sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7b3686dadb1deaaa75785d809356de25482c35dadd2a3658c940feb65c755bb8 | MATLAB | 5,560 | 164 | function [distance,units] = IsolationDistance(features,varargin)
%IsolationDistance - Determine the isolation quality for one or more clusters.
%
% Compute isolation distance, as defined by K. Harris (see Schmitzer-Torbert
% et al. 2005).
%
% USAGE
%
% [d,units] = IsolationDistance(features,<options>)
%
% featu... |
71dfadff47f12bb05d56b8cda24ba9f0f2228aed1a09071afb3e264aaa198d6e | MATLAB | 5,561 | 132 | function net = cnn_cifar_init_nin(varargin)
opts.networkType = 'simplenn' ;
opts = vl_argparse(opts, varargin) ;
% CIFAR-10 model from
% M. Lin, Q. Chen, and S. Yan. Network in network. CoRR,
% abs/1312.4400, 2013.
%
% It reproduces the NIN + Dropout result of Table 1 (<= 10.41% top1 error).
net.layers = {} ;
lr = [... |
ce986515957b00572d843daef6db22c1d2785b5f4686137bb0897a6e4d9127f0 | MATLAB | 5,563 | 84 | function outstr = GE_dumpExamHeader(exam)
%
% outstr = GE_dumpExamHeader(exam)
%
% Writes the exam header to the string outstr
%
% Souheil J. Inati
% Dartmouth College
% May 2000
% souheil.inati@dartmouth.edu
%
outstr = sprintf('ex_suid: %s\n' , char(exam.ex_suid));
outstr = strcat(outstr, sprintf('ex_uniq: %d\n' ... |
0d238b9c90975240ec2cf0333c979ac461b74c1aa8aacb082cbcc98737d3602a | MATLAB | 5,564 | 130 | % controls the user interface with keyboard and mouse callback for
% analyzing a FOV as quickly as possible; check the
% switchImage()-subfunction for further details and a brief manual
%
% open window of FOV which allows to zoom and pan and select neurons
% manually ('f' for freehand) or automatically ('x' for
% cross... |
35f502f7448c2d86466dafc6527a78866722e5bb9114b06bfd8d13af8a12701f | MATLAB | 5,568 | 155 | % analysis_FeaturePredictionAccuracy Calculate feature prediction accuracy
%
% Author: Tomoyasu Horikawa <horikawa-t@atr.jp>, Shuntaro C. Aoki <aoki@atr.jp>
%
clear all;
%% Initial settings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Data settings
% subjectList : List of subject IDs [cell array]
% ... |
734f1a5d899a256d079b595984ec2eecd1743a9ae3819cc5566e7c3e29ed4e94 | MATLAB | 5,570 | 171 | function brain3D_projections(params, vals, plotInfo)
% plots iEEG channel activations on 3D transparent brain model
% prints axial, sagittal and coronal views
% (c) Jiri, Apr17
%% color maps
clrmap.brain = gray(128); % colormap for brain (T1, T2, CT, ...)
if isfield(params.plot_brainTopo, 'c... |
47aa930e5458df47f3ea8a82cc4555666f6ae2a8fb3945fce31fd5ecc4a5bdc1 | MATLAB | 5,571 | 139 | function [formatted_method_string,options]=genMethod(method_name,varargin)
% EXAMPLE USE WITH ARGUMENTS
% [formatted_method_string,options]=genMethod(method_name)
% [formatted_method_string,options]=genMethod(method_name,options)
%
% HELP
% Generates class method template to be pasted into existing class file.
% Create... |
9c0e26f33a0d5ee90826545acc6062f01cb80ea34e0de7beab6ccc57c008c752 | MATLAB | 5,571 | 147 | function [IDs,notIDs] = TS_GetIDs(theMatchString,whatData,tsOrOps,nameOrKeywords)
% TS_GetIDs Retrieve IDs of time series (or operations) in an hctsa dataset
% using that matches a string in either the Name or Keyword
% fields.
%
%---INPUTS:
% theMatchString, the string to match
% whatData... |
ced99019c3d98339fbc5f390b1f5b4d93fdaf0da22a73fa16803f7919a4d9ec2 | MATLAB | 5,573 | 132 | %{
rf.Sync (imported) # mapping of h5,ca imaging, and vis stim clocks
-> rf.Scan
---
-> psy.Session
first_trial : int # first trial in recording
last_trial : int # last trial in recording
frame_times : longblob ... |
3efb2097186433b1bf4d4bddaee9835e82c6c9c9ff57f2e98898e6d1271409a3 | MATLAB | 5,579 | 110 | function out = EN_wentropy(y, waveletName, level)
% EN_wentropy Wavelet entropy of a time series.
%
% Decomposes y via the maximal-overlap discrete wavelet transform (MODWT)
% into a set of scales, computes each scale's share of the signal's total
% energy, p_j = E_j / sum(E), and returns the Shannon entropy of this
... |
74fc53c79104a3bdacd9301cccc61b2a2265395c7de507b7aa947936daefc164 | MATLAB | 5,580 | 199 | % [chi2,df,p,sig,warn,isnonparametric] = chi2test_massive(seedcounts, counts,[obs. weights],[nonpar flag])
%
% Weighted or unweighted Chi-square test
% from observations
% Optional nonparametric estimation for questionable results
% SEE CHI2TEST.M
% THE PURPOSE OF THIS FUNCTION IS TO IMPLEMENT A CHI2 TEST EFFICIENTLY W... |
a183bab0f79da13ec03bcac7653ccdc9ede3e33b29a5ed5dc937080220dba874 | MATLAB | 5,580 | 90 | % clean_rawdata(): a wrapper for EEGLAB to call clean_artifacts function
%
% Usage:
% >> EEG = clean_rawdata(EEG, arg_flatline, arg_highpass, arg_channel, arg_noisy, arg_burst, arg_window)
%
% ------------------ below is from clean_artifacts -----------------------
%
% This function removes flatline channels, low-fr... |
d4a2ab9be8d772c5be9d41068117c9750089ff8df0fa7704e4c45ecce6d6f49f | MATLAB | 5,580 | 146 | %% SpatialTuningCurve
% Draw firing map of units
%% Dataset Paths
datasetBasePath = 'D:\Data\Lobster\FineDistanceDataset\';
resultBasePath = 'D:\Data\Lobster\FineDistanceResult_syncFixed_May';
filelist = dir(datasetBasePath);
sessionPaths = regexp({filelist.name},'^#\S*','match');
sessionPaths = sessionPaths(~cellfun... |
33fcb3215c1e23c146344fe679c304d1081aac67d4f17eae5947f64d49a772bf | MATLAB | 5,583 | 145 | % STD_CHECKDATASESSION - Check/fill session field in STUDY. Based in the
% name and IC decomposition of datases, the function determine which
% ones are coming from the same sessions.
% It will assign the same index number to the sets from the same subject coming
% from the same session.
%
% Usage:
% >> clustinfo =... |
a1f85d65831dabf6f6a8f176436b4821b92e1fcca034c8c30d23840f0371dfea | MATLAB | 5,583 | 177 | function avi_filename = show_demixed_video(obj,save_avi, kt, frame_range, amp_ac, range_ac, range_Y, multi_factor, use_craw)
%% save the final results of source extraction.
%% inputs:
% kt: scalar, the number of frames to be skipped
%% author: Pengcheng Zhou, Columbia University 2017
% zhoupc1988@gmail.com
if ~exis... |
74d5da0372977e4cc997e55a0ca98216aae077db8502fc4125703ebc1dd18b90 | MATLAB | 5,593 | 141 | function [outFlag,theName] = BF_CheckToolbox(theToolbox,infoMode,doInstallCheck)
% BF_CheckToolbox Check for a Matlab Toolbox license
%
% Checks for the given Matlab Toolbox license and produces an appropriate error
% message if there's a problem.
%
%---INPUTS:
%
% theToolbox, the string identifying the toolbox (in f... |
9543b02940a65b7446d0ec5a3a21cc0c6a54f45c0e5b5e43736f882d53ac2527 | MATLAB | 5,595 | 183 | %January 2025 SW: Script that reads out a portion of the eye and reads the average
%brightness over time from a tiffstack (frames)
%%
%NOTE: BLUE and ORANGE do not cause a change, so focus only on RED
%darkness
%blue stack: 1-2274
%orange: 1-2434
%red : 1-4134
%ambient light_animal 676
%blue stack:1-16734
%orange: 1-... |
eeb8b3e2765f5c1654f89b1f49830d11b20957d69abd70ec3404c5666f244ee1 | MATLAB | 5,597 | 143 | function [dist,bin_centers,stats] = CircularDistribution(angles,varargin)
%CircularDistribution - Compute circular distribution and statistics.
%
% USAGE
%
% [dist,bin_centers,stats] = CircularDistribution(angles,<options>)
%
% angles angles in radians, which will be shifted in [0,2π)
% <options> ... |
62bc75f40172bc5d82b3821f5d1e15a9ec7db990bdd03eca15fae85fa87cfe69 | MATLAB | 5,599 | 138 | function [C3] = BIASED(C3,myelin,funcs,PB)
C3_x = C3.x;
C3_y = C3.y;
C3_bias_func = funcs.C3_bias;
% define step size
delta = 1;
% Create 2 column matrix where column 1 is x pos, column 2 is y pos
C3_xy = [C3_x;C3_y]';
% Create a mask of x,y pos where myelin is not dead
alive_my_x = myelin.xarray(m... |
ab917a8cc43c53f41791e0525eea0d36f3c01e61894fea969318b6c2480dba89 | MATLAB | 5,600 | 160 | function [convRVTOut, rvtOut, verbose] = tapas_physio_create_rvt_regressors(...
ons_secs, sqpar, model_rvt, verbose)
% computes respiratory response function regressor and respiratory volume per time
%
% [convRVTOut, rvtOut, verbose] = tapas_physio_create_rvt_regressors(...
% on... |
f93cd81d74dec8938e3bb45efa7e5db39c67a58569b2f059c416253940de20f2 | MATLAB | 5,600 | 161 | function EC_avg = plotEC_targetGroups_imagesc(params, M, EC_info, selCh_groups, subjTag)
% plots effective connectivity (EC) of selected channel group (= params.grup_source) to all other groups
% plots = imagesc (a-la spectra) for each class: src->trg & trg->src
% input: M = 5D: ch_src, ch_trg,freq, time, clz
% channel... |
fdcf5df3fec36f90272f0e0523bb574051db61062d3e4efc2b7a705cead299f5 | MATLAB | 5,603 | 155 | function allExpData = compileAllExpData(ExpName, experimentMatFileFolder, Params, metricLevel)
%COMPILENETWORKLEVELDATA Combines data from multiple NetMet structures
% INPUT
% ------------
% ExpName : cell
% cell where each entry is the name (without extension) of a file to
% compile the data for
% experimentM... |
098b5529c9ecaaf006eced8392c29f0ad59778e2d85f89d26f67b5ed2da4141e | MATLAB | 5,604 | 204 | %{
TO BE UPDATED / TO BE UPDATED / TO BE UPDATED / TO BE UPDATED
%%%%%%% Preprocessing of BFM data %%%%%%%%
*** INPUT ***
Point to the master folder that contains the .dcimg data to process
(green and red channels)
The convention imposes: 'basename + _G or _R + .dcimg'
*** OUTPUT ***
Unmixed voltage ... |
dd8805645f26396b6e21fd4014fff775009ed64a58fdb62cd09d04592f0b6550 | MATLAB | 5,604 | 157 | function [L,varargout] = defineSearchlight_volume(ROIMask,Mask,varargin)
% function L = rsa.defineSearchlight(Mask,Opt)
% Defines a volumetric searchlight using all voxels that are > 0 in both
% ROIMask and the Mask as centres for the searchlights and as potential voxels
% to be included in the searchlight.
% The Ma... |
c1d8163774ba865f347d20a5d1058ffbeeeb10d2f7ecfa4fb9cebca0128e4ada | MATLAB | 5,606 | 133 | function F = fit_nlinOspreyMultiplex(x, dataToFitInput, basisSet, spl_pos, fitRangePPM)
% This function receives the current set of non-linear parameters during
% every iteration of the non-linear least-squares optimization. The
% parameters are applied to the basis set.
%
% Subsequently, a fast non-negative l... |
60cd82955cb0d7b453d7d116d273e10c3b35544eda589886d6016c3a4252db6f | MATLAB | 5,607 | 171 | function fear_coactTrigWaveletHighThreshold(basename,varargin)
% basename='~/data/Fear/triple/karmeliet190901/karmeliet190901';
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName);
load([basicMetaData.AnalysesName '-nremWaveletPow.mat'])
param... |
16880e61fc9ddf51f7acfdf6205bbd2464371eeeaa30b90696846dc8eab91bbb | MATLAB | 5,611 | 144 | function M = euclideansubspacefactory(E, proj, dim)
% Returns a manifold struct to optimize over a subspace of a linear manifold
%
% The factory produces a manifold description M for a linear subspace S of
% a linear space E.
%
% Points and tangent vectors on M are represented in memory in exactly the
% same way as the... |
b22617a472fc2d9a5a99bdd1b7f3edab7800e7e69d8cd9b7a17ccd0fe32d8eb6 | MATLAB | 5,615 | 174 | %=============================================================*
% *
% run_1D_ST.m *
% Version: 1.2 (created on 11 June 2020) *
% AUTHORS: A.M. LaPole, M.J. Colebank, M.U. Qureshi, *
... |
efe90839b372afbd19298c71c95d774963d7b1a58ad253d54ecb6b0b2aa1a5d1 | MATLAB | 5,616 | 144 | function TS_CheckTimeSeries(whatData,whatID,doParallel)
% TS_CheckTimeSeries checks calculation of feature values for a given time series
% Specify the hctsa data file, and the ID of the time series to check against
% the operations.
%
%---INPUTS:
% whatData, the data to use (cf. TS_LoadData)
% whatID, the ID of the ti... |
29decd3c9e1dee98b76242c6b03be03df8e0fde1ca5875a6edfa0c2f595d897c | MATLAB | 5,618 | 180 | function [cognitiveX,BVstimProt,standardIndexSequence,hirf_ms]=generateCognitiveModel_fastButTrialsNeedToStartOnVols(sequence,stimDur_ms,trialDur_ms,nTRvols_final,TRvol_ms,nSkippedVols,monitor,scaleTrialResponseTo1)
% this function generates a design matrix of hemodynamic response
% predictors from a condition sequenc... |
aa6b653768ba0ae6bde38a6a2eb5d564e3921feae290ffeaafc6964b3336ba1a | MATLAB | 5,618 | 173 | function Calls=SqueakDetect(inputfile,networkfile,fname,Settings,currentFile,totalFiles,networkname)
% Find Squeaks
Calls = table();
h = waitbar(0,'Initializing');
% Get the audio info
audio_info = audioinfo(inputfile);
if audio_info.NumChannels > 1
warning('Audio file contains more than one channel. Detection w... |
519518e22cf89b36bbdd992bf8a8f549c5fbc2b02907d8f830eecb492a41fa15 | MATLAB | 5,620 | 146 | function userOptions = defineUserOptions()
%
% projectOptions is a nullary function which initialises a struct
% containing the preferences and details for a particular project.
% It should be edited to taste before a project is run, and a new
% one created for each substantially different project (though the
% op... |
6d6fa869bd58028ab7a060c323dd4727419c60f1faf619811672f21eb2a06c6c | MATLAB | 5,621 | 147 | function userOptions = defineUserOptions()
%
% projectOptions is a nullary function which initialises a struct
% containing the preferences and details for a particular project.
% It should be edited to taste before a project is run, and a new
% one created for each substantially different project (though the
% op... |
ee2ecd76e69d21b525267823289083196f8a9de6ead1f4ab0ee623dd724aa794 | MATLAB | 5,622 | 172 | % EEG_DECODECHAN - given an input EEG dataset structure, output a new EEG data structure
% retaining and/or excluding specified time/latency, data point, channel,
% and/or epoch range(s).
% Usage:
% >> [chaninds chanlist] = eeg_decodechan(chanlocs, chanlist);
%
% Inputs:
% chanlocs ... |
02bbe7f5756fe4fffbe31fc5dbf02d8ec578d1b8953b9eebacaee5a7d78aaf75 | MATLAB | 5,623 | 153 | % Script demo_segment
% Illustrates usage of segment for 3D and 4D images, and the additional
% parameters available in the batch editor
%
% demo_segment
%
%
% See also
% Author: Saskia Bollmann & Lars Kasper
% Created: 2019-12-01
% Copyright (C) 2019 Institute for Biomedical Engineering
% Uni... |
5606f46a520da0754a49f252c77a042d56a0d14e45b0bd0c24a6324f1a98f3cb | MATLAB | 5,623 | 157 | function c = tapas_hhmm_config
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Contains the configuration for the hierarchical hidden Markov model (HHMM)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Th... |
62c40ac3ae6b36bbfdd520384a25ebd542e0a86252598253648416d7dbee73af | MATLAB | 5,628 | 122 | function [fname_spikes,fname_events] = cellid2fnames(cellid,filename,CSC_chan)
%CELLID2FNAMES Convert cell IDs to data file names.
% [FNAME_SPIKES, FNAME_EVENTS] = CELLID2FNAMES(CELLID) returns spike data
% and event filenames for CELLID.
%
% [FNAME_SPIKES, FNAME_EVENTS] = CELLID2FNAMES(CELLID,FILENAME) uses
% ... |
02f078c4b7075e6e6e43cc038545278ad90d16b9bf1724bb3d397d59321aa23f | MATLAB | 5,629 | 140 | function [bandwidth,density,xmesh,cdf]=improvedSJkde(data,n,MIN,MAX)
% Reliable and extremely fast kernel density estimator for one-dimensional data;
% Gaussian kernel is assumed and the bandwidth is chosen automatically;
% Unlike many other implementations, this one is immune to problems
% cau... |
05bae8f58a2cd2788461acda4092550e715a48803314a26225cb1fd1a3ed00ec | MATLAB | 5,629 | 183 | function f = DBGetFigures(query,varargin)
%DBGetFigures - Get all figures that match given criteria.
%
% Open figures and get related information such as code used to generate them.
%
% USAGE
%
% f = DBGetFigures(query,<options>)
% f = DBGetFigures(figures,<options>)
%
% query optional figure list q... |
09ac0372f08352fb4330f1a549a2da3e527a1f43ac94482098138c8fd0911170 | MATLAB | 5,630 | 174 | %=============================================================*
% *
% run_1D_ST.m *
% Version: 1.2 (created on 11 June 2020) *
% AUTHORS: A.M. LaPole, M.J. Colebank, M.U. Qureshi, *
... |
700315131b39cfcd764a4ee049ff56983a42a6c45747bd3c74b335fddde2a18f | MATLAB | 5,632 | 145 | function [ons_secs, outliersHigh, outliersLow, verbose] = ...
tapas_physio_correct_cardiac_pulses_manually(ons_secs, thresh_cardiac, ...
verbose)
% this function takes the onsets from ECG measure and controls for
% outliers (more or less than a threshold given by a percentile increased
% or decreased by upperTr... |
290e60fdcaf04d0a78d59f6753e8fc92144ef94fa6a2b9d2b81bfdbe4253e859 | MATLAB | 5,634 | 144 | % BIDS_IMPORTEVENTFILE - create EEG.event from events.tsv and optionally events.json files
%
% Usage:
% [EEG, ~, ~, ~] = bids_importeventfile(EEG, eventfile, 'key', value)
%
% Inputs:
% 'EEG' - [struct] the EEG structure to which event information will be imported
% 'eventfile' - [string] path to the event... |
9693f6cbf6f50a81372d9d78a5b0870e4b8e20ce54015144a716c6f76273d911 | MATLAB | 5,635 | 196 | function out=icassoGet(sR,field,index)
%function out=icassoGet(sR,field,[index])
%
%PURPOSE
%
%Auxiliary function for obtaining various information from the
%Icasso result data structure. Using icassoGet, you can return
%information related to original data, e.g.: data matrix,
%(de)whitening matrix, total number of es... |
7da3eea8ccbc87f3bc7f5105e79243ed3c3aad9ef9681d45f567a6ae799cc657 | MATLAB | 5,636 | 127 | % IMAGESCLOGLOG - make an imagesc(0) plot with log y-axis and
% x-axis values
%
% Usage: >> imagescloglog(times,freqs,data);
% Usage: >> imagescloglog(times,freqs,data,clim,xticks,yticks,'key','val',...);
%
% Inputs:
% times = vector of x-axis values (LOG spaced)
% freqs = vector of y-axis value... |
9e686055399a8d1ce856130e5488d02e0d0a577bb748d2b5fb4e096cec3f2008 | MATLAB | 5,636 | 201 | function [cl,han,surfhan] = plot_points_on_subcortex(DB,name,colors,condf, varargin)
% [cl,han,surfhan] = plot_points_on_subcortex(DB,name,colors,condf, varargin)
%
% Extract and plot points for specific structure/structures.
%
% name input specifies structure to extract and plot on. Can be:
% - 'brainstem-thalamus', ... |
baa379bbbb63f0ba11fa3fb09d1ac2d9a99a1a9cb5d9b2b785573a7815477534 | MATLAB | 5,636 | 147 | %% |nanimresize| documentation
% The |nanimresize| function resizes an image using the Image Processing toolbox function
% |imresize|, but first fills NaNs to prevent missing data along NaN boundaries.
%
%% Requirements
% This function requires Matlab's Image Processing Toolbox. This function
% includes <http://www.... |
cbd75c76c9641c564c6bd69ed5c3846151335af0b0e1418af7c96653f287e98b | MATLAB | 5,636 | 131 | % STD_READTOPOCLUST - Compute and return cluster component scalp maps.
% Automatically inverts the polarity of component scalp maps
% to best match the polarity of the cluster mean scalp map.
% Usage:
% >> [STUDY clsstruct] = std_readtopoclust(STUDY, ALLEEG, clusters... |
04b5898dddef274e353d9ed55ed72c36d6051e103bc6c7365de804af35645833 | MATLAB | 5,638 | 163 | function diffStats = simplenn_caffe_compare( net, caffeModelBaseName, testData, varargin)
% SIMPLENN_CAFFE_COMPARE compare the simplenn network and caffe models
% SIMPLENN_CAFFE_COMPARE(NET, CAFFE_BASE_MODELNAME) Evaluates a forward
% pass of a simplenn network NET and caffe models stored in
% CAFFE_BASE_MODELNAM... |
5aca0e0f112e6366c0fc29581e3fa4b57d96a033b56f5555c9fd454a9ea33c8e | MATLAB | 5,641 | 130 | function out = SB_BinaryStats(y, binaryMethod)
% SB_BinaryStats Statistics on a binary symbolization of the time series
%
% Binary symbolization of the time series is a symbolic string of 0s and 1s.
%
% Provides information about the coarse-grained behavior of the time series
%
% ---INPUTS:
% y, the input time serie... |
ac491ec72f6dbb5d7a3654c3b0862856c93c31428660aa95a9cc424e01370977 | MATLAB | 5,641 | 153 | % POP_EVENTSTAT - Computes and plots statistical characteristics of an EEG event,
% including the data histogram, a fitted normal distribution,
% a normal distribution fitted on trimmed data, a boxplot, and
% the QQ-plot. The estimates value are printed in a panel a... |
6fc11fa74d0f94cedd3ac8a8376fb2b9384e884b08917c597dac65cbc1e58ad6 | MATLAB | 5,645 | 169 | % EEG_LAPLAC - gives the laplacian for the data contained in EEG
% for the values 1:stepl:end with electrodes position given by EEG.chanlocs.
% Step must be a number between 1 and length(EEG.data)
% The method used for computig the laplacian is the described by Perrin et al.
% 1989 using a spline interpolation betwee... |
b1d766c55f274bb4df570217d260ec585ffe0fcb573a9d0f17a764ff7a6cd5fd | MATLAB | 5,645 | 168 | function this = init_processing_step(this, module, varargin)
% initializes next processing step by creating folders for version tracking,
% shuffling data, and updating processing parameters
%
% MrSeries = init_processing_step(MrSeries, module)
%
% This is a method of class MrSeries.
%
% IN
% module 'realign',... |
f102b07a058b7e06a3287e6caf86317601a231f0e24bdb25d3021a3d521a03ba | MATLAB | 5,649 | 180 | function [pos,unit]=getpos(h,fmt,href,opt)
% GETPOS Get graphics object position in a flexible way.
% GETPOS(H,FMT) gets the position property of graphics object
% with handle H, according to FMT that can be expressed using different
% units. H must have a "Position" property.
%
% FMT is a char array con... |
d5ae8a99992535f182e78694dd2e16b5671e336a52fc65a507d0cb3bf19cf6c1 | MATLAB | 5,650 | 143 | function [] = plot_basic(xvals, yvals, name, pathstr)
%% plot_basic plots worm tracks as cm values without any gradient information
%% Make a plot with all the tracks, then save it.
global info
fig = DrawThePlot(xvals, yvals, name);
movegui('northeast');
ax=get(fig,'CurrentAxes');
setaxes = 1;
while setaxes>0 % loop... |
74a55d696d56f99139abe8bcb5d5a25892f0f1edeb2aeedba952e5de21a410db | MATLAB | 5,654 | 159 | function [U, cost] = robust_pca(X, d)
% Computes a robust version of PCA (principal component analysis) on data.
%
% function [U, cost] = robustpca(X, d)
%
% Given a matrix X of size p by n, such that each column represents a
% point in R^p, this computes U: an orthonormal basis of size p by d such
% that the column s... |
43423a36816c8b337d50ddb8336cdf4616e0f6528b92084f03735709ba5a5a29 | MATLAB | 5,660 | 145 | function [MRSCont] = OspreySettings
%% [MRSCont] = OspreySettings
% This function initialises default settings and variables required to
% run Osprey.
%
% USAGE:
% [MRSCont] = OspreySettings;
%
% OUTPUTS:
% MRSCont = Osprey MRS data container.
%
% AUTHOR:
% Dr. Georg Oeltzschner (Johns H... |
88e92f8397677e24ffcf4ec7a8b4606308c3cdf251085ef28ca164aa24c649f9 | MATLAB | 5,661 | 147 | function [meg] = read_ctf_meg4(fname, hdr, begsample, endsample, chanindx)
% READ_CTF_MEG4 reads specified samples from a CTF continuous datafile
% It neglects all trial boundaries as if the data was acquired in
% non-continuous mode.
%
% Use as
% [meg] = read_ctf_meg4(filename, hdr, begsample, endsample, chanindx)
... |
276e18e999ddd981e12a0f64d024181eecedee39b59d4db86954ec58b5ee7f21 | MATLAB | 5,662 | 153 | function download_atlas()
% Cross-platform (Windows/macOS/Linux) atlas downloader - replaces
% download_atlas.sh, which cannot run on Windows at all (no bash) and is
% unreliable on macOS (its `readlink -f` call depends on a GNU coreutils
% flag BSD/macOS readlink doesn't support).
%
% Downloads the CIT168, MuSus-100 a... |
1a1e2f3cdd14577ee80891ddaef939fc71e7143bbb3aa3e9351dca64d7752571 | MATLAB | 5,665 | 189 | function M = fixedrankfactory_2factors_preconditioned(m, n, k)
% Manifold of m-by-n matrices of rank k with two factor quotient geometry.
%
% function M = fixedrankfactory_2factors_preconditioned(m, n, k)
%
% This geometry is tuned to least-squares problems such as low-rank matrix
% completion with ell-2 loss.
%
% A po... |
966146028a19b3df850dc425c82cde5e57941d5008a2acde165e0f71962f92f1 | MATLAB | 5,666 | 202 | function [] = main(analysisName, jobID, testRun)
% test run = false by default
if nargin<3
testRun=false;
end
% add filepaths to matlab search path
paths = addPaths();
% create output directory
if ~exist(paths.outputs, "dir")
mkdir(paths.outputs)
end
% get configurations
config = getConfig(analysisName, tes... |
7efbdbf50f412740fb877dc78ac4f03bc2a8c0e9bddd456bc165da12ba88040a | MATLAB | 5,670 | 187 | function M = poincareballfactory(k, n, gpuflag)
% Factory for matrices whose columns live in the Poincare ball manifold
%
% function M = poincareballfactory(k)
% function M = poincareballfactory(k, n)
%
% Manifold of k-by-n real matrices whose columns live in the Poincare ball.
% By default, n = 1, which corresponds to... |
1b845b76d653a6051ce2eef528bf90094e95054e97d0afa558fdc8d00ba123b0 | MATLAB | 5,672 | 137 | function [k_fft2_wat_ref, k_fft2_wat_ref_no_k_zfill, k_sort_b4_2dfft] = process_wat_ref(this_file, k_zfill, seq_type)
fprintf('\nReading water scan parameters.')
[data] = loadRawKspace(this_file);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Determine dimensions of the acquisition
%%%%%%%%%%%%%%%%%... |
78f8c38b1088892101e35fc403dbb1d916d8e3640d4ff45a7de13e1a9f4fe208 | MATLAB | 5,673 | 149 | clear; clc;
morph_path = '/oak/stanford/groups/kalanit/biac2/kgs/projects/babybrains/mri/code/morphology_allparameters/';
addpath(morph_path)
set_participant_information
hemi= 'lh';
Correl_R1=[]; Correl_CT=[]; Correl_CU=[];
R1_data=[]; CU_data=[]; SD_data=[]; CT_data=[];
ALL_profiles_SD = []; ALL_profiles_CT = []; A... |
6285724d727022aa3a494605a48c9a752919624de0ce7668af6725712b1e38ec | MATLAB | 5,674 | 178 | function plot_brain3D_wrapper(params, vals, plotInfo)
% plots iEEG channel activations on 3D transparent brain model
% (c) Jiri, Jan17
%% color maps
clrmap.brain = gray(128); % colormap for brain (T1, T2, CT, ...)
if isfield(params.plot_brainTopo, 'colorMap')
clrmap.chnls = params.plot_b... |
73c7bf093e94b0422efa7112592f0ed87685bd13ca19becc59a519a139cb444f | MATLAB | 5,679 | 186 | function scatter_hsi(pts_2d,stride,hsi_img,rgb_img,wvl)
%
% utility to scatter plot 2d data points that correspond to
% pixels in an hsi image
%
% clicking on the scatter plot highlights the closest data point in the
% scatter plot and in the rgb image and plots the pixel's spectra,
% clicking on the rgb image highlig... |
1a50f856e23d7aa157eb0159d3a683a50508c73beb36148752986a0d0b1ca077 | MATLAB | 5,682 | 167 | classdef (Abstract) Environment
% Environmental dynamical system to be modelled by reservoir.
properties (Abstract)
D % system dimension
Ranges % range lengths and lower limits of system variables
Params % ODE parameters
H %... |
c24cec3c60ece197b96f5a7517726088c28073531f562e64ec877eff702f38bf | MATLAB | 5,682 | 140 | function [type] = ft_headmodeltype(headmodel, desired)
% FT_HEADMODELTYPE determines the type of volume conduction model of the head
%
% Use as
% [type] = ft_headmodeltype(headmodel)
% to get a string describing the type, or
% [flag] = ft_headmodeltype(headmodel, desired)
% to get a boolean value.
%
% For EEG the ... |
d71ca0228edcd8d66f526bbe51575d9998438d68621233140111f798835626b6 | MATLAB | 5,683 | 130 | %% pruneRunAll
% Script which calls pruneGetVals for specifed pruning method (saves
% having to repeat in every iteration of the preprocessing pipeline)
% whilst saving the .nirs files
%
% SLB 15/2/24
clear; close all;
%% Add relevant toolboxes to current path
% Underneath parameter settings for ease of access to ch... |
8a7d1c941690d454f076827e1eb69a6a4c53c6107213329bbcf09cfc9b3d9b1c | MATLAB | 5,684 | 144 | clear all
global clut2b timetracesX_X ROI_map_X movie_AVG_X
load clut2b
% load list of files
% cd distorted
FileList_0 = dir('Sag_Pos3_1-51_001*_.tif');
% cd ..
FileList = FileList_0;%dir('OB_4planes_paradigm1*_undistorted.tif');
FileListX = FileList;
% for k = 1:numel(FileList)
% FileList(k) = FileListX(numel(File... |
0152dee9a0b15b90923285eb1b628761c342a0764416f53864c35ff4f33d8d93 | MATLAB | 5,686 | 148 | function out = EN_SampEn(y, M, r, preProcessHow)
% EN_SampEn Sample Entropy of a time series
%
% SampEn(m,r), using code from PhysioNet.
%
% Uses a compiled C version of the code if available, otherwise uses a (slower)
% Matlab implementation (which can actually be faster for shorter time series
% due to overheads ... |
19925378fe14cfb2661db2b07791c6f0fc02fad87d4e9e6bae3f64d95eea6aea | MATLAB | 5,687 | 147 | %% %%%%% transfer all current ROIs to fsaverage
files = {'floc-places'};
hemis = {'lh' 'rh'};
vals = []; % V x hemis x 8 x quantities
for ff=1:length(files)
for subjix=1:8
for hh=1:length(hemis)
a5 = cvnloadmgz(sprintf('~/nsd/nsddata/freesurfer/subj%02d/label/%s.%s.mgz',subjix,hemis{hh},files{ff}));
... |
cf0ab2c65059ec75b535ca03607799e86b99e4fac574e612c306c3872b08e9ad | MATLAB | 5,689 | 151 | function [X, y] = generateEventClassifierDataset(tank_location, timewindow, timewindow_bin, kernel_size, kernel_std)
%% generateEventClassifierDataset()
% generate dataset for event(head entry, avoid, escape) classifier
% tank_location : string. location of tank
% timewindow : [TIMEWINDOW_LEFT(ms), TIMEWINDOW_RIGHT(ms)... |
ec0dc47d0e5177c01322065c558144590afdc93e498ee4c61565e200e7bfa6b8 | MATLAB | 5,690 | 168 | function idx2 = get_spike_pos(input_sig, fs, orig_sig, params)
% get_spike_pos computes spike positions from thresholded data
%
% This function computes the exact spike locations based on a thresholded
% signal. The spike locations are indicated as non-zero elements in
% input_sig and are accordingly evaluated.
%
% The... |
ba3bbae28871c7b28d1a967afa7e9788d689da523b700be730dc11851035cf1b | MATLAB | 5,691 | 127 | function dendrogramConditions(RDMs, userOptions, localOptions)
% Will generate a text-labelled dendrogram for each RDM in RDMs.
%
% dendrogramConditions(RDMs, userOptions[, localOptions])
%
% RDMs --- The RDMs to be operated on.
% RDMs is some kind of struct containing RDMs. It can be of
% ... |
ae66362b17ebd1c0cfd4f0749d75a3b318460c37c87814bccfb0c0055d95b932 | MATLAB | 5,693 | 182 | function runQAMPERBatch(batchStruct) %,csv_outdir)
batch_id = batchStruct.batch_id;
DWIstruct = batchStruct.DWIstruct;
% userCachePath = setUserCache;
% batchPath = [userCachePath filesep num2str(batch_id)];
batchPath = fullfile(batchStruct.currentNiiPath,num2str(batch_id));
csv_outdir = batchPath;
if ~exi... |
b62e0cae7be68236a348c5caec634766552a2eabe22b034ecca3536dbdad9289 | MATLAB | 5,699 | 90 | % Specialized analyses for FMAToolbox.
%
% Firing map and curves, etc. (place cells, grid cells, head direction cells).
%
% FiringCurve - Compute spatial firing curve (e.g. for a head direction cell).
% FiringMap - Compute spatial firing map (e.g. for a place cell).
% PhaseCurve ... |
a29c7221f321c4a834a33fb14933e87019298d8a75cda4055277607ba10cd2b1 | MATLAB | 5,701 | 189 | function [c, r, t, cpulse, acq_codes] = tapas_physio_read_physlogfiles_biopac_mat(log_files, ...
cardiac_modality, verbose)
% reads out physiological time series (ECG, PMU, resp belt) and timing vector for Biopac .mat
% files
%
% [cpulse, rpulse, t, c] = tapas_physio_read_physlogfiles_GE(logfiles, ...
% ... |
cfe2d8cda4276b018a2def456d89284598f64f126d56624e46a2c09873f51a87 | MATLAB | 5,701 | 136 | function hlp_worker(varargin)
% Act as a lightweight worker process for use with hlp_schedule.
% hlp_worker(Options...)
%
% Receives commands (string expressions) from the network, evaluate them, and send off the result to
% some collector (again as a string). Processing is done in a single thread.
%
% In:
% Options... |
e533405a442dfcba1a5f8277994324a22aa7c844aa529aca53bf4d71f8819613 | MATLAB | 5,702 | 177 | function [c, r, t, cpulse, acq_codes] = tapas_physio_read_physlogfiles_philips(log_files, cardiac_modality)
% reads out physiological time series and timing vector depending on the
% MR scanner vendor and the modality of peripheral cardiac monitoring (ECG
% or pulse oximetry)
%
% [c, r, t, cpulse] = tapas_physio_read... |
837edffdf77e8fcc078491d3fd9727ed22c005f083cb69a182a103c034e7e09f | MATLAB | 5,703 | 136 | function [ons_secs, verbose] = tapas_physio_read_physlogfiles(log_files, cardiac_modality, ...
sqpar, ons_secs, verbose)
% reads out physiological time series and timing vector depending on the
% MR scanner vendor and the modality of peripheral cardiac monitoring (ECG
% or pulse oximetry)
%
% [ons_secs, verbose] = ... |
e34ae87f4f3ef2a63c0a80a4aa9c885c3dbc47f0691c11531a29d135ce4161f8 | MATLAB | 5,704 | 139 | %% Create Dataset
function [vals_PPIX_all, vals_PPIX_visible, vals_background_all, vals_all, ...
vals_PPIX_all_test, vals_background_all_test, vals_all_test, labs_test, ...
features_region3, tsne_data, tsne_labs] = FD_clVAE_CreateDataset(data_path)
%% Load Data
liquid1 = imread(fullfile(data_path, 'liq... |
09f4d655f0b7b6fdb53f7663ef8889304b97f8e9ec0d44ea42e237a3d5440a6f | MATLAB | 5,709 | 227 | function R=surfing_suma_surfacefiles(specfn,trgdir,cpmethod)
% Finds AFNI SUMA surface files, and optionally copies them to another
% directory.
%
% [R]=SUMA_SURFACEFILES(SPECFN[,TRGDIR,CPMETHOD])
% INPUTS:
% SPECFN: SUMA .spec file; or if a directory is given, then all .spec
% files in that direc... |
095fb9c1fa15e72d9036aaa1a282f275f78f0b436b81cd5f55bf9673d1bc2ec8 | MATLAB | 5,715 | 107 | classdef McsCmosRecording < handle
% Stores a single recording for HDF5 files produced by the CMOS-MEA
% software
%
% The different data sources present in the file are represented by the
% different properties of this object. Typically, a file generated by
% CMOS-MEA-Control will only contain an Acquisition grou... |
ee3659b08fd14d8715e3dfb8410c022d3f3130c00dd747adf4dc47d0be067536 | MATLAB | 5,716 | 148 | %% WILL NOT WORK EXCEPT FOR CELIAN, ONLY AS A BACKUP
%% Get data
load('\\znas.cortexlab.net\Lab\Share\Celian\dataForPaper_ChronicImplant_stability_withQM_2024-11-08');
%% Define the rest
recInfo = cellfun(@(x) split(x,'__'),recLocAll,'uni',0);
subjectsAll = cellfun(@(x) x{1}, recInfo, 'UniformOutput', false);
probeS... |
94cfd34962d8aef66efbd7af531106c26dd6af7fd8df04ae45e50cd7c86d7ae0 | MATLAB | 5,718 | 189 | function r = tapas_sampleModel(inputs, varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Samples prior values from the prior provided in the configurations of the perceptual and
% (optionally) the response model and returns the implied belief trajectories... |
c530a4a26be834ec47f339a6d8a22f662f23d4e04eaa2145522ff9c4fd1fc889 | MATLAB | 5,718 | 187 | function [final_positions, overlap, fvf_historic] = process_packing(x0, d, gap, side, iter_max, iter_fvf, resolution)
% author : Tom Mingasson
% function that create the packing i.e disk migrations from intial positions
disp(' ')
disp('Packing in process...')
disp(' ')
N = length(d);
fvf_historic = [];
x = x0;
progr... |
8ce346155b733d9898666f5eac4789d0514efb1e07850a3972d865d6ca9ee57d | MATLAB | 5,725 | 145 | function [s, cfg] = ft_statfun_indepsamplesT(cfg, dat, design)
% FT_STATFUN_INDEPSAMPLEST calculates the independent samples T-statistic
% on the biological data in dat (the dependent variable), using the information on
% the independent variable (ivar) in design.
%
% Use this function by calling one of the high-lev... |
212af970fb015eeea36861757a6cbebe0619d5a5667d8c7b675fd70e47c15106 | MATLAB | 5,726 | 151 | function [events, ECG_min, kRpeak] = tapas_physio_find_ecg_r_peaks(t,y, ECG_min, kRpeak, inp_events)
% finds ECG-R peaks in a timecourse, if MR-scanner detection failed (esp. at high field >= 7 T)
%
% USAGE
% [events, ECG_min, kRpeak] = tapas_physio_find_ecg_r_peaks(t,y, ECG_min, kRpeak,
% inp_events)
%
% Give... |
e970ceff299a233e2ff8e0543db1818531f4db6562782fd5f076743065d6f764 | MATLAB | 5,726 | 156 | function [ data ] = nmri_parse_stimuli( subject, data, params )
% will parse the info_ markings (from subject) to estimate trial-based
% stimuli markings
%
% Implemented for
% Augen auf / zu
% HV Beginn / End HV
% End HV / Post-HV 90 Sek
% ?? Hz / Aus
% call the subject and params include
nmri_include_read_ps
%% Get... |
7cddbd1bc456dbeaa4303680b44167b924bc9ec86a741835d8b511ebac829d2f | MATLAB | 5,728 | 168 | function [P,Label]=DiffAnalysis(op,file,molec,model,ds,M,S0,U,UT,RTI,radius,ax,NumAnalysis,fit)
[color, MOLEC] = colorcodefunction (model, molec);
%Define axes units and labels
xlabstring=['Time [' UT ']'];
ylabstring = [molec ' [' U ']'];
str=[model ' Simulation'];
p=gobjects(1,7... |
a1b0717918923bc21bb06d347c0e50f962a1082031cc7bc7fac5151e694205fd | MATLAB | 5,728 | 135 | % Script demo_save
% Shows how to save (image) data to one or multiple files (split!)
%
% demo_save
%
%
% See also
% Author: Saskia Bollmann & Lars Kasper
% Created: 2016-09-22
% Copyright (C) 2016 Institute for Biomedical Engineering
% University of Zurich and ETH Zurich
%
% This file is part... |
bbad37d917f9e7a51f0291f1f5218acf601000f5a2aff9d2c22275e6d36de43c | MATLAB | 5,730 | 149 | function [Y,Info_all,proc_paths] = inscopix2mat(isx_file_names,varargin)
%% input movies should be of the same size!
spatial_ds_factor = 1; temporal_ds_factor = 1; dcrop = [];
crop_x_offset = 0; crop_y_offset = 0;
Y = []; save_path = [];
num_planes = 1; get_info_only = 0;
for v = 1:numel(varargin)
if strcmpi... |
298bd6389a2ab1f5a875da4393b1ebcd4af6de203b19812d7eb315cb9365e545 | MATLAB | 5,731 | 107 | function [pnt, tri, srf] = read_bv_srf(filename)
% READ_BV_SRF reads a triangulated surface from a BrainVoyager *.srf file
%
% Use as
% [pnt, tri] = read_bv_srf(filename) or
% [pnt, tri, srf] = read_bv_srf(filename)
% Copyright (C) 2005, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtr... |
e2afb34edfcd607365ba3d8a47574d49861032fee0aa7eae3eba4126a96a341b | MATLAB | 5,736 | 143 | function [pulseCleanedTemplate, pulseTemplate, verbose] = tapas_physio_get_template_from_pulses(...
c, cpulse, halfTemplateWidthInSamples, verbose, varargin)
% Computes mean pulse template given time stamp of detected pulses and raw
% time series; removes outlier pulses with correlation to initial guess of
% mean ... |
db7af13b7f4c981c2ba61671dcc6d34aa8485011d15580c20c71de3766dde639 | MATLAB | 5,738 | 172 | function this = read_gifti_file(filename, this)
% Low level reader of GIfTI 1.0 files
% FORMAT this = read_gifti_file(filename, this)
% filename - XML GIfTI filename
% this - structure with fields 'metaData', 'label' and 'data'.
%__________________________________________________________________________
% Cop... |
f31a40585d60fec57003e831da4edbe90572c88396f2593dbbc79f6ead4ec960 | MATLAB | 5,739 | 167 | % EEG_MERGELOCS - merge channel structure while preserving channel
% order
%
% >> mergedlocs = eeg_mergelocs(loc1, loc2, loc3, ...);
%
% Inputs:
% loc1 - EEGLAB channel location structure
% loc2 - second EEGLAB channel location structure
%
% Output:
% mergedlocs - merged cha... |
d4baf0bc1b884720dfe7305bfd790e8a9e517345f02c49da5fd5a65edecb1b8a | MATLAB | 5,742 | 161 | % POP_SIGNALSTAT - Computes and plots statistical characteristics of a signal,
% including the data histogram, a fitted normal distribution,
% a normal distribution fitted on trimmed data, a boxplot, and
% the QQ-plot. The estimates value are printed in a panel a... |
1edc3ee288dc533537710b18647f9006e6892794bef678f3d70b7199a229f096 | MATLAB | 5,743 | 156 | %% function [chi, lambdaOptimal] = qsmClosedFormL2(localField,mask,matrixSize,voxelSize,varargin)
%
% Description: compute QSM based on closed-form solution
% Ref : Bilgic et al. JMRI 40:181-191(2014)
% : Bilgic et al. MRM 72:1444-1459(2014)
%
% Input
% -----
% localField : local field perturb... |
09d08c00ebecd065b59cc081146c9da38490160a1e63ccc0123d26c31b2988e6 | MATLAB | 5,744 | 157 | function [f,J,D] = tapas_ceode_fx_erp(x,u,P,M, xtau)
% [f,J,D] = tapas_ceode_fx_erp(x, u, P, M, xtau)
%
% Computation of the dynamical (state) equation for a neural mass model
% (ERP model). Compatibile with continuous extension for ODE
% methods. Adapted from spm_fx_erp.m (original function license below).
% Function... |
c5f5b9cbc45c2928711e15365163912e1e9d30f11b2e6798d7f3545cbe2c937f | MATLAB | 5,745 | 198 | addpath(genpath(pwd));
clear; clc; close all;
% set the info of data
% global path
path = fullfile('./', 'data', './');
neuron = {'Or42a'};
title_str = 'Or42a-10-73pentanol';
% set the parameters about the filters
lfilter = 937; %30s, at the time resolution of 32ms.
lunstable = 1900; %depend on the output data.
r... |
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