2fixedtrx(inmatname,outmatname)
% inmatname: name of a matfile created by mtrax
% outmatname: name of a matfile to save results to
% results will be saved in the format returned by fixerrorsgui
function mtrax2fixedtrx(inmatname,outmatname)
load(inmatname);
load(inmatname,'angle'); % because matlab is retarded :... |
04dbb5913e1d608a3196ed1543bd4cfa29aaa7f4feb3ac6626085532910f2739 | MATLAB | 1,195 | 65 | function [inF, n_r] = extend_dcm(inF,hA,hB,hC,hD,dim,sources)
%%- get dimensions
n=dim.n;
n_u=dim.n_u;
n_r = get_dims(hA,hB,hC,hD) ;
sourcesDim = cellfun(@numel,{sources(2:end).out});
for i=1:sum(sourcesDim)
respSource(i) = sum(i>cumsum(sourcesDim))+1 ;
end
%%
[inFtemp] = prepare_dcm(hA,hB,hC,hD,respSource);
%... |
1698cc503e7e5f52313ad1fff66c8f909c32110a92123cb816d7016a945df789 | MATLAB | 1,195 | 39 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
function EEG = find_exactRpeaks(EEG, trigger_name, ecg_chanName, debug_mode)
% if data was down-sampled it is necessary to search for more exact R-peaks
% data needs to have an ECG channel!
% BN, 06,2020
idx_ecg = find(ismember({EEG.chanlocs.labels}, ecg_chanName));
% ge... |
3d69f48465e164483c8e5c9ed5e729b811d8e2620e80b7b1a21c7eb81c2b7ffa | MATLAB | 1,195 | 33 | function h_setROIProperties3(handles, flag)
[currentInd, handles, currentStruct, currentStructName] = h_getCurrendInd3(handles);
roi = findobj(handles.imageAxes, 'Tag', 'annotationROI3', 'Selected', 'on');
if length(roi)>1
error('more than one ROI selected! this should not happen!');
elseif length(roi)==... |
884136247b04124b784ebe5ea76a9a4b4f37cfbc2837daa126f5a4603a53d810 | MATLAB | 1,195 | 30 | function nc_copy_file_list(fromdir, folder_prefix, file_prefix, file_suffix, todir, newprefix, insubfolder)
from_folders=dir(fullfile(fromdir, [folder_prefix, '*']));
if isempty(folder_prefix)
from_folders(1:2)=[];
end
if exist('insubfolder', 'var') == 0
insubfolder = 1;
end
for i=1:length(from_folders)... |
9fc0e55af8463ce81d1ed0ac8eb4dd35b1f4c9d29bf90eb9001f4f2d89a63e8d | MATLAB | 1,195 | 32 | function [SNReff,bEff,Delta] = DWSE_SNREfficiency(x,optSample,optScanner,b,~)
%%
% calculates DW-SE SNR Efficiency
%
% input:
% x = array with diffusion gradient (mT/m), duration of diffusion gradient (ms) and repetition time (ms)
% optSample = T1 (ms), T2 (ms) & D (um^2/ms)
% optScanner = Maximum readout duratio... |
1f88c59bcf0fece961c17190b491989a8b953714126355548a3d3d08067cb559 | MATLAB | 1,196 | 34 | classdef (Sealed) AdjMatrixLinLatt < adjmatrix.AdjMatrix
methods
function this = AdjMatrixLinLatt(params, loadOnInit)
% creates a complete graph (mean-field network)
%
% params {AdjMatrixParams}: params of the adjacency matrix
% loadOnInit {boolean}: loads the... |
288701239c69a8c7057065ae7edb9aa8445ac1798ceb9d0e42ebed880cbe5c8e | MATLAB | 1,196 | 48 | function u = SB_ITV(g,mu)
% Split Bregman Isotropic Total Variation Denoising
%
% u = arg min_u 1/2||u-g||_2^2 + mu*ITV(u)
%
% Refs:
% *Goldstein and Osher, The split Bregman method for L1 regularized problems
% SIAM Journal on Imaging Sciences 2(2) 2009
% *Micchelli et al, Proximity algorithms for image models: ... |
a07841e5116c74e9bb011bc875cdfeafb72260fd50250a4e0bc59e461e69701b | MATLAB | 1,196 | 77 | function [hits,task,choice,gfreq,gdir,side,nta,vecr,vecl,vechi,veclo] = ...
get_trials_stim(sessions,trials,minperf,mintri,minbe)
ind=find([sessions.hit]>=minperf & ...
[sessions.valid]>=mintri & [sessions.good]==1 & ...
([sessions.bdir]+[sessions.bfreq])/2>=minbe);
tr=trials(ind);
hits={tr.hits_all};
h... |
2233be9df0778b70f8afa1edecd181728cd71995a7ac5649fe8f8cf5004fd14d | MATLAB | 1,197 | 30 | % ISCUDA Determines if there is a NVidia CUDA enabled GPU in the system.
% Also, checks if the compute capability is at least 3.0.
%
% SYNTAX:
% ISCUDA
% [IS] = ISCUDA
% [IS, INFO] = ISCUDA
% [IS, INFO, MESSAGE] = ISCUDA
%
% ISCUDA Returns logical true or false:
% 0 - no available NVidia GPUs with ... |
4484525a8dab47201251c42b1ab9e86fd7890d826c47c49f2fd9893d229228df | MATLAB | 1,197 | 42 | clear;
basefolder = fileparts(fileparts(fileparts(mfilename('fullpath'))));
codefolder = [basefolder,'/code'];
addpath(genpath(codefolder));
config1_path = [basefolder, '/tests/fixtures/config.json'];
config2_path = [basefolder, '/tests/fixtures/config2.json'];
config5_path = [basefolder, '/tests/fixtures/config5.jso... |
7466bb0bd9ffd96c210bc635dc100aeddbfbf8021d0bcfd3d0c225735fc13581 | MATLAB | 1,197 | 34 | % pstCoincidenceHistogram calculates a psth coincidence histogram of
% a given width for a JPSTH
% pstCoincidenceHistogram.m
%
% Copyright 2008 Vanderbilt University. All rights reserved.
% John Haitas, Jeremiah Cohen, and Jeff Schall
%
% This file is part of JPSTH Toolbox.
%
% JPSTH Toolbox is free software: you... |
c975fc8e0b109469de65005b245b18383575efdd5092b91f51df13beb2610aa6 | MATLAB | 1,197 | 51 | function [L, Lij] = discreteLogprob(arg1, X)
% Compute the log probability of the data. X must be in 1:K.
% [L, Lij] = discreteLogprob(model, X) or
% [L, Lij] = discreteLogprob(T, X)
%
% model is a structure with a field T, a K-by-d stochastic matrix,
%(as returned by discreteFit).
%
% X(i, j) is the ith case from the ... |
f8ea82ab3c95293bb4634af8ccdbc34441c824b442439de342604f5aa2624745 | MATLAB | 1,197 | 45 | function C = minus(A,B)
%MINUS Binary subtraction for ktensor.
%
% C = MINUS(A,B) computes C = A - B. A and B must both be ktensors
% and have the same size, and the result is another ktensor of the
% same size.
%
% C = MINUS(A,B) is called for the syntax 'A - B' when A or B is a
% ktensor.
%
% See also ... |
0b7c1b92a7717c8244dc7327ae4bbbec879e711347140c1382dee4eceb418325 | MATLAB | 1,198 | 62 | function [om3,T3,dom3dom1,dom3dT1,dom3dom2,dom3dT2,dT3dom1,dT3dT1,dT3dom2,dT3dT2] = compose_motion(om1,T1,om2,T2);
% Rotations:
[R1,dR1dom1] = rodrigues(om1);
[R2,dR2dom2] = rodrigues(om2);
R3 = R2 * R1;
[dR3dR2,dR3dR1] = dAB(R2,R1);
[om3,dom3dR3] = rodrigues(R3);
dom3dom1 = dom3dR3 * dR3dR1 * dR1dom1;
dom3dom2 =... |
a9ebfe9aeef675401200917fb815d1ce8d3935a7d7247d0d45c6a2e8e2bd39a8 | MATLAB | 1,198 | 41 | % slightly more robust version of matlab's waitbar
function varargout = mywaitbar(varargin)
if nargin >= 2 && ischar(varargin{end-1}) && ...
strcmpi(varargin{end-1},'interpreter') && ...
ischar(varargin{end}),
interpreter = varargin{end};
leftovers = varargin(1:end-2);
else
interpreter = 0;
l... |
7880af5612f4c9430babbb75c6cfd06a9ed03bdaa459d9058e5e7bf4753bf90d | MATLAB | 1,199 | 30 | classdef dectree < handle
%Decision tree data structure.
properties
isRegression; %0 for classification, 1 for regression.
examples; %Indicies of the training examples directed to this node during fitting.
features; %Indicies of all available features remaining at ... |
f915aba5fbf8aab04343d498628e9e9e995009d3f7b5cd668037001c334fbedd | MATLAB | 1,199 | 35 | %% dataAtPercentile
% Simple macro for establishing a cdf of the observed data, setting up
%the appropriate percentile search, and returning value which is at x% of
%the data amplitude
%// Data should be rectified prior to percentile search if absolute
%magnitude of percentile is sought
% Copyright (C) 2023 T... |
07da21e3fd148edb2d65bca6dbe69bee8da4918699cbca77413c3ffbb6e71331 | MATLAB | 1,200 | 46 | %%
% ================= EXPORT CONN CONDITION FILE =================
%%
clear all; close all; clc;
%%
part = 1;
idx=1;
for s = 1%subs
if s < 10
sub = strcat('P0',num2str(s));
else
sub = strcat('P',num2str(s));
end
dir_files = strcat('F:\SEM_mri_rawdata\', sub, '\'); ... |
6244867d3934172151fa63e93da675f415f953110b046b58105c6559fa40a60d | MATLAB | 1,200 | 50 | function [locs pks]=peakseek(x,minpeakdist,minpeakh)
% Alternative to the findpeaks function. This thing runs much much faster.
% It really leaves findpeaks in the dust. It also can handle ties between
% peaks. Findpeaks just erases both in a tie. Shame on findpeaks.
%
% x is a vector input (generally a timeco... |
70cce2d814dabceab6505c8ea7d9aaf2bdcdf4532793e52cebc7fe148fa92098 | MATLAB | 1,200 | 43 | function dgm = dgmRebuildJtree(dgm, varargin)
% Rebuild the precomputed jtree after CPD params have changed
% The jtree structure does not change, just the clique potentials.
% This file is from pmtk3.googlecode.com
% In this implementation, we start from scratch,
% and ignore any existing jtree structure
%{
factors... |
77cb85bafb3acdf152decd543f367e53ff2ffe140e9688f410b30b14265b8352 | MATLAB | 1,200 | 54 | function y = costdist (x, numstat, cdf)
% function y = costdist (x, numstat {, cdf})
%
% Function calculates the distribution of the cost function
% Inputs:
% x - the value of cost function
% numstat - number of statistics being fitted by fitparam
% cdf - if = 1 cumulative distribution is found; default = 0
if exi... |
78767a1332c0fd4a9a9ea574af16a68d30387eba07535eece447ad37b5486383 | MATLAB | 1,200 | 38 | function [fi,ind] = interpF2d(F,n,s1,s2,h)
%% returns interpolated function value fi = F(s1,s2,s3)
% where s1 = row index, s2 = col index, s3 = depth index
%interpF(V,n,xi,xj,xk) == interp3(par.Yc,par.Xc,par.Zc,V,xj,xi,xk)
if nargin < 5
h = [1,1];
end
fi = zeros(length(s1),1);
[n1,n2]=deal(n(1),n(2));
% conv... |
c3cff33483b0303457bcdc878beb97fe50b637d409a2cddeaf9d5c956f2fce25 | MATLAB | 1,200 | 35 | % fixedtrx2mtrax(inmatname,outmatname)
% inmatname: name of a matfile created by fixerrorsgui
% outmatname: name of a matfile to save results to
% results will be saved in the format returned by mtrax
function fixedtrx2mtrax(inmatname,outmatname)
load(inmatname);
nflies = length(trx);
nframes = 0;
for fly = 1:nflies,
... |
039e893248d7e929a1cb53e04e8b0f30a91ec4cbfe3b9a4bad5fa9028c975e71 | MATLAB | 1,201 | 56 | function [xc,yc,radius,h] = fitcircle_manual(hfig,color,ti)
xc = [];
yc = [];
radius = [];
h = [];
if nargin < 1,
hfig = gcf;
end
hold on;
if nargin < 2,
color = 'm';
end
if nargin < 3,
ti = 'Click points on circle';
end
title(ti);
try
[x,y] = getline(hfig,'closed');
catch %#ok<CTCH>
return;
end
if isemp... |
6721610ce87a9406bc3adf4a692caae2c4b698ee1162ab0c3a3d9038395164b6 | MATLAB | 1,201 | 45 | function [mask] = image_stack_adjust_nucleus(stack, name)
% TODO: optimize
%load parameters
parameters;
% number of z-slices
Nz = length(stack(1,1,:));
%% ------------------------------ 3D matrix ------------------------------
tic
fprintf('Contrast enhancemenet: ')
% Allocate 3d matri... |
6be0094391094ea1f7f18c15a0fa840cbfad7b6b043e7588298d6b3de93f2f21 | MATLAB | 1,201 | 36 | function out = pointprop_gaussaperture(x,y,c1,c2,c3,x1a,y1a,dz1)
% analytical solution of a point source propagating through a gaussian aperture
% -> analytical solution for phase as a function position has the the same
% quadratic factor, but now also has a linear slope as well
offrad = sqrt(x1a.^2+y1a.^2);
o... |
728ab4a9910920eb8c739a2b848251df59dc7e2e68171f223423901bb0d24331 | MATLAB | 1,201 | 27 | function max_run_jobs = concurrency_size_in_colorcorrection_3D_cuda(cond)
loadParameters;
if ~isfield(params,'COLOR_CORRECTION_MAX_RUN_JOBS')
bead_downsample_imgsize_dbl = cond.downsample_imgsize_dbl * (cond.dim(3) - params.BEAD_ZSTART)/cond.dim(3);
main_mem_usage = params.MATLAB_PROC_CONTEXT... |
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