sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d3dbe9d6821233406f0f01c55a98ad4b0c7b9a2dd6467e18e80a223f80874103 | MATLAB | 733 | 27 | function [t] = normalized(v)
%% Normalize the input vector or matrix such that the rows sum up to 1.
%% authors: Stefano Diomedi
%% date: 22nd February 2024
%
%% Input:
% - v: Input vector or matrix to be normalized.
if size(v, 1) == 1
% If v is a row vector
k = length(v);
su = 0;
for i = ... |
2e96ae83893b825bf3a829374401a34de416c56b4dfa471c4843392f050faebb | MATLAB | 734 | 32 | % mglMetalCleanup.m
%
% usage: mglMetalCleanup()
% by: justin gardner
% date: 09/29/2021
% purpose: Helper function to clean-up directories for digital
%
function mglMetalCleanup
% get mgldir
mgldir = mglGetParam('mgllibDir');
% change directory
curdir = pwd;
cd(mgldir);
% get all recompiled fi... |
ae92ab61112cd5451bedb86b679bef1a0895aa9dfaa9b81c1966d5a0cce00f8e | MATLAB | 734 | 35 | function varargout = scl_slope(varargin)
% Format
% For getting the value
% dat = scl_slope(obj)
%
% For setting the value
% obj = scl_slope(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: privatescl_slope.m 8776 20... |
42dc322b75dd017c91d206fbee32a24e1d108848ebac103af45ee71998b47ef7 | MATLAB | 735 | 24 | function [S] = smallworldness(mat)
% This function calculates the small-worldness of a given connectivity
% matrix.
% Calculate C and L of original matrix
len_mat=1./mat; % conection-length matrix
d_mat= distance_wei(len_mat);
C=mean(clustering_coef_wu(weight_conversion(mat, 'normalize'))); % clusterin... |
97782e91ccd4d4dfff04479577e80799a01472314ac9609ed20e1932afd30555 | MATLAB | 735 | 31 | function [fim] = fbRun(fb,im)
% function [fim] = fbRun(fb,im)
%
% Run a filterbank on an image with reflected boundary conditions.
%
% See also fbCreate,padReflect.
%
% David R. Martin <dmartin@eecs.berkeley.edu>
% March 2003
% find the max filter size
maxsz = max(size(fb{1}));
for i = 1:numel(fb),
maxs... |
b358e8ba369749676e375ed80029ef00b15a157c286bada80981168f03481d80 | MATLAB | 735 | 36 | function varargout = scl_inter(varargin)
% Format
% For getting the value
% dat = scl_inter(obj)
%
% For setting the value
% obj = scl_inter(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: privatescl_inter.m 8776 20... |
f70a627d8c61c73f236fba04b6b17d980f29c471566b975917b485ca66317107 | MATLAB | 735 | 35 | function [video] = ml_cai_io_scopereadavi(filename)
%v1 = VideoReader(filename, 'VideoFormat', 'Grayscale', 'BitsPerPixel', 8);
%frames = zeros(v1.Height, v1.Width, 1);
% v = VideoReader(filename);
%
% i = 1;
% while hasFrame(v)
% frames(:,:,i) = uint8(readFrame(v));
% i = i + 1;
% end
% i = i - 1;
o = Vide... |
00064b4cb153e9b0c1c1f3bbfab39aa2a1e8a16d296abf2009ab3c3f466d25db | MATLAB | 736 | 23 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function T = calcium_compute_fraction_occupied(folder, useSmoothed)
tmp = load(fullfile(folder ,'calcium_occupancy_maps.mat'));
T = table2struct(tmp.OccupancyMaps);
for iRow = 1:length(T)
if useSmoothed
... |
29530c2f7885a7f3ade12a3fa66f3d31aca7c77b4f94efee4fe6aff954e291e4 | MATLAB | 736 | 20 | function flag=SONSave(fh, chan, sTime, bKeep)
% SONSAVE sets the write state for a channel from a specified time
%
% FLAG=SONSAVE(FH, CHAN, STIME, BKEEP)
% INPUTS: FH is the SON file handle
% CHAN is a channel number (0-SONMaxChans()-1) or -1 for all
% channels
% STIME the time for this write... |
33b28893d641f931becd982d7bf8e7cd1b6723a9537bb940640a6880aa660452 | MATLAB | 736 | 23 | function handles = SelectFly(handles,fly)
% change the selected fly to a specified one
% splintered from fixerrorsgui 6/23/12 JAB
if ismember(fly,handles.selected),
% set the current fly as unselected
fix_SetFlySelected(handles,fly,false);
i = find(handles.selected==fly,1);
handles.selected(i) = [];
else
% s... |
0f50d72bf4ca3db1e2777f02f81808b3fc9fdd9d460c38662e96d6e9621cdec2 | MATLAB | 738 | 19 | function [edges_s,edge_type,myosin2,P] = remove_myosin2(edges_s,edge_type,myosin2,P)
% randomly remove one myosin rod
aux = find(edge_type == 4);
if ~isempty(aux)
aux_e = randi(length(aux));
aux_r1 = find(myosin2 == edges_s(aux(aux_e),1));
if ~isempty(aux_r1)
aux_r2 = find(m... |
2362c91be0abc402641e5f1177ac013eb3ea24274d8f38e6edea2b64cd799b02 | MATLAB | 738 | 30 | function lkh = calcLH4(data, kk, idx, chr)
train = [chr(kk).distG, chr(kk).distP];
train = sortrows(train,1);
%Region for normalization
LG = 0-0.01;
UG = chr(kk).length;
LP = 0;
UP = max(chr(kk).distP)+1;
[distP_construct,distG_construct] = genomicAndPhysicalDist(data, [], [], []);
for ii = 1:max(idx) %loop through... |
4b4e719a37b5c6a0209d60bc5b7ea295028ad7367508763e6d8d903746c86ce1 | MATLAB | 738 | 28 | function f = zeromean(m,dim)
% function f = zeromean(m,dim)
%
% <m> is a matrix
% <dim> (optional) is the dimension of interest.
% if supplied, subtract off the mean of each case oriented along <dim>.
% if [] or not supplied, subtract off the global mean.
%
% subtract off the mean of <m>, either of individual case... |
6b4aa7560f22de1c39764e1de2dd9a92d9ee1bf8eb4bd79cbbc445af1c5217aa | MATLAB | 738 | 23 | function Protated = qRotatePoint( P, Qrotation )
% qRotatePoint: rotate a point according to rotation quaternion
% Protated = qRotatePoint( P, Qrotation )
% IN:
% P - point which is rotated
% Qrotation - quaternion describing the rotation (axis and angle)
%
% OUT:
% Protated - rotated point
%
%... |
256562ace20b73afbd4e2bd4b9968c69f939b34850fe6455c25d28847ccc07a0 | MATLAB | 739 | 26 | function F = isfield(tree,uid,parameter)
% XMLTREE/ISFIELD Is parameter a field of tree{uid} ?
% FORMAT F = isfield(tree,uid,parameter)
%
% tree - a tree
% uid - uid of the element
% parameter - a field of the root tree
% F - 1 if present, 0 otherwise
%________________________________________________... |
2635dbabfc0f6aee7504c5d9d4340e13cdb76eaea36b456637ea048489b4dd17 | MATLAB | 739 | 18 | function [informationRate, informationPerSpike] = ml_placefield_informationcontent(meanFiringRate, meanFiringRateMap, positionProbMap)
% Compute the information rate (bits per second)
% Find the non-zero entries of the position probability
[nzi, nzj] = find( positionProbMap > 0 );
informationRate = 0;
... |
941d627c049100bc9c11317156603eec18c70458df2fbbca7d6d1715167a195a | MATLAB | 739 | 26 | function filename_censored_data = make_filename_censored_data(handles)
ix=find(handles.mc.motions);
mc_method=char(handles.mc.methods{ix});
fd=num2str(handles.mc.FD_th,'%4.2f');
fd(fd=='.')='_';
min_frames=num2str(handles.mc.min_frames);
skip=num2str(handles.mc.skip);
tr=num2str(handles.mc.TR,'%4.2f');
tr(tr=='.')='_... |
ff30db35b07ea4858ffdf7da4d970a271b70c2998ff3ef31199166ded383e5d6 | MATLAB | 739 | 25 | % Calculate the critical value and p-value
function [HRT, HRTpvalue] = ml_stats_hermansrassonp(sample)
n = length(sample);
m = 1000;
rt = nan(1,m);
for i = 1:m
rsample = ml_stats_gen_uniform_samples(n, 0, 2*pi);
rt(i) = HermansRassonT(rsample); % from random samples
end
HRT = Her... |
2036eeca729af95ce0511a599c7d13a26d8c9c64bb50db4b58383e7e9c9fe5af | MATLAB | 740 | 28 | % mglSocketReadString.m
%
% usage: s = mglSocketReadString(socketInfo)
% by: justin gardner
% date: 01/26/23
% purpose: Reads a string from the socket
%
function s = mglSocketReadString(socketInfo)
% get scoket
if nargin < 1 || isempty(socketInfo) ... |
2442ebba55a76e92380af281a066803d076b689b7da07344d311116c55f7fed8 | MATLAB | 740 | 19 | function [clusterFiles] = ml_nlx_mclust_dir_clusters(folder)
% Returns a 'dir' result for MClust cluster files that have the standard
% names like TT4.clusters. This is used so that we can filter out odd names
% like TT4hull_maybe.clusters.
% Get all of the regular cluster files. Do not keep autosave.clusters or
... |
753e5ed8c0a6810d3bb3c87789934ae8c8af2339d6ff8f43491026b8436a5f28 | MATLAB | 740 | 23 | function rate=SONIdealRate(fh, chan, newrate)
% SONIDEALRATE gets or sets the ideal sampling rate on a channel
%
% RATE=SONIDEALRATE(FH, CHAN)
% returns the current rate on channel CHAN in file FH
%
% RATE=SONIDEALRATE(FH, CHAN, NEWRATE)
% returns the rate at the time of the call an sets a new rate if NEWRATE>0
% Cauti... |
1d96fd00dd4ad119cf70e82640e6a43cbdcef5a94b3ecfd39056d89830fe3b31 | MATLAB | 741 | 24 | function fh=SONOpenOldFile(filename, iMode)
% SONOPENOLDFILE opens an existing a SON file and returns a handle
% from SON32.DLL. Note that this is not a MATLAB handle.
% FH=SONOPENOLDFILE(filename, iMode)
% filename is a string
% iMode = 0 for Read/Write
% ... |
648be76746a02108a26db7fbfb62577858e4d242d89abf7db4a3bac2328f7596 | MATLAB | 741 | 35 | function varargout = offset(varargin)
% Format
% For getting the value
% dat = offset(obj)
%
% For setting the value
% obj = offset(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: offset.m 8776 2013-11-14 09:04:48Z ... |
9b97a45b8034f964333fa45d7557ccff55d99dcfb0720fe4b8a6e1c840c43a40 | MATLAB | 741 | 20 | function bemf2_graphics_vol_field(temp, th1, th2, levels, a, b)
% Volume field graphics: plot a field quantity temp in the observation
% plane using a planar contour plot. Revision 071318
%
% temp - quantity to plot
% th1, th2 - two threshold levels introduced manually
% levels - number of levels in the cont... |
5416e37784afae808aa037527307f5a5312aa26e10bc50cd35afd6a05eed3bdd | MATLAB | 742 | 32 | function [beta, intercept, R2, MSE] = my_linreg(X, y)
if length(X) ~= length(y)
error('X and y must have the same number of elements.');
end
X = [ones(length(X),1) X(:)];
beta = X \ y(:);
intercept = beta(1);
y_pred = X * beta;
RSS = sum((y - y_pred).^2... |
7c930d92f46e80985c20ad07f8cb0c3f0418c29e71fdcc27bfff22c40e6df423 | MATLAB | 742 | 34 | %
% Computer effective diameter.
%
% PARAMETERS
% $network
% $percentile (between 01 and 99)
%
% INPUT FILES
% dat/hopdistr.$network
%
% OUTPUT FILES
% dat/statistic.diameff$percentile.$network
%
network = getenv('network');
percentile_text = getenv('percentile');
percentile = str2double(percentile_text);
if ... |
97746315c5fa72bb090e99282b68e319d090770882674a69b0aea4da774670b6 | MATLAB | 742 | 23 | function newRect = CenterRectOnPoint(rect,x,y)
% newRect = CenterRectOnPoint(rect,x,y)
%
% CenterRectOnPoint offsets the rect to center it around an x and y position.
% The center of the rect is reported by RectCenter.
%
% See also PsychRects, RectCenter
% 9/13/99 Allen Ingling wrote it
% 10/6/99 dgp With permis... |
4920d0d7aca0ff9aee7420f80ef06d828c07616518acd251d2238b84da65e985 | MATLAB | 743 | 33 | function om_save_full(data,filename,format)
% OM_SAVE_FULL Save full Matrix
%
% Save full Matrix
%
% SYNTAX
% OM_SAVE_FULL(DATA,FILENAME,FORMAT)
%
% FORMAT : can be 'ascii' or 'binary' (default)
%
% Created by Alexandre Gramfort on 2007-11-27.
% Copyright (c) 2007 Alexandre Gramfort. All rights r... |
a40649db1a340a87e6941e4ad00ca6676fac0e92ba0db49271e80ad73e7c7093 | MATLAB | 744 | 44 | function varargout = myparse_nocheck(params,varargin)
nout = nargout;
% set defaults
ncopy = min(nout,floor(length(varargin)/2));
doreturnleftovers = ncopy < nout;
% parameter names
names = varargin(1:2:end);
varargout = varargin(2:2:2*ncopy);
% go through parameters
i = 1;
leftovers = {};
while true,
if i > le... |
ce61cefac1ca5447843d5fa9342feebe26325e9c27c972b61d12b41d73324e81 | MATLAB | 744 | 16 | clear; close all; clc;
% Get the metadata for a dataset from the HDF5 file
h5disp('data_motor_unit.h5','/')
% We can see that the dataframe is organized in two 'groups' (FDI and TA)
% and inside each group there are two 'datasets' (PRE and POST). Each
% 'member' within a dataset is the data of one participan... |
3c7d04fe7007e6987081e45da6b48e898c655cc1416bf75ed468a79ad5cb4ad6 | MATLAB | 745 | 23 | function state=SONExtMarkAlign(fh, n)
% SONEXTMARKALIGN gets and sets the alignment state for marker channels
% This is a feature of V7 of the SON filing system
% Using aligned markers improves cross-platform portability of SON files
% STATE=SONEXTMARKALIGN(FH,N)
% FH= SON file handle
% N = -2, Check ch... |
55431f41b4092eade26cdf563e37c95d1f9895b0fe9e7b2e98c1c27176799269 | MATLAB | 745 | 32 | function [sig,mixedsig]=demosig();
%
% function [sig,mixedsig]=demosig();
%
% Returns artificially generated test signals, sig, and mixed
% signals, mixedsig. Signals are row vectors of
% matrices. Input mixedsig to FastICA to see how it works.
% @(#)$Id: demosig.m 8776 2013-11-14 09:04:48Z roboos $
%create source s... |
7322eda5c1a1a0c4ed6cf7a2b254bc32fabb096825f47c43a40004b8f01ec6da | MATLAB | 745 | 26 | function [p,t,pix]=meshfix(p,t,ptol)
%MESHFIX Remove duplicated/unused nodes and fix element orientation.
% [P,T]=MESHFIX(P,T)
% Copyright (C) 2004-2012 Per-Olof Persson. (See DISTMESH/FIXMESH)
if nargin<3, ptol=1024*eps; end
if nargin>=2 & (isempty(p) | isempty(t)), pix=1:size(p,1); return; end
... |
26ef4bb3d339bc14e5303694233e3be1dacccb7a0459bc5dc27a8042b84a949e | MATLAB | 746 | 24 | function [slice] = ml_util_timeseries_split_into_slices( ts_ms, x, slice_separation_threshold_ms )
% Check that the inputs are fine
if slice_separation_threshold_ms <= 0
error('The slice separation threshold must be >= 0, but is (%d).', slice_separation_threshold_ms);
end
inds = ml_uti... |
1cff2a3a018ef1dfdbbbb7d0d7d6de62a18dadd6cad1dbefa289941e78dd497e | MATLAB | 747 | 32 | % mglHFlip.m
%
% $Id$
% usage: mglHFlip()
% by: justin gardner
% date: 09/06/06
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: flips coordinate frame horizontally, useful for when
% the display is viewed through a mirror
% e.g.:
%
%mg... |
42fc819d01120c93d8f356dfd91698c9bd166b90acf76399058985545af631fa | MATLAB | 747 | 44 | %
% Read metadata from a data file.
%
% RETURN VALUE
% A struct where field names are the keys and the values are
% strings. In key names, '-' is replaced with '_'.
%
% PARAMETERS
% network Network name
%
function ret = read_meta(network)
filename = sprintf('uni/meta.%s', network);
FILE = fopen(filename, 'r');
... |
43bffa0b78dcb85da76bb8fbf08747339d5f2ab242650df443fc024e30cd526a | MATLAB | 747 | 20 | function quoted = shellQuote(text)
% Quote text as one word for the POSIX shell that MATLAB's system() uses on unix
%
% function quoted = shellQuote(text)
%
% Purpose
% Private to +webupload. Inside single quotes the shell reads nothing specially, so only
% a ' in the text needs care: it is ... |
5b5cc96f444c80ba0e130714647116716dc295a61cee8f42ecc64efa26aed3f4 | MATLAB | 747 | 25 | % sankey demo2
% -----------------------
% @author : slandarer
% 公众号 : slandarer随笔
% 知乎 : slandarer
figure('Name','sankey demo2','Units','normalized','Position',[.05,.2,.5,.56])
links={'a1','A',1.2;'a2','A',1;'a1','B',.6;'a3','A',1; 'a3','C',0.5;
'b1','B',.4; 'b2','B',1;'b3','B',1; 'c1','C',1;
'c2',... |
7de67f01b3eac0b8db305f4e036a516126ddfb4670b65cb3b48349591594827e | MATLAB | 747 | 32 | function f_SaveF64File(pv_Data, pstr_FileName, ...
ps_FirstIndex, ps_LastIndex, ps_Append)
if nargin < 2
return;
end
s_FirstIndex = 1;
s_LastIndex = length(pv_Data);
s_Append = 0;
if nargin >= 3 && ~isempty(ps_FirstIndex)
s_FirstIndex = ps_FirstIndex;
end
if... |
51c25b635f033f841fb325f266b2f1f318c8487d052ace0b65d13688e0d6ea33 | MATLAB | 748 | 29 | function sTracks = storeTracks(tracks,sTracks,counter,del_ids)
if counter == 1
% create an empty array of tracks
sTracks = struct(...
'id', {}, ...
'data',{},...
'trackedFrames', 1);
else
ids = vertcat(tracks.id);
for i = 1:length(ids)
IDpos = ids(i);
sTrack... |
85483f93a61db5402bf10930ab52e62b9762d2efed9a3166512cc83d324f2417 | MATLAB | 748 | 28 | function newStack = preprocessImages(stack, pos, enchanceContrast)
% Upsample image for better detection of CR
newStack = imresize(stack,2);
% Gaussian Filter
newStack = imfilter(newStack, fspecial('gaussian',3,.5));
% Enhance Image Contrast
% (cannot be done to stack, must loop)
if encha... |
8e6c695d06d3545b5863a663c59d76621435ec3b2344fe73fd087bb2535fcdf1 | MATLAB | 748 | 35 | function varargout = offset(varargin)
% Format
% For getting the value
% dat = offset(obj)
%
% For setting the value
% obj = offset(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: privateoffset.m 8776 2013-11-14 09:... |
b58a746f02bfb27327ec28bbc23ee3ff41fcffbc0ca195c1df7d4725bf0836cb | MATLAB | 748 | 25 | function repforce = repel(P, cd, mu)
%find the self repel forces between each point to each other
nPoints = size(P,1);
force = zeros(size(P));
for i = 1:nPoints
for j = 1:nPoints
if j >= i
break;
elseif i-j == 1
%there is no repel forc... |
1417596a73876f41d3f6914c6e28eda038017acbd0d57d3ac1bbf681e7a9bbda | MATLAB | 749 | 29 | % initTempProbe.m
%
% Function to initalize National Instruments USB-TC01 device (thermocouple
% temperature probe)
%
% Input:
% settings - struct from twoPhotonSettings() containing all DAQ settings
%
% Output:
% tempDAQ - handle to temperature DAQ
% tcCh - handle to thermocouple analog acquisition channel
%
% ... |
20bcbf207bbfd045a631267113c6906e223a098a78c73da118632657528903e1 | MATLAB | 749 | 48 | %{
Arifact @ ~3183.5Hz
%}
%% load
cd Z:\1_Maxwell_Gagnon\ProjectData_Sriram\Granule_cell_recording\NR2_F_10_S1
load('testData.mat')
tv = amplifier_data(2,:);
samplerate = 30000;
%% BANDPASS FILTER
N = 3;
fc = [7 200];
[bb,aa] = butter(N, fc/samplerate, 'bandpass');
tv_filt = filtfilt(bb,aa,tv);
%% LOW PASS FILTE... |
90e4d7410ca49c3fc37d3c4554fa3567d6d96cfbfda311dc27e6d6b9044cfefc | MATLAB | 749 | 26 | function [medianFrame] = ml_cai_behavcam_median_frame_compute(video)
I1 = zeros(size(video.mov(1).cdata,1), size(video.mov(1).cdata,2));
I2 = zeros(size(video.mov(1).cdata,1), size(video.mov(1).cdata,2));
I3 = zeros(size(video.mov(1).cdata,1), size(video.mov(1).cdata,2));
for n = 1:length(video.mov)
... |
e31de4ffad34447f76b8d6b1129c08c7f94e9f2d07ef0c47a2e869167e23a71b | MATLAB | 749 | 25 | function [blobs, na, nb] = SegmentIndices2Blobs(indIm, boxes, neighbours)
% This function converts a segmentation index image to blobs
% Note that this is made by mexFelzenSegmentIndex
%
% indIm: index image in range 1:n, each int denotes segment label
% boxes: Bounding boxes of the segments
% neigh... |
ea285c5f9fab77a5e8a9f26f0fba01a9f79e9b8ffc6870fcfaeb63455c15fd5b | MATLAB | 749 | 33 | function [stats] = ml_cai_spatialfootprint_stats_compact(sfp)
%sfp = ml_core_remove_zero_padding(sfp);
% SFP must aleady be compact
X = sfp;
p = prctile(X(X ~= 0), 50);
% M1
BW = bwperim(X>0, 8);
P = sum(BW == 1, 'all');
A = sum(X>0, 'all');
M1 = 4 * pi * A / P.^2;
CC ... |
0b30a278c47425df8935ed786d1b44998c19a8b57c32b2c2e86f8e88a83bf0d1 | MATLAB | 751 | 24 | function makeprettyfigures()
% general graphics, this will apply to any figure you open
% (groot is the default figure object).
set(groot, ...
'DefaultFigureColor', 'w', ...
'DefaultAxesLineWidth', 0.5, ...
'DefaultAxesXColor', 'k', ...
'DefaultAxesYColor', 'k', ...
'DefaultAxesFontSize', 15, ...
'DefaultAxesFontName'... |
33e8567a658f897894f408cb0c6dbfb94c06abe4d83a8833bc63d2bc151604dd | MATLAB | 751 | 27 | function [HistSpl] = getSplines(method,lag,c_pt,s)
% calls functions from
%https://github.com/MehradSm/Modified-Spline-Regression
% ref:
%Sarmashghi, M., Jadhav, S. P., & Eden, U. (2021).
%Efficient spline regression for neural spiking data.
%Plos one, 16(10), e0258321.
switch method
case 'modcard'
if nu... |
8ab773d12ae937e0d9d345fe9938191609d05f05042b6b5140d316b5e830b6d7 | MATLAB | 751 | 17 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [M] = get_match_table_by_sessions(TableA, TableB)
% Get matching sessions between the two tables
matchingRows = ml_util_find_row_matches([TableA.animalName, TableA.sessionName], [TableB.animalName, TableB.sessionNam... |
a3f610d45d4c2db92c1399fa92e7c3230463f0a2803e8619dbe8027f567ac1a3 | MATLAB | 751 | 18 | function spring_force = spring(P, l0, nu)
%calculates the spring force forcing the centerline to be a preferred
%length
displacement = P(1:end-1,:) - P(2:end,:);
distance = sqrt(sum(displacement.^2,2));
direction = [displacement(:,1)./distance, displacement(:,2)./distance];
%caculate a vect... |
ccc150aaf6644d721fb046da188eff8dfb19109587e59f6e5af5f8290715451b | MATLAB | 751 | 35 | % VL_DEMO_SIFT_EDGE Demo: SIFT: edge treshold
randn('state',0) ;
rand('state',0) ;
I = zeros(100,500) ;
for i=[10 20 30 40 50 60 70 80 90]
d = round(i/3) ;
I(50-d:50+d,i*5) = 1 ;
end
I = 2*pi*8^2 * vl_imsmooth(I,8) ;
I = single(255 * I) ;
figure(1) ; clf ;
imagesc(I) ; colormap gray ;
axis equal ; axis off ; a... |
e7889549c28155ac4eda6a0bdad6f47c8f7b827e37a56d3a000cbf9c8038cebb | MATLAB | 751 | 18 | % VL_SAMPLINTHIST Sample integral histogram
% HISTS = VL_SAMPLINTHIST(INTHIST, BOXES) samples the integral
% histogram INTHIST to obtain the histograms of the specified
% BOXES.
%
% INTHIST is a MxNxK array, where M x N are ``spatial'' dimensions,
% and K is the number of histogram bins. INTHIST may be of cl... |
509665011c2e4ac6ab421d16971c82bad821a30b4f1e28a62b014e1c7642cc90 | MATLAB | 752 | 27 | %VL_DEMO_PLOTS_RANK Demonstates VL_ROC, VL_DET, VL_PR
randn('state',0) ;
numPos = 20 ;
numNeg = 100 ;
labels = [ones(1, numPos) -ones(1,numNeg)] ;
scores = randn(size(labels)) + labels ;
figure(1) ; clf ;
vl_roc(labels,scores) ;
vl_demo_print(1,'plots_rank_roc', 0.5) ;
figure(2) ; clf ;
subplot(2,2,1) ; vl_roc(labe... |
af38b5e1be7d3b7cda08d8cd5410a79c5b83d948c8d06b9404db04a2eb30792a | MATLAB | 752 | 25 | function [cinew,idx] = fcn_sort_communities(ci)
%FCN_SORT_COMMUNITIES reorder community labels by size
%
% [cinew,idx] = fcn_sort_communities(ci) takes a partition, ci, and
% relabels its communities so that the largest community is labeled 1,
% next largest labeled 2, next largest 3, and so on.
%
% Inputs:
%... |
02fbca3f646fe738db544ff982b36f684de27a28f6b2b3735f3b3e29f67be289 | MATLAB | 753 | 22 | function areaErrorbar(x,data,i)
%20151130 modified areaErrorBar
X = [x,fliplr(x)];
%colorOrder = [0,0,0;0,0.447,0.741;0.850,0.325,0.098;0.929,0.694,0.125;0.494,0.184,0.556;0.466,0.674,0.188;0.301,0.745,0.933;0.635,0.078,0.184];
%colorOrder = [0,0,1;0,0.5,0;1,0,0;0,0.75,0.75;0.75,0,0.75;0.,0.75,0;0.25,0.25,0.25];
cColor... |
3308e54528023539d1a8789d2dcdad916f1c17a9f7ff7af26b7eae79f6788ecd | MATLAB | 753 | 29 | function Uout = applyZernike(Uin,X,Y,k,abb)
% Uout = applyZernike(Uin,X,Y,k,abb)
%
% Applies the Zernike aberration given an input field, position and
% aberrations. The inputs are:
%
% - Uin - Input scalar field
% - X - X field positions
% - Y - Y field positions
% - k ... |
4a1312b514ea555da262688585bd1bd5446d3f86ba12121edd7a298733fc8a12 | MATLAB | 753 | 20 | function aug_names = feat_augment_names(names)
[logfeat, normfeat] = feat_augment_log_and_norm() ;
% update names to match their augmentation
simple_aug_names = cell(1,0) ;
diff_aug_names = cell(1,0) ;
for i=1:numel(names)
name = names{i} ;
if ismember(names{i},normfeat)
... |
6cbb4b7430d94cc92cc7fcd542a2689e7245f022e5c881ec3b1a53c7e3da62b6 | MATLAB | 753 | 21 | function compute_sfp_celllike( obj, session, trial )
% % Trained on session 1, trial 1 of CMG169_CA1
% tmp = load('trainedModel.mat', 'trainedModel');
% trainedModel = tmp.trainedModel;
% clear tmp
if isempty(obj.SpatialFootprintTrainedModel)
warning('Can not compute if spatial footprints ... |
1928a272462e087a54252102743da427917d5b62ec7bdd1e520a1b191f07a301 | MATLAB | 754 | 16 | % Author: Zachary Chiang, Buenrostro Lab, Harvard University
% Crops an image in 3D using a rectangle (x_start, y_start, z_start, x_len,
% y_len. z_len) regardless of the number of dimensions
function[cropped_img] = imcrop_xyz(img, rect_3d)
if ndims(img) == 3
cropped_img = img(rect_3d(2):rect_3d(2)+rect_3... |
75ac956ce2bf8960cd3ccb47026d06d57a06c7dfa74100f49e7baac5b9c1bf6b | MATLAB | 754 | 19 | function [INsummary, summary] = TRAP_Remove_INs(summary)
%This code removes the interneurons (INs) from the summary struct. INs are
%identified using Plexon Offline Sorter, comparing their average waveform
%to previous characterizations of PV and ACh striatal interneurons (Barnes et
%al., 2005).
%Created by Mi... |
8bf286a3305571c1ab1ee531701f42abdda8a72004105a2a8a11c1083017e6c1 | MATLAB | 754 | 21 | function [params, beta] = beta_pow3(params, state, denf)
% Local spectral shift function for denoise_tanh denoising function.
% [s_new, params] = beta_pow3(params, state, s)
% params Function specific modifiable parameters
% state DSS algorithm state
% denf Tanh denoising function
% beta Deno... |
8cbe636622a1e020d5ad2bfb20af131bf6ba91a4483bafbba64422812b006e6e | MATLAB | 754 | 21 | function [comment]=SONGetChanComment(fh, chan)
% SONGETCHANCOMMENT returns the comment string for the specified channel
%
% COMMENT=SONGETCHANCOMMENT(FH, CHAN)
% FH SON file handle
% CHAN Channel number (0 to SONMAXCHANS-1)
% Returns the channel comment as a string.... |
8e5aa258fa0a1ace6fc57d6d5418e68d4fe20e5f93208b518e272362adb4b326 | MATLAB | 754 | 34 | function [simulation_voxels_axDKI_table] = simulation_load_paper_synth_datasets()
MA(1,1)=1.557; % Dpara
MA(2,1)=1.048; % Dperp
MA(3,1)=0.396; % Wpara
MA(4,1)=0.708; % Wperp
MA(5,1)=0.330; % Wmean
LA(1,1)=0.457;
LA(2,1)=0.408;
LA(3,1)=2.901;
LA(4,1)=2.702;
LA(5,1)=2... |
c25d0a4989f95f26e742f68a078b478efaca2908f4539cf13b6f85b10cfb9cf9 | MATLAB | 754 | 34 | function [LL, sse] = indepGaussEval(X, params)
%
% [LL, sse] = indepGaussEval(X, params)
%
% Evaluate log likelihood and sum-of-squared prediction error given
% an independent Gaussian model
%
% xDim: data dimensionality
% N: number of data points
%
% INPUT:
%
% X - data matrix (xDim x N)
% params - parame... |
26508e14889501fbba1de546a0773dbe39bf234b9bfa79725fa9635514d03961 | MATLAB | 755 | 20 | function flag=SONSave(fh, chan, sTime, bKeep)
% SONSAVE sets the write state for a channel from a specified time
%
% FLAG=SONSAVE(FH, CHAN, STIME, BKEEP)
% INPUTS: FH is the SON file handle
% CHAN is a channel number (0-SONMaxChans()-1) or -1 for all
% channels
% STIME the time for thi... |
2d47cce492fa717b2a7e6c1b208085c8c50742148e9d6293aec4a7d6a6d34457 | MATLAB | 755 | 31 | % lowPassFiler.m
%
% LOWPASSFILTER Filters the data using a lowpass butterworth filter of
% specified cut out
%
% INPUTS:
% data - trace to be filtered
% lowPassCutOff - value (Hz) that will be the top limit of the filter
% sampleRate - rate data is sampled at to allow correct conversion in to
% Hz.
%
%... |
6181b07c15acb50cb11da2c3d350dca6cae9ba8a7e28612799f6125752ceb9a1 | MATLAB | 755 | 20 | function flag=SONSaveRange(fh, chan, startTime, endTime)
% SONSAVERANGE sets the write state to save for a channel in the given time range
%
% FLAG=SONSAVERANGE(FH, CHAN, STARTTIME, ENDTIME)
% INPUTS: FH is the SON file handle
% CHAN is a channel number (0-SONMaxChans()-1) or -1 for all
% channels... |
a12a4fd46b3cfcf43112f205aeda60bd10488c79fd3213a00a0b8a462ee42154 | MATLAB | 755 | 26 | function CC = largeBWConnComp(x,minLength,vals,minVal)
%returns a structure containing only 1d connceted components above a given
%size (output structure is identical to bwconncomp)
CC = bwconncomp(x);
lengths = zeros(CC.NumObjects,1);
for i=1:CC.NumObjects
lengths(i) = length(CC.PixelIdxList{i... |
bdbd99d9a63ad9a00726ca801e20caf62248e0420e658ca0d10dbd66c04115bd | MATLAB | 755 | 22 | function [y,varname]=xml2struct(filename_or_xml_string)
%XML2STRUCT reads non-MbML compliant xmlfile into matlab structure
%
% Syntax: [y,varname]=xml2struct(filename_or_xml_string)
%
% Description:
% 1. Convert any non-MbML xml into MbML compliant string
% 2. Stores consecutive structures in the a dimensional str... |
d6d0351538804a409c252b61e373f9d33cb65faf9a1d0b8275370080b37f7c98 | MATLAB | 755 | 24 | % Get header of the trigger event
% [ Yokogawa MEG Reader toolbox for MATLAB ]
%
% brief:
% This function retrieves information about trigger event in the specified file.
%
% usage:
% event = getYkgwHdrEvent(filepath)
%
% arguments:
% filepath : file path
%
% return values:
% event : structure array of... |
12b911357eb9a4a1e2f89cda1a44b129962830e5fb69c5dc30e6bbdd260519de | MATLAB | 756 | 24 | function [BW] = segmentImage5(X, erode, sens)
%segmentImage Segment image using auto-generated code from imageSegmenter app
% [BW,MASKEDIMAGE] = segmentImage(X) segments image X using auto-generated
% code from the imageSegmenter app. The final segmentation is returned in
% BW, and a masked image is returned in MASK... |
1b23044edc512d471281d6ecc16756314a1d4b5204644aa1ff165b651895617f | MATLAB | 756 | 36 | %savesmall
%save small structures
clear all; %close all;
base_folder = 'T:bnehud\data';
%Session = 'pom36';
%Session = 'pom31';
Session = 'vpm28';
Lsessionfolder = [base_folder '\LargeStructs\' Session];
Files = getFiles(Lsessionfolder);
Nmovies = length(Files);
mms=1:Nmovies; %matlab bug in cell ac... |
99dae4c035f7d8d57926fa97a5dbbcd18f526b766b5f8afe6eb9aad2d661d129 | MATLAB | 756 | 37 | function paramFile = getRecipeFileName(supressWarning)
% Look for a the acquisition system's parameter file in the current directory and return its name
%
% function mosaicFile = getRecipeFileName(supressWarning)
%
% Purpose
% Return the recipe file name.
%
%
% Inputs
% supressWarning - optionally supress warning abou... |
ea3a18e5c3ea7aab5ef8f4968f397d44e6165bd22cefe9722bfec5f3023b2e5f | MATLAB | 757 | 20 | function wrapped = inBinSh(cmd)
% Command line that runs cmd under /bin/sh whatever shell MATLAB's system() uses
%
% function wrapped = inBinSh(cmd)
%
% Purpose
% Private to +webupload. On unix MATLAB's system() hands the line to $MATLAB_SHELL or
% $SHELL, which can be csh or tcsh, where syn... |
fd5b219c4cff7e858d3a1a4b81b7db1c99b48f373fd77836970f3f3941b8115f | MATLAB | 757 | 17 | % Author: Zachary Chiang, Buenrostro Lab, Harvard University
% Crops an image in 2D using a rectangle (x_start, y_start, x_len, y_len)
% regardless of the number of dimensions
function[cropped_img] = imcrop_xy(img, rect_2d)
if ndims(img) == 3
cropped_img = img(rect_2d(2):rect_2d(2)+rect_2d(4)-1, rect_2d(... |
f6a29869b1eb9e5b195ef85a0629b385e7bf252266706c77ae5e021023bfb357 | MATLAB | 758 | 27 | function Q = qGetRotQuaternion( teta, rotationVector )
% qCreateRotQuaternion: outputs a quaternion which is used to perform
% rotation
% Q = qGetRotQuaternion( teta, rotationVector )
% IN:
% teta - rotation angle
% rotationVector - vector around which the rotation will be performed
%
% OUT:
% Q ... |
2b81ab786db84d35a9de8339d1968e7e5dd969c312058eaff5d05f3d9fb8e191 | MATLAB | 759 | 20 | function [UniqueIDConversion, MatchTable] = AssignUniqueID(SaveDir)
disp('Loading match table to assign Unique IDs...')
tmpfile = dir(fullfile(SaveDir,'UnitMatch.mat'));
load(fullfile(tmpfile.folder,tmpfile.name))
if exist('TmpFile', 'var')
UniqueIDConversion = TmpFile.UniqueIDConversion;
MatchTable = TmpFile.M... |
491ef11135f285ac2706db8ab85f4ffb58784e43b80e24b1871fe98b9a5cb9b5 | MATLAB | 760 | 22 | function [map, C] = vl_flatmap(map)
% VL_FLATMAP Flatten a tree, assigning the label of the root to each node
% [LABELS CLUSTERS] = VL_FLATMAP(MAP) labels each tree of the forest contained
% in MAP. LABELS contains the linear index of the root node in MAP, CLUSTERS
% instead contains a label between 1 and the num... |
5c483d7f69cf5746cbdbfc0fa96090a04d4017a4ff2fc6d6bee9e72a580fa384 | MATLAB | 760 | 38 | % plotFreqSpec.m
%
% Function that takes in time series and its sampling rate and plots the
% one-sided frequency spectrum
%
% INPUTS:
% in - time series to get frequency spectrum of
% sampRate - sampling rate of time series
%
% OUTPUTS:
% none, but generates frequency spectrum plot
%
% CREATED: 8/27/19 - HHY
% ... |
5fb827abb7e3f9527df24837a6720f68acf5761b152f655157222044e9cbecaa | MATLAB | 760 | 36 | function om_write_cond(condfile,c,names)
% OM_WRITE_COND
% [] = OM_WRITE_COND(CONDFILE,C)
%
% Write conductivity file for OpenMEEG
%
% Authors: Alexandre Gramfort alexandre.gramfort@inria.fr
ndomains = length(c);
if nargin < 3
names = {};
for k=1:ndomains
names{k} = ['domain', num2str(k)];... |
0666853169223ca7896507178416554f635a915e325801c0a2d9f2bef8b99e07 | MATLAB | 762 | 34 | function [S1,f] = runWelch(delta_mat_T,nfft,noverlap,FS,wintype)
%runWelch.m 6/6/22
% note delta_mat assumes time down *rows*, windows in columns
if ~exist('wintype','var')
wintype = 'hamm';
end
switch wintype
case 'hamm'
winarg = nfft;
case 'rect'
winarg = ones(nfft,1);
end
data1 = delta... |
2acdc2c308e77183e97c722600fe9be233efd01a751b8982e223aa70b9be9b7a | MATLAB | 762 | 17 | function [stimWidthPx, stimHeightPx] = convertDVAToPixels(stimWidthDVA, stimHeightDVA, screenWidthPx, screenWidthcm, distanceFromScreen)
% Convert screen dimensions from cm to mm
screenWidthmm = screenWidthcm * 10;
% Calculate the pixel density (pixels per mm)
pxPerMmX = screenWidthPx / screenWidthmm;... |
66e4e1c21d129ae183e4212bb34baa96d91f533ddf4f709011fe409e8ad996db | MATLAB | 762 | 23 | function rate=SONIdealRate(fh, chan, newrate)
% SONIDEALRATE gets or sets the ideal sampling rate on a channel
%
% RATE=SONIDEALRATE(FH, CHAN)
% returns the current rate on channel CHAN in file FH
%
% RATE=SONIDEALRATE(FH, CHAN, NEWRATE)
% returns the rate at the time of the call an sets a new rate if NEWRATE>0
... |
3551c4383c3090031b890ad486289acee1a64e786026c53dcc4a0eef29845911 | MATLAB | 763 | 17 | function success = video_transcode(input_video_file)
output_video_file = [input_video_file(1:end-4), '.mkv'];
if strcmp(computer, 'PCWIN64')
%windows
%ffmpeg -r 30 -i TestCameraFrames\Frame_%06d.tif -c:v hevc_nvenc -rc:v vbr_hq -preset:v slow CameraFrames.mp4
system([fileparts(mfilename(... |
e8a6128c1c686b4642a44b7ab5f165b200f56e04fca7b18bc41153f72f9873e1 | MATLAB | 763 | 25 | % basic_example.m This script shows a bare-bones example of creating and
% plotting ternary data
% (1) Add paths
% add_ternary_paths
FIG = figure();
% (2) Create Basic Ternary Axes (Sides Ranging from 0-1)
handle_base = ternary_axes;
% (3) Get a set of A,B,C Test points, assuming 20 points along ea... |
059e71d9afb4bb9e90b5240890b1696005b3574fb2d0bf2476b825a0e8912299 | MATLAB | 764 | 24 | % plotFreeWalkReviewerResponseFig.m
%
% Quick script to plot reviewer response figure for free walking bouts
% Distribution of change in forward velocity for turning bouts
fullFilePath = '/Users/hyang/Dropbox (HMS)/FreeWalkLegAnalysis-Helen/AnalyzedData/condBouts_allDFwd_240526/angVel50-150_iFwdVel10-15_allDFwdVel.mat... |
1129620bd870683526f83fce6ae7058003cda0d8ec1a71016b51b1a3b7378099 | MATLAB | 764 | 24 | function fh=SONOpenOldFile(filename, iMode)
% SONOPENOLDFILE opens an existing a SON file and returns a handle
% from SON32.DLL. Note that this is not a MATLAB handle.
% FH=SONOPENOLDFILE(filename, iMode)
% filename is a string
% iMode = 0 for Read/Write
% ... |
3cbcd18e7f44472393f9ff954065dc60eadb8a0127c88c083ecfe4fe22ccf277 | MATLAB | 764 | 25 | function [entropyXY] = ml_it_entropy_joint(x,y, binMethod)
if length(x) ~= length(y)
error('x and y should be the same length.');
end
if strcmpi(binMethod, 'uniformly_spaced')
[edgesX, edgesY] = ml_it_edges_xy_uniformly_spaced(x,y);
elseif strcmpi(binMethod, 'uniform_density')
... |
5c092dadd89dcaf17c17ee81d0f3646ac067a0bbcfb355887dbce9897acc6336 | MATLAB | 764 | 24 | % this script create a 3-D scatter plot showing different pattern of the
% dynamics, including ON-ON, OFF-ON, OFF-OFF and ON-OFF
% 3 dimensions are: DeltaE (x), DeltaI (y), and Isens(z)
rootFolder = "figure_Iattn_0.02_2d/";
% ON-ON
data = readFilename(rootFolder+"asAllCriteria/*_*_*_*.png",'%f_%f_%f_%f');
data( all(~da... |
6e8a766e4176f9c00b512b17976a535fa9029d61b99526bd853194f66881a119 | MATLAB | 764 | 33 | function [textons] = unitex(fb,k)
% function [textons] = unitex(fb,k)
%
% Compute universal textons from the training images.
iids = imgList('train');
n = 100000;
nper = round(n/numel(iids));
n = nper * numel(iids);
d = numel(fb);
data = zeros(d,n);
c = 0;
for i = 1:numel(iids),
iid = iids(i);
... |
816b36a91c798b4214ba57f07954579c52586c531acb65f34037524659e7eb1c | MATLAB | 764 | 29 | function B = randomize_symmetric_matrix(A)
% RANDOMIZE_SYMMETRIC_MATRIX shuffles the upper triangular part of a
% symmetric matrix and returns a new symmetric matrix with the shuffled
% values.
%
% Input:
% - A: a symmetric matrix
%
% Output:
% - B: a new symmetric matrix with the upper triangular part of A
% ran... |
c7b9076502075129d78c5bd689843a6806dcb07bed6373fe3598f1afaadb376b | MATLAB | 764 | 28 | function [y]=VMFMeanDirDensity(x, k, p)
% This is the tangent direction density of VMF distribution. See the
% SphereDistributionsRand.pdf file for detail description and formulas.
%
% Usage:
% [y]=VMFMeanDirDensity(x, k, p);
%
% Inputs:
% x: The tangent direction value. should be in [-1 1].
%
% k: The kappa par... |
d751ef8359ade88664e495854d0586b086d1ba79d1e5fd4a8a300ff69859d5bb | MATLAB | 764 | 20 | function [edges_s,edge_type,myosin,P] = remove_small_myosin(r_s,edges_s,edge_type,myosin,P)
% check the length of the myosin linkers
aux = find(edge_type == 3);
d = r_s(edges_s(aux,1),:) - r_s(edges_s(aux,2),:);
d = sqrt(dot(d,d,2));
aux_r = find(d < P.min_r);
% remove those myosin linkers that ... |
c965dd86622575395853ec1bcd29cefed8087e08ad546ae494ce20611a973230 | MATLAB | 765 | 21 | function job_ID = get_job_ID(folder_name, script_name)
% get the SLURM job ID so we can update our log
try
% update the logs on cluster
log_name = [folder_name,filesep,'status.csv'];
[~, last_log_line] = system(['tail -n 1 ', log_name]);
if isstrprop(last_log_line(end), 'cntrl'), la... |
c100d8aeaaa559530f802f1d08d8bc68c48c274a7a1452f30b290724ee012528 | MATLAB | 766 | 35 | function Play(handles,hObject)
% play through a sequence
% splintered from fixerrorsgui 6/23/12 JAB
handles.isplaying = true;
set(handles.playstopbutton,'string','Stop','backgroundcolor',[.5,0,0]);
guidata(hObject,handles);
f0 = max(1,handles.seq.frames(1)-10);
f1 = min(handles.nframes,handles.seq.frames(end)+10);
fo... |
1b40c22abb18ca9a46b44be93fcde9fb37df4e3b464f19e9abd29696da29b210 | MATLAB | 767 | 42 |
%
% Minimal and maximal numbers, cutting the extreme points.
%
function [min_w, max_w] = map_minmax(ww)
% cut ALPHA points from each side
enable_cut = 1;
% use the L1 deviation instead of the standard deviation
enable_l1 = 0;
% amount of points to cut
alpha = .06;
% number of st... |
db34389a9cf85dd10595d70e563d230c476adcaf0b4cd426fce4b718eb1220d6 | MATLAB | 767 | 33 | function C = ROY_BIG_BL(N)
% ROY-BIG-BL, extracted from Washington-University/workbench.
roy_big_bl = [
0 1 1
0 1 0
0 0.784313725490196 0
0.294117647058824 0.490196078431373 0
0.490196078431373 0 0.627450980392157
0.294117647058824 0 0.490196078431373
0 0 0.666666666666667
0 0 0.313725490196078... |
28e77c85378b659f4111eb5ceb51b074b14f1eb04e3a3a256d646ba5a6f253c8 | MATLAB | 768 | 23 | function state=SONExtMarkAlign(fh, n)
% SONEXTMARKALIGN gets and sets the alignment state for marker channels
% This is a feature of V7 of the SON filing system
% Using aligned markers improves cross-platform portability of SON files
% STATE=SONEXTMARKALIGN(FH,N)
% FH= SON file handle
% N = -2, Ch... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.