sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0f597fd445fba5762cdf528f6139b066d0ec0815f5f240eae2209a6484d1072a | MATLAB | 538 | 15 | function [lp,dlp] = priorSameMulti(x)
% Dummy hyperparameter prior distribution to have a group of hyperparameter
% share the same value.
% The function is not intended to be evaluated but exists merely to make
% the user aware of the possibility to use it. The function is equivalent
% to priorEqualMulti.
%
% ... |
77d09db4f71f672bc837e0953611db733d8a57da404823bebd47b1b2881bf235 | MATLAB | 538 | 14 | function [lp,dlp] = priorDeltaMulti(x)
% Dummy hyperparameter prior distribution to fix the value of a hyperparameter.
% The function is not intended to be evaluated but exists merely to make
% the user aware of the possibility to use it. The function is equivalent
% to priorClampedMulti.
%
% For more help on d... |
dbe7ed50ccccbdb14acc9a28839cb15dc85f73b812da1f738a45f030a12e52af | MATLAB | 538 | 27 | function vrot = rodriguesRot(v, k, theta, angle_type)
% rotate a vector v in R3 by theta around the axis of rotation defined by
% unit vector k in R3, in degrees or radians
if nargin < 4
angle_type = 'degrees';
end
if strcmp(angle_type, 'degrees')
cos_theta = cosd(theta);
sin_theta = sind(theta);
else
... |
f5e3e3c256a5838faebc5923341f9e4acb8693de3ce321b7113e905cbc703b91 | MATLAB | 538 | 15 | function [lp,dlp] = priorEqualMulti(x)
% Dummy hyperparameter prior distribution to have a group of hyperparameter
% share the same value.
% The function is not intended to be evaluated but exists merely to make
% the user aware of the possibility to use it. The function is equivalent
% to priorSameMulti.
%
% ... |
fd2300ab9c728920a57e7b283d2018f4fdf4bf01eeb2553ce15858253da66514 | MATLAB | 538 | 14 | function [lp,dlp] = priorClampedMulti(x)
% Dummy hyperparameter prior distribution to fix the value of a hyperparameter.
% The function is not intended to be evaluated but exists merely to make
% the user aware of the possibility to use it. The function is equivalent
% to priorDeltaMulti.
%
% For more help on d... |
09b17f081e47eb3c691f4566162f126edf4b149ec291b12bbd113589a96e1bdd | MATLAB | 539 | 13 | %{
experiment.TreadmillSpecs (lookup) # methods for extraction from raw data for either AOD or Galvo data
-> experiment.Rig
treadmill_start_date : date # first day in use on this rig
---
diameter : float # treadmill diameter where mouse sits in cm
counts_per_revo... |
03a1c85b0a7563e7fe3f3eef59839a630384e6b98c786b63232712277ea1e88a | MATLAB | 540 | 26 | function [data] = tapas_sem_multiv_data(data, model, pars)
%% Get the date from the hgf.
%
% Input
% hgf -- Array of complete hgf models.
% pars -- Parameters structure
% Output
% data -- Structure with the data
% aponteeduardo@gmail.com
% copyright (C) 2016
%
data = data;
ns ... |
61632750d02a5a1d6488e44970f3b794131fbdadf9b92dd00cc51629d07856bd | MATLAB | 540 | 16 | function save_struct_by_level(S, levels, out_dir, suffix)
% SAVE_STRUCT_BY_LEVEL Save tables from a struct by level to CSV files.
%
% S : struct with fields for each level (e.g., .global, .rsn_pairs)
% levels : cellstr of level names to consider
% out_dir: output directory
% suffix : char/string appended to filen... |
ae9ab47503172415aca01bc87e1a48309d6b0a5784192083eec344306c3c6d2c | MATLAB | 540 | 25 | load('fort.101')
fort(:,1)=fort(:,1)/1000-2;
a1=find(fort(:,2)<=200);
x_ec=fort(a1,:);
scatter(x_ec(:,1),x_ec(:,2),2)
hold on
a2=find(fort(:,2)>200 & fort(:,2)<=700);
x_gc=fort(a2,:);
scatter(x_gc(:,1),x_gc(:,2),2)
a3=find(fort(:,2)>700 & fort(:,2)<=800);
x_hil=fort(a3,:);
scatter(x_hil(:,1),x_hil(:,2),2)
a4=find(fo... |
e896adde2a48d6f360e0c3004db12a5b8d1f6f1234d128766a9fa27325e01462 | MATLAB | 540 | 14 | function whichRuns = nsd_et_lookup
% ----------------------------------------------------------------------- %
% Look-up: Which runs should be analyzed for each of the 8 NSD subjects
% ----------------------------------------------------------------------- %
whichRuns{1} = [21:44];
whichRuns{2} = [21:44];
whichRuns{4}... |
5a0fdfda86b6e74398a670403a67389c7440a1d87644c982bafb1016f9f688bd | MATLAB | 541 | 24 | %28Mar14 Para encontrar el numero de rutas diferentes en un experimento.
%times_secb tiene que ser un arreglo
[ d_sec,times_sec ] = d_assemblies( Pks_Frame,sec_Pk_edos );
d_sec_time=cat(2,d_sec,times_secb);
d_st_1=sortrows(d_sec_time);
N=size(d_st_1,2); %Número de rutas
j=1;
for i=1:(N-1)
SRRa=d_st_1(:,i);
SR... |
d702e7998722fdf673a807d75add1008bed473953e8e71f80b11fd95697b68ce | MATLAB | 541 | 14 | %{
# current setup parameters for each rig
-> experiment.Rig
---
monitor_distance : float # (cm) eye-to-monitor distance
monitor_size=19 : float # (inches) size diagonal dimension
monitor_aspect=1.25 : float # physica... |
288b19df218ed9f0c5cea7ec8526660bc3031ec09dac7bc13c233b1f154925e7 | MATLAB | 542 | 20 | function tapas_BLT_logEvent(eventName, params)
% tapas_BLT_logEvent logs timing of the event specified in eventName
%
% Inputs:
% store: data storage file
% eventName: string with event name
%
% Outputs:
% store: data storage file
%
% About:
% Coded by F.Petzschner 19. April 2017
% Last change: F.Petzschner 19. A... |
046783071984c8235fb8aca59ef60c864c92f220198f4f221228e432e22af09b | MATLAB | 543 | 34 | function Residualscombined = concatresiduals(Residuals)
Residualscombined = cell(1, length(Residuals));
for sub = 1:length(Residuals)
datatoconcat = [];
tempresidualsepoch = [];
tempresidualsepoche = cell(1, 2);
for epoch= 1:2
tempresiduals = [];
if epoch == 1
e = 1:4;... |
a2eb21b8880b186e0976735780db1dd5337c9027e3a4253b8e1b322e56ed5df6 | MATLAB | 543 | 29 | function RHS = constantSourceTerm(phi)
% RHS vector for an explicit source term
% k is a cell variable
%
% SYNOPSIS:
% RHS = constantSourceTerm(k)
%
% PARAMETERS:
% phi: Cell Variable
%
% RETURNS:
% RHS: vector
%
% EXAMPLE:
%
% SEE ALSO:
%
% Copyright (c) 2012-2016 Ali Akbar Eftekhari
% See the license file
d =... |
a4a0b38765b2eef6415dba9e7dd805dfa573d6916b964801bf7c13e01569a6d5 | MATLAB | 543 | 21 | %Creado por LC
%Encuentra el porcentaje de celulas compartidas entre los diferentes
%estados.
function [Shared_Cells]=SharedCells(Cells_edos_active)
S=size(Cells_edos_active,2);
for ss=1:S
for zz=(ss+1):S
Sa=Cells_edos_active(:,ss);
Sb=Cells_edos_active(:,zz);
Sc=size(find(Sa==ss),1); %... |
e550a0d3667906b305f718974303c31b8de8cf6aeec4799551fd7635968ced0f | MATLAB | 543 | 15 | folder_name = uigetdir('C:\Projects\Valencia\results\ctr\ctr_subset_results','Select folder to save reference contours in');
if (~folder_name); return; end;
cd (folder_name);
% workspace MUST contain the NET variable for this to work
contours=NET.weight;
[~,numContours]=size(contours);
for i=1:numContours
outputFi... |
1e5c1bdea92c7bec7e44665b61ef2973766c83c5170d5c6103e6d55717329f3c | MATLAB | 544 | 17 | function r = is_stateful(f,varargin)
% check whether a filter function is stateful (for some arguments)
% stateful filter functions are characterized by a second output
nout = nargout(f);
if nout >= 0
% usually, nargout tells us this
r = nout > 1;
else
% but in some cases (e.g., when the function is wrappe... |
46c865ccbd3056d0b4a74a5e0b4addaf04bbbb82a55ee1524f5dd597e443ad60 | MATLAB | 544 | 14 | function fear_separate_reactInfo(basename)
% basename='~/data/Fear/triple/achel180320/achel180320';
load([basename '.basicMetaData.mat'])
fprintf(' %s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
load([basicMetaData.AnalysesName '-icaReac.mat'])
icaReacInfo=rmfield(icaReac,'strength')... |
9db787140261a4493be01d9d14d3c2eb1875b60019ca13714a6867a8e55e8688 | MATLAB | 544 | 29 | function f = fillmatrix(v,msize,dim)
% function f = fillmatrix(v,msize,dim)
%
% <v> is a vector
% <msize> is a matrix size
% <dim> is the dimension along which <v> is oriented
%
% return a matrix of size <msize> filled with <v>.
%
% example:
% isequal(fillmatrix([1 2 3],[3 2],1),[1 1; 2 2; 3 3])
% calc
len = length(m... |
153359e54999b71d95c88721ed48b3e8a0d5d8c87d35dabe242e23fc9f3d4c09 | MATLAB | 545 | 13 | function synchronized = fastPETH(spiketimes,events,interval)
try
if length(spiketimes)*length(events)<10000,
synchronized =mainFastPETH(spiketimes,events,interval,1,length(spiketimes),length(events));
elseif log10(length(spiketimes)*length(events))<10 ,
synchronized = mainFastPETH(spiketimes,ev... |
176bd34ecfa08a0467f7e29d9a1e4a81e976782d247361124962aa8cb01fe195 | MATLAB | 545 | 18 |
function metrics = evaluate_metrics(pred, true_labels)
TP = sum(pred==1 & true_labels==1);
FP = sum(pred==1 & true_labels==0);
TN = sum(pred==0 & true_labels==0);
FN = sum(pred==0 & true_labels==1);
precision = TP/(TP+FP+eps);
recall = TP/(TP+FN+eps);
f1 = 2*precision*recall/(precision+recall+eps);
ba = 0.5*(recall ... |
2792eeb0f46619ce28f631be7e0a03b25c98b374ab429f4954f704a431dbc996 | MATLAB | 545 | 26 | function scut = calc_scut(data)
% calculate threshold of similarity values from shuffled data
num_shuff = 20;
p = 0.98;
dims = size(data);
% calculate similarity matrix
warning('off')
S = zeros(dims(2),dims(2),num_shuff,'single');
for n = 1:num_shuff
data_shuff = shuffle(data,'time');
S(:,:,n) = 1-pdist2(data... |
5c7d9b458a37d9f6995486bf66419add436be9759b9f013162b8c733259593e3 | MATLAB | 545 | 24 | function bb = get_bb(imgname)
% world-bb -- get bounding box in world (mm) coordinates
V = spm_vol(imgname);
d = V.dim(1:3);
% corners in voxel-space
c = [ 1 1 1 1
1 1 d(3) 1
1 d(2) 1 1
1 d(2) d(3) 1
d(1) 1 1 1
d(1) 1 d(3) 1
d(1) d(2) 1 1
d(1) d(2) d(3)... |
523430f1cf657037ad413b23d18df48eb6297f490df8e55b23e02a4a2ef3875c | MATLAB | 546 | 16 | function S=dataframe2struct(D);
% function D=struct2dataframe(S);
% Converts a structure-array into a dataframe structure.
% The pre-requisite is that all fields in the structure a 1xK matrices or
% cell arrays, so that they can be vertically concatenated
fields = fieldnames(D);
numStruct = length(D.(fields{s}));
for ... |
13bbbf431d1ea10b9973740d5063936a79ff4d80bec0403556d0757a749485b3 | MATLAB | 547 | 19 | function [imgdata] = meta_read_image(name,mask)
% [imgdata] = meta_read_image(name,mask)
%
% gets image data in a v x 1 voxel list (for fast processing)
% compatible with Meta_Activation_FWE subfunctions
%
% This is the inverse of meta_reconstruct_mask
% image (name) and mask (mask) must have same dimensions and origi... |
3be917340bdcc8f6a9df29a63e4763044af84b9326930bc0a73a141af59d2a3a | MATLAB | 547 | 26 | function isNew = tapas_uniqc_isNewGraphics()
% returns true, if Matlab version is R2014b or new (different handling of
% figure handles)
%
% isNew = tapas_uniqc_isNewGraphics()
%
% IN
%
% OUT
%
% EXAMPLE
% tapas_uniqc_isNewGraphics
%
% See also
% Author: Lars Kasper
% Created: 2014-11-05
% Copyright (C) 2014 Ins... |
4d8256a722ab1f0bc3453ce262daaeea63d29b0809a65670962c6d8afa7ce346 | MATLAB | 547 | 15 | %{
# scan stim type, visual or auditory
-> experiment.Scan
-> experiment.StimTypes
---
speaker_id : int # id of the speaker
location : tinyint # 1 = Left, 2 = Right
calib_trial : int # calibrati... |
5d38f63d358dd63f8db16b725d8f2aedeb4072ec2b12b0f5171d4e18093967ec | MATLAB | 547 | 19 | function [wMLnew,opsnew] = removeParams(wMLold,index,ops)
%will remove params and update the ops struct
opsnew = ops;
opsnew.nkern = ops.nkern-1;
opsnew.ls = [ops.ls(1:index-1),ops.ls(index+1:end)];
opsnew.dimst = [ops.dimst(1:index-1),ops.dimst(index+1:end)];
opsnew.dimbcst = [o... |
83dc6c7a5691f095d493533a73b120025547d340dc19d1931a992b7d3bebc09e | MATLAB | 547 | 22 | %{
# single slice of one stack
-> stack.CorrectedStack
-> shared.Channel
islice : smallint # index of slice in volume
---
slice : longblob # image (height x width)
slice_z : float # slice dep... |
a3eae72bf9d1c1a2a45c01e8654e37c7eee0c3bf1d9969228d09d3f5a07e5074 | MATLAB | 547 | 21 | %{
preprocess.PrepareAodPoint (imported) # points in 3D space in coordinates of an AOD scan
-> preprocess.PrepareAod
point_id : smallint # id of a scan point
---
x : float # (um)
y : float # (um)
z ... |
ea7fd097fd99346b36c86ba118ecc7d159f9cf55f5f6273e3b0fc605b204ac91 | MATLAB | 547 | 34 | function [llh] = tapas_vlinear_hier_llh(data, theta, ptheta)
%% Linear model with variance and identity covariance matrix.
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
y = data.y;
u = data.u;
theta = theta.y;
[np, nc] = size(y);
llh = zeros(np, nc);
ln2pi = log(2 * pi);
for j = 1:nc
% Precision
mu =... |
4cabd9bc19b6deaa6633b65b68c6e3e6cb0af0763b7087d4b978b2104d98826d | MATLAB | 548 | 18 | %Author: Kim Kundert-Obando for questions please reach out to me at k.rogge.obando@gmail.com
%This code will be a function that derives 4D nifti file of data that is in 2D format, v1 v2 v3 are
%voxel dimensions of original nifti data
function nifti_map = derive_4Dmaps(file,file_name,brainVox,mask_info,v1,v2,v3)
for i... |
04949d7444b004b40387079742bbe55c18c8acce195cc0b13dd792606f665cd5 | MATLAB | 549 | 30 | %
% Open the QT-NIRS GUI for data quality check
%
% Parameters
% ----------
% participant: integral number
% Participant to process.
%
% Outputs
% -------
% The outputs are saved as .csv files.
%
% Author
% -------
% Ségolène M. R. Guérin
% June 29, 2023
% RnB-Lab (Institute of Neuroscience, UCLouvain)
%
function... |
7acb72864ed49718c8c39b6434f30b42f75e87da3aee6e38a1f3c3ab479e4ec4 | MATLAB | 549 | 21 | function varargout = covConst(varargin)
% Wrapper for unit constant covariance function covOne.m.
%
% Covariance function for a constant function. The covariance function is
% parameterized as:
%
% k(x,z) = sf^2
%
% The scalar hyperparameter is:
%
% hyp = [ log(sf) ]
%
% For more help on design of covariance functions... |
a8a9ec9ddc400d23432d065dd382e7996ab1dcc7b45086e963c24c4fd2fbfe05 | MATLAB | 549 | 15 | function [lp,dlp] = priorDelta(x)
% PRIORDELTA fix the value of a hyperparameter.
%
% This is a summy hyperparameter prior distribution.
% The function is not intended to be evaluated but exists merely to make
% the user aware of the possibility to use it. The function is equivalent
% to priorClamped.
%
% For m... |
5b1b716507470260d495a24364c166b4c81eaa881dc638070ea3c34226274787 | MATLAB | 550 | 30 | %close all
%clear all
path(path,'.\FUZZCLUST')
%the data
data.X = Z(:,[1 2]);
[N,n]=size(data.X);
%data normalization
data = clust_normalize(data,'range');
plot(data.X(:,1),data.X(:,2),'.')
hold on
%parameters given
%param.c = [0.51 0.91
% 0.14 0.79
% 0.6 0.17
% 0.05 0.25]
param.c=4;
para... |
8184ed53bbd32022dbeac1fc0374f39f416bafb4b8a01c9892c8b2354d7959df | MATLAB | 550 | 26 | function ListSubj(SubjsDir,outname)
if nargin==0
SubjsDir= uigetdir([],'select a input folder') ;
outname='SubjList.txt' ;
elseif nargin==1
outname='SubjList.txt' ;
end
[DirPath, fileN, extn] = fileparts(SubjsDir);
list = dir (SubjsDir) ;
% if exist ([SubjsDir,filesep,'SubjList.txt'])
% delete ([SubjsDir... |
9f206919fc0ad06125ae377b6c93a8005fe195dedc5c57f877b80b8893848938 | MATLAB | 550 | 28 | function [J,h_theta] = jointcostaccfun(param,x,y,task)
if nargin<4
task = ones(size(x));
end
sigma = param(1);
lapses = param(2:3);
if length(param)==4
mu = param(4);
else
mu = 0;
end
m = length(y);
h_theta = nan(m,1);
utask = unique(task);
ntask = length(utask);
for itask = 1:ntask
itrl = task == u... |
e061958876b80d2951485af54d95f835048d21398e06a529a1232dd28c10efc3 | MATLAB | 550 | 16 |
function changeslice(src,evt,safter,Ftrace,traceX,traceY)
evname = evt.EventName;
switch(evname)
case{'SliderValueChanging'}
% f = sbefore.SliceNumber;
% safter.SliceNumber = f;
% disp(['Slider value changed event: ' mat2str(evt.CurrentValue)]);
safter.Slice... |
3ccdc0a73388f9f24b2d152422c726ff7061564ffd2a6aa7e59f94ca125b6cfd | MATLAB | 551 | 31 | function [llh] = tapas_vlinear_llh(data, theta, ptheta)
%%
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
y = data.y;
u = data.u;
theta = theta.y;
[~, nc] = size(y);
llh = zeros(1, nc);
ln2pi = log(2 * pi);
for i = 1:nc
pe = y{i}.pe;
lpe = log(pe);
tllh = theta{i}.k * log(theta{i}.t) - gammaln(th... |
85806da3ce64f9ed1f4b2a58b046445a611e4900a23f242f24f14ad6f33370ef | MATLAB | 551 | 15 | function [lp,dlp] = priorClamped(x)
% PRIORCLAMPED fix the value of a hyperparameter.
%
% This is a dummy hyperparameter prior distribution.
% The function is not intended to be evaluated but exists merely to make
% the user aware of the possibility to use it. The function is equivalent
% to priorDelta.
%
% For... |
ed004fb7985f2b468b53c1d8dec264ba3a249790cd0504af16c4ff79aa6d33ad | MATLAB | 551 | 25 | function task_indicator_table(connames,taskstr,taskindic,tasknames)
% header 1
fprintf(1,'Task types in analysis\n\nContrast Name\tTask type\tTask indicators with sample sizes\n')
% header 2
fprintf(1,'\t\t')
for i = 1:length(tasknames)
fprintf(1,['%s\t'],tasknames{i})
end
fprintf(1,'\n')
% prin... |
0a5a7b12d9d04e979896fbedc8bbd77e7a2693c9c703973964de9e66ca59a554 | MATLAB | 552 | 32 | function [template] = tapas_load_template(fname)
%% Loads a file that work as a template for filling.
%
% Input
% fname -- File name.
%
% Output
% string -- An array containing the string.
%
% aponteeduardo@gmail.com
% copyright (C) 2017
%
fid = fopen(fname);
try
template = {};
... |
ec1da39e1b9c9aa421c51edfc4c7388446be174df1bfa1f9975b7d291edc9e9b | MATLAB | 552 | 20 | function y = linTransform(x, fromLimits, toLimits)
% linearly transforms values x lying in interval 'fromLimits' into another interval 'toLimits'
% eq: y = k*x + c
% (c) Jiri, Mar11, Nov16
% input
x1 = fromLimits(1);
x2 = fromLimits(end);
y1 = toLimits(1);
y2 = toLimits(end);
% linear transformation
k = (y2-y1)/(x2-... |
1022c179946a679f57fa42e036bbe8334e7056da542fe4ccd06a065f80f0c2ef | MATLAB | 553 | 19 | function [data, spans, names] = read_analog_stream(stream)
response = stream.next();
stream_data = response.getDataList();
length = stream_data.size();
data = zeros(length, 1);
for i = 1:length
data(i) = stream_data.get(i-1);
end
stream_spans = response.getSpansList();
length = stream_spans.size();... |
1804a05116ce434e1c22db104e0c1f40647da8eff42b67d5c576327e41b38ce7 | MATLAB | 553 | 25 | %{
monet.DriftTrialSet (computed) # all drift trials for this scan
-> rf.Sync
---
%}
classdef DriftTrialSet < dj.Relvar & dj.AutoPopulate
properties
popRel = rf.Sync & (psy.MovingNoise & 'speed>0');
end
methods(Access=protected)
function makeTuples(self, key)
... |
27e67580c4568a6c2f2430c59c48c37859ca1947b51b1c66569e98f7fdef8b22 | MATLAB | 553 | 15 | %{
vis.MovieSeqCond (manual) # random sequences of still frames
-> vis.Condition
---
-> vis.Movie
rng_seed : int # random number generator seed
pre_blank_period : float # (s)
duration : float # (s)... |
606c41af4704b0f07fad96438f0fd299a01fb58e923a7a05c1507fe8d4514043 | MATLAB | 553 | 35 |
% Panel gives you figure-wide control over text properties.
%
% (a) Create a grid of panels.
% (b) Change some text properties.
%% (a)
% create a grid
p = panel();
p.pack(2, 2);
% select all
p.select('all');
%% (b)
% if we set the properties on the root panel, they affect
% all its children and grandchildre... |
7f6accef62aae4f6e66b780d5b92c9087bf9663d0e909f51e58f0d15bb0f9d80 | MATLAB | 553 | 20 | function fn = tapas_uniqc_str2fn(str)
% reformats string so that it could be a filename (without space colon etc)
%
% output = tapas_uniqc_str2save(input)
%
% IN
% str string
% OUT
% fn file-name compatible string without spaces, dots, slashes etc.
% EXAMPLE
% str2save
%
% See also
% Author: Lars Ka... |
0a31c5e22b0cf6c0067014e29bb43839a3223b215738163bf351e19f65cb7857 | MATLAB | 554 | 25 | function result = is_symmetric_matrix(A)
%
% Symmetric Matrices
%
% is_symmetric_matrix(A) determines if the matrix A is a symmetric
% matrix. An error is returned if a matrix that is not square is attempted
% to be determined for symmetry.
%
% Function written by Anthony Russo, downloaded from MatlabCentral.... |
62f154c5b6767b01c59f23cb15520560aad11fba25fc3b82a1a75b02870e64c2 | MATLAB | 554 | 20 | %{
preprocess.ExtractRawGalvoROI (imported) # region of interest produced by segmentation
-> preprocess.ExtractRawGalvoSegmentation
-> preprocess.ExtractRawTrace
---
mask_pixels : longblob # indices into the image in column major (Fortran) order
mask_weights=null : longblo... |
63a2c722c314e1d7ffc230807fa0c01c1db2eef9b95ddea151bc14113403e66b | MATLAB | 554 | 25 | % handy function to save variable in nifti format
function save_nii_quick(templateHeader,img,filename,datatype,voxelsize)
if nargin < 4
datatype = 16;
end
nii = templateHeader;
nii.img = single(img);
nii.hdr.dime.datatype = datatype;
nii.hdr.dime.dim(5) = size(img,4);
nii.hdr.dime.dim(1) = ndims(img);
nii.hdr.dim... |
d8aec31325022bdebe41d7b1c3d5c4581bb79121a8ccd02e6b3f41d25d343358 | MATLAB | 554 | 19 | function candoit = canGetCost(problem)
% Checks whether the cost function can be computed for a problem structure.
%
% function candoit = canGetCost(problem)
%
% Returns true if the cost function can be computed given the problem
% description, false otherwise.
%
% See also: getCost canGetDirectionalDerivative canGetGr... |
e2309a01785892dcf25bea06b4d35d2a6aea3a299532ea7610253c81fd104f90 | MATLAB | 554 | 11 | % This script is taken from the old 'callback1' variable, and is called
% when the main ARTwarp GUI figure is closed. It saves the network
% parameters used to a file named 'ARTwarp.mat'
global vigilance bias learningRate maxNumCategories maxNumIterations sampleInterval resample;
shh=get(0,'ShowHiddenHandles');
set... |
ed05395267d9e3776aee49d2cfc640a5f9afa6593c28666457ffab05bba77a24 | MATLAB | 554 | 18 | %% BatchScript
% Script for batch running other scripts or functions
basePath = 'D:\Data\Lobster\Lobster_Recording-200319-161008\Data';
filelist = dir(basePath);
sessionPaths = regexp({filelist.name},'^#\S*','match');
sessionPaths = sessionPaths(~cellfun('isempty',sessionPaths));
fprintf('%d sessions detected.\n', nu... |
7cd7cd87c11579841dca446dd3b7637eb7bafc611f059d1ed0b278b327b93497 | MATLAB | 555 | 25 | %{
aod_monet.DriftTrialSet (computed) # all drift trials for this scan
-> aodpre.Sync
---
%}
classdef DriftTrialSet < dj.Relvar & dj.AutoPopulate
properties
popRel = aodpre.Sync & (psy.MovingNoise & 'speed>0');
end
methods(Access=protected)
function makeTuples(self, key... |
a68739d995a3de3aed2de7dac859c7a55f943b32c522270dddf6cda06bfcfa52 | MATLAB | 555 | 13 | function res = hlp_sort_namevalues(varargin)
% Sort name-value pairs by name.
% Sorted-NVPs = hlp_sort_namevalues(NVPs)
%
% Since the toolbox occasionally caches results of function calls,
% this is practical to uniformize arguments that lead to the same results, but look superficially different.
%
% ... |
4b97be7e22126ae1f2ffaa9fc1470411d97bbc506ae718d2b2c9d9767abb73e1 | MATLAB | 556 | 11 | function dataout = LargeCluster(data, dim1, dim2, dim3)
[theObjMask, theObjNum]=bwlabeln(reshape(data, dim1, dim2, dim3),26);
for x=1:theObjNum,
theCurrentCluster = theObjMask==x;
ClusterSize(x,1) = length(find(theCurrentCluster)) ;
end
[maxa maxb] =max(ClusterSize); % get t... |
bdb06cadb2d1f35345f81bd723434520766608f3b9b0e6745c45def0ef76314f | MATLAB | 556 | 22 | function h=setfsize(wx,wy)
% h=setfsize (wx,wy)
%
% Set figure position.
%
% h = setfsize(X,Y)
% X - Horizontal length.
% Y - Vertical height.
% h is the figure handle to the figure just handled
% Sets current figure lower left position to X by Y pixels (measured from
% lower left corner of screen. On image, max p... |
bf7c4516cf97d57ad7500b5da156cfb34818cc92e4af513944570c173bc46ae6 | MATLAB | 556 | 12 | function y = tapas_sgm(x, a)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2012-2013 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Licence (GPL), version 3. ... |
846289f281e4208738419fb6329adfe46f61038a76cf291bc3453c689da4c0c1 | MATLAB | 557 | 36 | function phi = solvePDE(MS, M, RHS, varargin)
%SOLVEPDE solves the linear system M x \phi = RHS and returns the value of
%\phi reshaped based on the structure of the MeshStructure variable. The
%default solver is the matlab '\' linear solver
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE ALSO:
%
... |
fcbbf284ff461452e73a46f1855541753ec2ee55cf57a974bd268ed2815f1cf3 | MATLAB | 557 | 20 | %{
# some intermediate results from affine registration
-> stack.FieldRegistration
---
score_map : longblob # 3-d map of best correlation scores for each yaw, pitch, rol combination
position_map : longblob # 3-d map of best positions (x, y, z) f... |
4f1185b4d7defef58b0d792c4269984d27a1929f3455b2d6c6d058d5c1c14e22 | MATLAB | 558 | 18 | function balanced_accuracy = balanced_accuracy_score(y_true, y_pred)
%% balanced_accuracy_score
% same function used in the sklearn.metric.balanced_accuracy_score
% but only works for the two classs.
if numel(unique(y_true)) ~= 2
error('Number of class is not two.');
end
classNames = unique(y_true);
balanced_ac... |
59a84c71523f2b53ddbf5bd953989ae3e46ef3f5997aede21c0abfe4e290fdf7 | MATLAB | 558 | 25 | function fn = getImFiles(params)
contents = dir(params.pth);
good = false(numel(contents), 1);
disp('Image files: ');
for i = 1:numel(contents)
if contains(contents(i).name, params.imtoken) && ~contains(contents(i).name, 'reg_')
if ismember(str2double(contents(i).name(end-8:end-4)), params.nums)
... |
6fd1be88f19dc83d8fc66e766b62e74ae23ac0d0bfbc5d76a1df83778be07dc2 | MATLAB | 558 | 29 | function [Y]=sindex(A)
% Calculate similarity of tf-idf normalized matrix
% INPUT:
% A: N-by-T tf-idf normalized matrix
% OUTPUT:
% Y: N-by-N similarity matrix
%
% Luis Carrillo-Reid, 2014; Shuting Han, 2017
N = size(A,2); %Número de picos
Y = zeros(N,N);
for i=1:N
for j=i:N
Aa = A(:,i);... |
ead4b246b2e09a9ae7a48d75cb75af2cb563abd0e528135f92b8e2da7bdb857f | MATLAB | 558 | 34 | function X = myTEOcircshift(Y,k)
% circshift without the boundary behaviour
% Parameters
% ----------
% Y :
% k :
%
% Output
% ------
% X :
colshift = k(1);
rowshift = k(2);
temp = circshift(Y,k);
if colshift < 0
temp(end+colshift+1:end,:) = flipud(Y(end+colshift+1:end,:));
elseif colshift > 0
temp(1:1... |
0ac212d1ac69db0ec1edf60fb791ff45980002f8fbcdf746c4bf27ae3480fc41 | MATLAB | 559 | 23 | function [rand_nums] = rand_with_int(N,delta)
% Reference paper: Herzog et al. 2020 "Scalable and accurate automated method
% for neuronal ensemble detection in spiking neural networks"
% https://www.biorxiv.org/content/10.1101/2020.10.12.335901v1
% Rubén Herzog October 2020
N = 10; % number of integers required
delt... |
d15274a2e3624ff2e370061f987830eb2651aca09a80e24391e5ec6a2650862b | MATLAB | 559 | 22 | %{
# Inferred background components with the CNMF algorithm
-> preprocess.ExtractRaw
-> preprocess.Channel
-> preprocess.Slice
---
masks : longblob # array (im_width x im_height x num_background_components)
activity : longblob # array (n... |
0f9059d02d0d84c0a64e3d30baa97342f595ff55cd6c8d670cbe7bf950365e75 | MATLAB | 560 | 27 | function uidents = re_sort_uidents(uidents, identifiers)
% %for testing_______________
% clear all
% close all
% clc
% %this fbmm file was generated from the data in CPH_003_datalist
% load repackData_testfile
% % load lightcurvefbmm.mat
% identifiers=fbmm.szGenotype;
% uidents = unique(identifiers)
% %end testing___... |
62982038671a7fef06bd2aa4f2c14e3ca0ac3a148a4f329c2f9e1a8dc21c7934 | MATLAB | 560 | 23 | function V0 = initialize_membrane_potentials(params)
% INITIALIZE_MEMBRANE_POTENTIALS - Set initial voltages
%
% H1 Line: Initialize membrane potentials randomly
%
% Syntax:
% V0 = initialize_membrane_potentials(params)
%
% Description:
% Generates random initial membrane potentials between reset
% and threshold ... |
b5bf42497dad03480a9af0c1d8f8c0a588c36279d8f8b4fd1dd4a8e263419991 | MATLAB | 560 | 24 | function im = loadTifFramesFast(FileTif, info, frames)
xpix=info(1).Width;
ypix=info(1).Height;
bitdepth = info(1).BitsPerSample;
Nframes = numel(frames);
if bitdepth == 32
im=zeros(ypix,xpix,Nframes,'uint32');
elseif bitdepth ==16
im=zeros(ypix,xpix,Nframes,'uint16');
elseif bitdepth ==8
... |
bcb1ddb39d6b87d03122b7ed6724d23db6f8dcc3335d5a06d1b1b4e7f96c64e4 | MATLAB | 560 | 20 | function spike_matrix = spikeTimeToMatrix(spikeTimesStruct, start_time, end_time, sampling_rate)
%{
%}
channel_names = fieldnames(spikeTimesStruct);
bin_edges = start_time:1/sampling_rate:end_time;
num_bins = length(bin_edges) - 1;
num_channels = length(channel_names);
spike_matrix = zeros(num_bins, num_channels);... |
e0f6eb682f76867d2a86f18d1031f70ed33e2a587a1761b5f8269280a5996235 | MATLAB | 560 | 31 | function [posterior] = tapas_linear_estimate(y, x, model, inference, pars)
%% Estimate a linear model
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
n = 3;
if nargin < n
model = struct();
end
n = n + 1;
if nargin < n
inference = struct();
end
n = n + 1;
if nargin < n
pars = struct();
end
[pars] = t... |
fd95d556bf0a660ea203a428dc4df9ebf23cee81095aaf528825003c08444134 | MATLAB | 560 | 17 | function edge_thresh = getEdgeThreshold(adjM, Params)
%GETEDGETHRESHOLD Summary of this function goes here
% Detailed explanation goes here
if isfield(Params, 'networkPlotEdgeThresholdMethod')
if strcmp(Params.networkPlotEdgeThresholdMethod, 'Absolute Value')
edge_thresh = Params.networkPlotEdgeThreshold;... |
ef206c739cf560e763dd3873ce178fc663aa76fb00e316bd7a0cfe2fd8b69364 | MATLAB | 561 | 20 | function aux_stackwrite(stack, filename)
%AUX_STACKWRITE Write a 3D matrix as a stack of images (.tif)
% AUX_STACKWRITE(stack, filename) write the 3D matrix stack as filename
%
% Input:
% - stack: 3D matrix
% - filename: string containing the name of the stack.
%
% Example:
% aux_stackwrite(stack, '3dou... |
4f007775d1a48c2c2fdb8b2262054b3a6c752c72e2a1374a2fb43c374a262b38 | MATLAB | 562 | 32 | n = 3;
m = 3;
p = 3;
k = 2;
X = randn(n, m, k);
Y = randn(m, p, k);
t = tic();
for K = 1 : 100000
XY1 = multiprod(X, Y);
end
toc(t)
t = tic();
for K = 1 : 100000
XY2 = multiprod_ez(X, Y);
end
toc(t)
t = tic();
for K = 1 : 100000
XY3 = mmx('mult', X, Y);
end
toc(t)
fprintf('Relative difference: %g\n', no... |
81af80bc9080fb1a5433f54936edc25c50709e51de6f5c484ff46f7c62861706 | MATLAB | 562 | 20 | function aux_stackwrite(stack, filename)
%AUX_STACKWRITE Write a 3D matrix as a stack of images (.tif)
% AUX_STACKWRITE(stack, filename) write the 3D matrix stack as filename
%
% Input:
% - stack: 3D matrix
% - filename: string containing the name of the stack.
%
% Example:
% aux_stackwrite(stack, '3dou... |
d6a75935fb186f1f9957dd87632805b4a11f657d4f1bada6dabb38e15bf44d71 | MATLAB | 562 | 14 | function[rawdata] = CleanData(orgrawdata, column1_index, column2_index, column3_index)
% clean rawdata from messy start/finish
firstdatapoint = max(orgrawdata{1,column2_index});
q = find(orgrawdata{:,column2_index} > firstdatapoint - 25E-9);
if (~isempty(q))
w = q(end);
else
w = 1;
end
[maxrawdata,ma... |
dfb332bde52e551cb21290d25949ad368ac95ccbcf35b39d84d7764d3e03d77f | MATLAB | 563 | 19 | function plot_eigs(ax,eigs,seleig)
% Reference paper: Herzog et al. 2020 "Scalable and accurate automated method
% for neuronal ensemble detection in spiking neural networks"
% https://www.biorxiv.org/content/10.1101/2020.10.12.335901v1
% Rubén Herzog October 2020
cla(ax);
hold(ax,'on');
plot(ax,1:length(eigs),eigs... |
038bd0e6ed8fe4088f9ff638605755f3e055b7715908065556f388121d9e7ede | MATLAB | 564 | 31 | function [posterior] = tapas_vlinear_estimate(y, x, model, inference, pars)
%% Estimate a linear model
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
n = 3;
if nargin < n
model = struct();
end
n = n + 1;
if nargin < n
inference = struct();
end
n = n + 1;
if nargin < n
pars = struct();
end
[pars] = ... |
8dbfacd18771d54dc0021f886b3e7e049d50c950cc872cb204e751932597cbc7 | MATLAB | 564 | 15 | function [dc, rho] = paraSetv2(dist, percNeigh)
% using the modified version of Yger et al 2016, related to spike sorting.
%
% Reference paper: Herzog et al. 2020 "Scalable and accurate automated method
% for neuronal ensemble detection in spiking neural networks"
% https://www.biorxiv.org/content/10.1101/2020.10.12.3... |
9259f01605abdf25df342019a0f5f9def211b36e5f34c3d02f6f2761cef27bf6 | MATLAB | 564 | 20 | function stackedbar2(v,colors,labels)
% stackedbar(v,colors,labels)
% plots a stacked bar plot, so you can see proportions of each variable out
% of whole
% useful for plotting p(task|act)
% columns of v are tasks, rows are regions
% labels are labels for regions
figure('Color','w'); set(gca,'FontSize',18); hold on;
... |
40994c8c99ecfd6d0f6808340897170739a89b49f53c2091880bc8fd3254f9af | MATLAB | 565 | 29 | function [theta] = tapas_mh_mc3_propose_gaussian_sample(data, model, ...
inference, state, node)
%%
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
otheta = state.graph{node};
nc = numel(otheta.y);
theta = otheta;
% Default if not no update values
if isfield(state.kernel{node}{1}, 'nuk')
nup = state.kern... |
58632296670cc018096f9b95ba0126fd07faeb24bf17adb4caa7f8286e9b52f4 | MATLAB | 565 | 26 | function [A,W,SW,S,Q,ix_act] = ...
compo_delete_act(XX,A,W,SW,S,Q,SY,i_del,jx,ix_act)
% Delete component
% XX = X(ix_act,:)*X' [M_act x M_all]
A(i_del) = 0;
M = length(ix_act);
jj = [1:(jx-1), (jx+1):M];
% New active index
ix_act = ix_act(jj);
% Weight & variance update
ss = 1./SW(jx,jx);
SX =... |
80f2ab518fcb657de1cbc41fd26737aec51f2706fcdabd4f5cc2b83540a8edcd | MATLAB | 565 | 28 | function b = regressVolume(data, trials, varargin)
if strcmpi('low', varargin)
use = find(data.block == 3 & data.optout == 1 & ...
data.catch == 1);
elseif strcmpi('high', varargin)
use = find(data.block == 2 & data.optout == 1 & ...
data.catch ==1);
else
use = find(data.block==1 & data.op... |
a9a24087782485555204552519b9b2274490f06c51a68a9daf8f7dd9d37e29ab | MATLAB | 566 | 16 | function d = log_det(sxx)
% Log( det(sxx) ) for Positive definite matrix
% ¶¦Ê¬»¶¹ÔÎó¤Ï¾ï¤ËÀµÄêÃÍÂоιÔÎó
% Gauss ¤Î¾ÃµîË¡¤Ë¤è¤ë»°³Ñ¹ÔÎó°ø»Ò
[L,U] = lu(sxx);
eig_val = abs( diag(U) );
eig_val = eig_val(eig_val > 0);
d = sum( log( eig_val ) );
% ¥³¥ì¥¹¥Ê¬²ò : X ¤¬ÀµÄê¹ÔÎó¤Î¤È¤¡¤»°³Ñʬ²ò¤è¤êÁᤤ
%R = chol... |
b09ee1f649801eebcc821d5788869b8057eac00f0714575c83387d7b8e1c6247 | MATLAB | 566 | 27 | function PlayBeep(w,t)
%USAGE:
% beep
% beep(w) specify frequency (200-1,000 Hz)
% beep(w,t) " " and duration in seconds
%
fs=65000; %sample freq in Hz (1000-65535 Hz)
% it was 8192 when using SOUND command at the end of this code
if (nargin == 0)
w=1000; %defa... |
f68c176a2dd64bcc6e8a30772ec41df7f364ef63d1a6281b8f5681c8e8b2cbbb | MATLAB | 566 | 31 | function [y] = rngits(dim,x,p)
% RNGITS Random number generator using inverse transform sampling
% [y] = rngits(dim,x,p)
if nargin < 3
error('Missing input argument(s).');
end
if size(x) ~= size(p)
error('x and p should have the same size.');
end
p = p/trapz(x,p);
c = cumtrapz(x,p);
imin = f... |
1b0063430989b68a5918417b826ef233c25e21188652aad75aab07643d9df350 | MATLAB | 567 | 24 | function cl2area=surfing_clusterarea(clu,node2area)
% quick wrapper function to find areas of clusters.
%
% CL2AREA=SURFING_CLUSTERAREA(CL,NODE2AREA)
%
% INPUTS:
% CL Nx1 cell for N clusters, where CL{K} are the indices of
% the nodes in the K-th cluster
% NODE2AREA Mx1 areas of each node
% ... |
51ee7e458e412c58714cd3aca8bcecc8237a504c85af637f5f175459e20d3a3f | MATLAB | 567 | 24 | function data = getData( obj,channel )
if nargin<2
channel = 1;
end
import vis2p.*
assert( length(obj)==1 );
[path,name] = fetch1( Experiments*obj, 'directory','file_name' );
scan_prog = fetch1(obj,'scan_prog');
if strcmp(scan_prog,'MPScan')
filename = getLocalPath([path '/' name 'p%u.h5']);
tpr = tpRea... |
57aa63f5d0744e495819d269914ea352143e9c00af585cfb06107ebb6f65875d | MATLAB | 567 | 25 | function niml=afni_niml_read(fn)
% simple function to read niml files
%
% P=AFNI_NIML_READ(FN) reads a file FN and returns a NIML structure P.
%
% NNO Dec 2009 <n.oosterhof@bangor.ac.uk>
bytes=read_bytes(fn);
niml=afni_niml_parse(bytes);
function s=read_bytes(fn)
fid=fopen(fn);
if fid==-1
if... |
75d5c9a6ad0cdbbcb9b91d0cff1262254cf4929d17721807801ea6f1013f46b0 | MATLAB | 567 | 32 | function tableExamples
% % Table call format
%
% clf
%
% albert=[1,1,1,3,2,1,3,3,3,2,2,3,3]';
% victoria=[7,8,6,1,5,7,2,1,3,4,5,2,4]';
% M = table(victoria,albert); %place data in first column and groups in the second
%
% subplot(1,2,1)
% notBoxPlot(M)
%
% subplot(1,2,2)
% notBoxPlot(M,'jitter',0.5)
help(['NBP.',mfi... |
e6ab13b2e88763e1a7843467a20819d47a41e6cd6b78dbbcabe208f537d6e362 | MATLAB | 568 | 19 | function class_calc = knnclass(neighbors_class,neighbors_distance,num_class,K)
% find class on the basis of K neighbors
for g = 1:num_class
freq(g) = length(find(neighbors_class == g));
end
unique_class = find(freq == max(freq));
if length(unique_class) == 1
[M,class_calc] = max(freq);
else
mean_dist = o... |
a2de1dc9a085dac4d7cacca0fdf5b9de532bbb53ccff3eee184b4b298d18ff6a | MATLAB | 570 | 21 | function f = nsd_datalocation(dir0)
% function f = nsd_datalocation(dir0)
%
% <dir> (optional) is [] | 'betas' | 'timeseries' | 'stimuli'
%
% Return full path to the nsddata directories.
% Edit this to suit your needs!
if ~exist('dir0','var') || isempty(dir0)
f = '/media/charesti-start/data/NSD/nsddata/';
else
sw... |
e8b419e7db44b37548c252b7b84498608417cbd7b2c6fd30becd630fc2186eaa | MATLAB | 570 | 12 | function pstruct = tapas_softmax_mu3_namep(pvec)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2017 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Licence (GP... |
23a6e3a93c15ed4c310e8608dfb6b772cbe7663ee443012465bdb4197f1466d6 | MATLAB | 572 | 22 | function [q,r] = divmod(x,y)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% divmod divides X and Y and return the quotient and the remainder.
%
% Arguments:
% x = Numerator
% y = Denominator
%
% Output:
% q = quotient
% r = remainder
%
% Emin Serin - 14.08.2019
%
%%%%%%%%%%%%%%%%%... |
e781407af14086f4ebb371de2b0745463a9d9233867ee49d7743946d23aa4116 | MATLAB | 572 | 12 | %{
# projector configuration
projector_config_id : tinyint # projector config
---
-> ProjectorColor.proj(channel_1="color_id") # channel 1 means 1st color channel. Usually red
-> ProjectorColor.proj(channel_2="color_id") # channel 2 means 2nd color channel... |
e951fbaa6d0bec6614538c66a0b90b7b5284afad11533b8b359b6248141b7014 | MATLAB | 572 | 19 | load(which('invMLEFitResults.mat'))
load(which('MLEFit.mat'))
%%
x0resid = cellfun(@(x0i,x0bar)x0i-x0bar,x0inv,num2cell(cMatrixMLE),'UniformOutput',false);
%%
Adist = cell2mat(cellfun(@(x)x(:),Ainv(:)','UniformOutput',false)');
ndist = cell2mat(cellfun(@(x)x(:),ninv(:)','UniformOutput',false)');
x0dist = cell2mat(cellf... |
ef45c74c14560cbe9d69301aed9809a76abdbbbb80d5f2c31faa219448761adb | MATLAB | 572 | 25 | function [fits] = tapas_sem_normalized_fits(data, fits)
%% Normalize the fits according to the data.
%
% Input
% data -- Data structure with field y and u
% fits -- Fits structure with fields pro and anti
%
% Output
% fits -- Normalized fit structure
% aponteeduardo@gmail.com
% c... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.