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b2712ca7703b53330137ee078330754fa16957e3111924687a2a375c9b5b743a
MATLAB
528
18
function [I_Kr, dP_a, dP_i] = fast_delayed_rectifier_k(V, P_a, P_i, E_k) g_Kr = 3.5; % Condactance of the fast delayed rectifier k+ [nS] I_Kr = g_Kr.*P_a.*P_i.*(V - E_k); alpha_p_a = 9.0.*exp(V./25.371); beta_p_a = 1.3.*exp(-V./13.026); p_am = 1./(1 + exp(-(V + 5.1)./7.4)); tau_p_a = 1./(alpha_p_a + beta_p_a); dP_a =...
e68b022fa176bfcd12ebf2b26c941e87b344c5cdca666cb2389cfe8675f8dedb
MATLAB
528
24
function transformByuLinearXfm ( in_byu, in_xfm, out_byu, invertXfm) %Given xfm that takes images from A to B, takes a surface from A to B T=importdata(in_xfm); if (exist('invertXfm')) T=inv(T); end [faces,vertices]=readTriByu(in_byu); transformed=inv(T)*[vertices';ones(1,length(...
81e06b34414c98e675c9810b2405e019bc3145a1f84fa156eb7f03b9a633061e
MATLAB
532
45
function [ROI INCLUDE] = fb_clean_roi(ROI) % % % nrois=length(ROI.coordinates); counter=1; nrois=length(ROI.coordinates); TO_DEL=[]; % find matches nmatches=1; roi=ROI; idx=1:nrois; while nmatches>0 nmatches=0; nrois=length(ROI.stats); pairs=nchoosek(1:nrois,2); for i=1:size(pairs,1) x=pairs(i,1); ...
a19253f22448be4e6de76693c58ce5eec116b256bef047eba501787bb83375a0
MATLAB
532
21
function [d] = subsetNested(d,select,dims) %subsetNested Select from particular indices of particular dimensions % Operates on matrices or structures containing matrices d = doSubset(d,select,dims); end function [x] = doSubset(x,select,dims) if isstruct(x) f = fieldnames(x); for ii=1:length(f) ...
502fdaf87437c303e1c0e784ca6271133565473d1f63e13c18c56a5bf13ffed6
MATLAB
534
18
function plotSave(plotHandle, condition, savePath, dim, plotLegend) if ~exist('plotLegend', 'var'); plotLegend = 0; end set(plotHandle, 'HandleVisibility','on'); width = dim(2); % 10 % Width in inches height = dim(1); set(gcf,'InvertHardcopy','on'); set(gcf,'PaperUnits', 'centimeters'); papersize = get(gcf, 'Pa...
b5272e2c30ee479a64c0910a09c606907711413f934d081c536eb6bb431faad0
MATLAB
534
15
function delete_raw_and_bin_NA_kilosort2(output_dir, do_delete_NA_raw_files) % Delete temporal files - Cleaning the data after the run ks_output_dir = fullfile(output_dir, 'ks_output'); if do_delete_NA_raw_files try delete(fullfile(output_dir, 'raw_*')); delete(fullfile...
e8a36804c83fcace580a0891eaea5ddd279e652f6cef271290732d52fdf081e5
MATLAB
535
19
function [label_dir] = natsort_label_dir(input_label_dir) % load_label_natsort - arrange image files of image directory based on natural order % input: % input_dir : a string of label directory % output: % label_dir : natsorted label dir % Written by: % Jiachen, 06/10/2021 % load label images for ground...
50e5f1569eff6ffe5760564317f04dfaa062f9ab71f3156e81f7434d3fda529f
MATLAB
537
25
function plot_2bars(data, SD, ylabel_string, ylimit) number_subjects = size(data,1); figure ax = axes; bar(1, mean(data(:,1)), 'k'); hold bar(2, mean(data(:,2)), 'r'); %Plot confidence intervals for i=1:2 plot([i,i], [mean(data(:,i))-SD/sqrt(number_subjects), ... mean(data(:,i))+SD/sqrt(number_subjects)]...
58aa522953ecefbcd3644a0e15edff386c9732699673825efdb1ffafbe8782a1
MATLAB
537
16
function val = get(new_signal,prop_name) % GET Get PULSE property from the specified object % and return the value. Property names are: % Name, Signal, Level_comp, STime_comp, ETime_comp, Ramp_comp, Phase_comp, Envelope_list, % Num_of_env, Comp_list, Num_of_comps, Comp_list_str. if isa(prop_name,'char') switch pr...
86feaee943a9932a9a6abc5c1c5f9bd1f7cf67729269e137eb2881b8965f56b2
MATLAB
541
16
function val = get(new_signal,prop_name) % GET Get NEW_SIGNAL property from the specified object % and return the value. Property names are: % Name, Signal, Level_comp, STime_comp, ETime_comp, Ramp_comp, Phase_comp, Envelope_list, % Num_of_env, Comp_list, Num_of_comps, Comp_list_str. if isa(prop_name,'char') switc...
ab71171635ee0912aa9320068d2122147c80e8f3392b4250089faff7ff83324d
MATLAB
546
22
function write_data(out) fid=get(out,'Fid'); d=datestr(now); date_line=['% ',d]; fprintf(fid,'%s',date_line); fprintf(fid,'\n'); meta_data_title=['%% MetaBlock data : %%%%%%%%%%%%%%%%%%%%%%%']; fprintf(fid,'%s',meta_data_title); fprintf(fid,'\n'); meta_data_title2=['%% METADATA FILE VERSION = 2.0 %%%%%%%%%%%%%%%%%%%%%...
b7b706c493b112b7c2542d004883566c6a79d8fd87fe1933821fae447b5a2a9d
MATLAB
548
18
function table = get_session_table(experimenter, year, month) % JN 2019-04-03 [riff_folder, ~, ~] = fileparts(which('main')); log_folder = fullfile(riff_folder, '..', 'session_logs'); if ~isfolder(log_folder) error('Folder %s not found, needed for database mode', log_folder) end % Read session database fname = f...
efb8ac23e6e0494e0b231d813f59ab467152f7e35c90cfed5f4a7fb75f24f7e8
MATLAB
548
16
function flank = set(flank,varargin) % SET Set NEW_SIGNAL properties and return the updated object % Property names are: % Level_comp, STime_comp, ETime_comp, Ramp_comp, Phase_comp,Envelope_list. property_argin = varargin; while length(property_argin) >= 2, prop = property_argin{1}; if ~isa(prop,'char') ...
eb31260fd8b815ee923257f2b87184111bad5a79d60dfbdb5ce19060a0ed03c9
MATLAB
549
16
function flank = set(flank,varargin) % SET Set NEW_SIGNAL properties and return the updated object % Property names are: % Level_comp, STime_comp, ETime_comp, Ramp_comp, Phase_comp,Envelope_list. property_argin = varargin; while length(property_argin) >= 2, prop = property_argin{1}; if ~isa(prop,'char') ...
aa738272258a8f0ad6cb40734f05cf970befb31668f4528d1153e9249c45ecfd
MATLAB
550
16
function val = get(new_signal,prop_name) % GET Get NEW_SIGNAL property from the specified object % and return the value. Property names are: % Name, Signal, Level_comp, STime_comp, ETime_comp, Ramp_comp, Phase_comp, Filename,Envelope_list, % Num_of_env, Comp_list, Num_of_comps, Comp_list_str. if isa(prop_name,'char') ...
b9b7e63d8970dd6fdb3c99a59d965169c6e4fdd66df9232f2a5f076e0f587bcf
MATLAB
552
19
function [Result] = AO_StopSave() % Function to stop saving on the SnR/Neuro Omega %% Result is an integer result of the AO_StopSave, 0 = no function errors %% % Copyright (C) 2011 AlphaLabSnR EthernetStandAlone % Author: Majid Mechael % Last modification: 13/03/2013 Result=MexFileEthernetStandAlone(5); ...
074953ff7fdcbdf91d19a11e96d91297b617bb5732d447be8ad5876f2dea24ed
MATLAB
553
28
function animal_sorted_CeF = extract_animals (CeF) % puts data after the SPL analysis into a format for IQR analysis. Not only % CeF, BF as well CeF_animals = CeF; CeF_animals(:,6) = round(CeF_animals(:,6)/100000); animal_numbers = unique(CeF_animals(:,6)); animal_sorted_CeF = {}; for n = 1:length(anim...
9efecc1882a1eb03e6bcb771fb46e290f5e29fde1bf59a9fe5546bca0c1eba98
MATLAB
553
22
classdef TestClassA < handle %TESTCLASSA Class for testing createObjFromTree() % This class is used on the first layer of a tree struct. It % containts a simple property and an object of TestClassB, which will % represent a second layer. % Author: Lasse Osterhagen properties ...
03ed06a7278587758d6ca6fb6de3351cdf8ef4ca7909635ad2505dea3b986d59
MATLAB
554
19
%% % Generate spike times for the ffwd network %% function [ sF ] = ffwd_spikes(T,rF,NF,NF1) % rF*NF*T is the mean number of spikes that will occur tempspikes=sort(T*rand(poissrnd(rF*NF*T),1)); % Store in the data format expected by the C code, % where neuron indices are assigned randomly sF=zeros(3,numel(tempspikes...
65989852918c7a0f81ff9e874accf1282c8f8fb174ae2a876c2a67938a7a589c
MATLAB
557
19
function [db1YL, dbScale] = NS_PlotLFP(db2LFP, db1Time, dbScale) %Checks number of arguments narginchk(2, 3) %Gets the number of channels inNChan = size(db2LFP, 1); %Sets the scaling between channels if nargin < 3, dbScale = 0.7 * max(range(db2LFP, 2)); end db1YL = dbScale * [-.5 inNChan + 1.5]; %Plots the...
853e4fc96314b977037448852860b15b6097c244657c57aab0778ea05b0a6a4a
MATLAB
557
16
function new_signal = set(new_signal,varargin) % SET Set NEW_SIGNAL properties and return the updated object % Property names are: % Level_comp, STime_comp, ETime_comp, Ramp_comp, Phase_comp,Envelope_list. property_argin = varargin; while length(property_argin) >= 2, prop = property_argin{1}; if ~isa(prop,'cha...
d6d8d097777b0ded7aecc4ad50cb2ef12b479ddd28521303a0a5b0ec8c88ab0c
MATLAB
558
21
% check for button down [xblah,yblah,buttons] = GetMouse(whichScreen); if any(buttons) if ButtonDown==0 numResp=numResp+1; RespT(numResp)=GetSecs; % RespTcopy(numResp)=GetSecs; if buttons(1) RespLR(numResp)=1; disp('Button 1') elseif butto...
ab38e8e548c547f546348e7e3bb354a0af749c0cfc20a63d4bb2737df10e2356
MATLAB
559
23
classdef AscendState < LogbookState %ASCENDSTATE is the state that happens when a subject initialized a trial. % Author: Lasse Osterhagen methods function this = AscendState(evaluator) this@LogbookState(evaluator) end function evaluate(this, ~) nextEvent = this.evaluator.getNextE...
e5d09459f6377e451f81977c4dd2655d8b3d0dea0e1e8d26c8196811ac7eea21
MATLAB
560
16
function data=mAO_getData(ich) global mAO difftime=mAO.mt-mAO.PrevTrig; num_samples=ceil(difftime*mAO.RX8sfreq); t=(1:num_samples)*difftime/num_samples; ft=find(mAO.LFPtime{ich}(1:mAO.LFPind(ich))<=mAO.PrevTrig,1,'last'); if isempty(ft) disp('mAO_getData: wrong start'); end lt=find(mAO.LFPtime{ich}(1:mAO.LFPind(ich...
09c630c69e741d10f2171a1c4fb8a1a0ce1b1ed2fa6cdab0f5cfab02b69144fc
MATLAB
562
16
function new_signal = set(new_signal,varargin) % SET Set NEW_SIGNAL properties and return the updated object % Property names are: % Level_comp, STime_comp, ETime_comp, Ramp_comp, Phase_comp,Envelope_list. property_argin = varargin; while length(property_argin) >= 2, prop = property_argin{1}; if ~isa(prop,'cha...
cf948404aca82473ed97b58f7c5e631b53d6a5367f55d2f074e93c9cc4b8c0f9
MATLAB
563
27
% This function defines the position of the search window function Window_location = Define_SearchWindow(noisyImg, BlockPoint, WindowSize, Blk_Size) point_x = BlockPoint(1); point_y = BlockPoint(2); LX = point_x + Blk_Size/2 - WindowSize/2; LY = point_y + Blk_Size/2 - WindowSize/2; RX = LX + WindowSize; RY = LY + W...
f917abc04d8701e94a5ca768d5d71741445305f54d4eaf12890db8a5c557116e
MATLAB
565
16
function new_signal = set(new_signal,varargin) % SET Set NEW_SIGNAL properties and return the updated object % Property names are: % Level_comp, STime_comp, ETime_comp, Ramp_comp, Phase_comp,Filename,Envelope_list. property_argin = varargin; while length(property_argin) >= 2, prop = property_argin{1}; if ~isa(...
3ef37cbb006cf6a865cadf4c608ffa9474159d108065ffd9d0650b75a9b17fa7
MATLAB
567
21
function val = get(comp,prop_name) % GET Get Trial_dur_comp property from the specified object % and return the value. Property names are: % Sig_comp,Swp_on,Seq_on,Static_value,Sweep,Seq_values. global TRIAL_DUR_COMP_DEFAULT; if isa(prop_name,'char') switch prop_name case 'Sig_comp' val = comp.Sig_com...
241c8640a9b75b4a7c24e39c5eab449603d9776e9b56fa2805a7c4fc2e755fa3
MATLAB
570
22
function [nMDPState,=nextStateAction(MDPState,RATState) nMDPState=MDPState; if nMDPState.type=='att_play' || nMDPState.type=='reward_play' if soundIsPlaying return; end nMDPState.type='check_poke'; end if RATState.action==0 if nMDPState.pokeInProgress nMDPState.nPoke=nMDPState.nPoke+1; ...
c4998c20abf26d922daa582a6970d37190a3eb6898c5c2aeec2b3abe17f64a4f
MATLAB
571
21
% function err=get_coord_errors(s_coord) % % if nargin==1 % %coord=s_coord.Coordinator; % n=get(s_coord,'Num_coord_groups'); % group_error=get(s_coord,'Group_error'); % tmp=group_error{1}; % if n==1 % err=tmp; % end % valid_group=get(s_coord,'Valid_group')...
c8ced66559db2dfe04957b662eef256cb474599d8c35d0d896c62087aaf82b58
MATLAB
571
8
%Reads channel indices from the .txt file function data=load_data(file_path,channelNum) % input: the file path of where the .txt file is and the channels numbers to pull %channelNum=[1:10] for left hemisphere and 11:20 for right. HbOInd=[10,4,1,13,22,7,16, 28, 25, 19, 40, 34, 31, 43, 52, 37, 46, 58, 55, 49]...
7e403cf0792625aef234df0a6980ccde6bcee9164b47c0493d53177849289ea5
MATLAB
572
29
function plotSDF_AllTrialsForCondition(SDF,TM,textForSave) global OUTDIR cd(OUTDIR) spkMax = max(SDF,[],'all'); count = 0; clear trlLoop for trlLoop = 1:size(SDF,1) close all count = count + 1; figure plot(TM,SDF(trlLoop,:)) ylim([0 spkMax]) vline(0) titleText = strcat('StimPresentation #'...
aa2d8633d8de9c2c75692c1bed1d880c6d15179bdbf4735e02e76deeb9b8b903
MATLAB
576
19
function new_sig=FILE(varargin) % FILE class constructor. switch nargin case 0 % if no input arguments, create a default object m_sig=Main_signal('FILE'); new_sig.num_of_comps=5;%assuming NEW_SIGNAL have 1 more unique component beside the basic 4. new_sig=class(new_sig,'FILE',m_sig); % assuming tha...
f4ad14d8e665315654ed89903c855e83a7658c48d51a4a42d0fd9c38c30dec48
MATLAB
576
20
function [condition,conditionarray] = getAdaptorCond(DE,NDE,PS,NS) condition= table(... [NDE DE ]',... %the eye is identified by the suppressor [PS PS ]',... %the tilt must be identified by the adapter or the suppressor [1 1 ]',... %tiltmatch [1 1 ]',... %adaptor [0 0 ]',... %suppressor [800 800 ]',......
04e1949b2a19e7f6b07a2b5074d8823207ea8faade19269cd135490f8dbdf752
MATLAB
579
26
function [T, paramGap] = createGapRow(Told,paramGapold,gaplen) type = categorical({'gap'}); speaker = 3; samp_rate = 192000; trial_dur = 500; stime = 100; etime = 300; ramp = 10; % played = 0; played = categorical({'no'},{'yes','no'}); att = 40; Tsize = size(Told,1); paramsize = size(paramGapold,1); paramline = para...
a2a6871cfa0e0b3be55bce4c08848f2d827cc3f38cfabb6ffad12fcf84fa1070
MATLAB
579
25
classdef NullStimulusSampleFactory < AudioObjectSampleFactory % NULLSTIMULUSSAMPLEFACTORY creates audio samples for NullStimuli. % It just returns the raw samples it got from the SampleSource. % Author: Lasse Osterhagen methods function this = NullStimulusSampleFactory(~) % Empty contructor to allow us...
2efc4ef9623ab52a04b09fd841e85ff6b81736ce7cf9687dce8af4aba8a5538f
MATLAB
580
23
function pa5= set(pa5,varargin) % SET Set PA5x properties and return the updated object % Property names are: property_argin = varargin; while length(property_argin) >= 2, prop = property_argin{1}; if ~isa(prop,'char') treat_error(['The property input is not a valid PA5 property']) end val = pr...
8983334a05728fe91b85fb2d0b1549e6897849780b3c55b2919d2000c603c058
MATLAB
580
14
function def=get_default(m_sig,index) % GET_DEFAULT returns Main_signal default value for the relevant component. % DEF=GET_DEFAULT(M_SIG,INDEX) returns Main_signal default value for the relevant component. % according to the given index. num_comps=get(m_sig,'Num_of_comps'); index_opt=(1:1:num_comps); if (~isint(index...
21dc45c31f8676981a9b023284c2302c674a70dd4d12c10b55db4ebcfec1afd7
MATLAB
581
23
function rx8=RX8(varargin) switch nargin case 0 % if no input arguments, create a default object rx8.device_num=1; rx8.controler=actxcontrol('RPco.x',[5 5 26 26]); rx8=class(rx8,'RX8'); case 1 if (isa(varargin{1},'RX8')) rx8 = varargin{1}; else % treat_error('Input argument is...
5a546fdda0f1e095725425f6dda42bbf5ba43f96cba93cf5e4cecf5dd18fb63f
MATLAB
583
26
function [ filt_out ] = myFilt( data ) %UNTITLED Summary of this function goes here % Detailed explanation goes here %filter the data % All frequency values are in Hz. Fs = 4/3; % Sampling Frequency N = 50; % Order Fc1 = 0.01; % First Cutoff Frequency Fc2 = 0.2; % Second Cutoff Frequency %design a butterwo...
39d0461c621a3a0f5046e4413838e784e040073a9fe53101845943715aea012e
MATLAB
584
21
function val = get(comp,prop_name) % GET Get Ramp_comp property from the specified object % and return the value. Property names are: % Name,Sig_comp,Swp_on,Seq_on,Static_value,Sweep,Seq_values. global RAMP_COMP_DEFAULT; if isa(prop_name,'char') switch prop_name case 'Sig_comp' val = comp.Sig_c...
47dc4e73a7ff0a89e4e55828b115d8c6d5ab4762949528c92ec97060c792b266
MATLAB
584
25
function val = get(comp,prop_name) % GET Get Level_comp property from the specified object % and return the value. Property names are: % Sig_comp,Swp_on,Seq_on,Static_value,Sweep,Seq_values. global LEVEL_COMP_DEFAULT; global MAX_LEVEL; if isa(prop_name,'char') switch prop_name case 'Sig_comp' val = comp.Sig_comp;...
3bb90783d95d84ffaa5f1072a2187b63b8bd6a50b767ef7221d5c77ab5010211
MATLAB
586
18
function log_msg(folder, type, argument) % JN 2019-03-06 % type can be 'start-part' 'finish-part' 'save-file' etc. % argument should explain what file we are logging about log_fname = 'logfile.txt'; fid = fopen(fullfile(folder, log_fname), 'a'); t = now(); date = datestr(t, 'yyyy-mm-dd'); time = datestr(t, 'HH:MM:S...
62ae1250cbe55899632acc4682cc9d4ccffe6d1ef188077db2a3f48b47536eba
MATLAB
586
26
function [ filt_out ] = myFilt( data ) %UNTITLED Summary of this function goes here % Detailed explanation goes here %filter the data % All frequency values are in Hz. Fs = 1/0.72; % Sampling Frequency N = 50; % Order Fc1 = 0.01; % First Cutoff Frequency Fc2 = 0.2; % Second Cutoff Frequency %design a butte...
65a5749ed5a62cd7f8a5cf05f4ead6e0ba954da0a6e0e2672f7030f19b51cc71
MATLAB
587
23
classdef ExperimentEventData < event.EventData % Holding data for events that should be registered by the LogBook % Author: Lasse Osterhagen properties % datacell must be a m-by-2 cell matrix containing m attributes % (string) - value (any data type) pairs. datacell end...
939962cee5108fd82f42783e96e909351ed050b6e455482a2c92536f6774af42
MATLAB
587
26
function Monoc = visIDX_Monoc_fromAUTO(sdf,info) SDFmax = max(sdf,[],'all'); TM = info.TM; Monoc = figure; condNum = [1,2,3,4]; for i = 1:4 subplot(4,1,i) plot(TM,sdf(condNum(i),:),'-k','LineWidth',2);hold on; title({info.conditNameForCC{condNum(i)},strcat('TrlNum=',string(info.CondTria...
aa2068579fcdcaf2c581b25dfed7b215b277917aa1b495a7a48508dae5cbf43a
MATLAB
587
23
% Fast evaluation of psychometric function for tone detection experiments % Author: Lasse Osterhagen % Unselect practice trials fh = @(x) x.ID > 0; % Evaluate log files fsa = FileStatsAccumulator('Level', fh); [out_mean, group] = funcByGroup(fsa.dPrime, fsa.header, @mean); % Draw plots subjectNo = fsa.files.name{1}...
197e7d28089278dd67fa11639b5c8d07151be9f0eb3070ed8951ebe45d214d48
MATLAB
588
7
function [] = parsave_generate_ml_model_preds(subdir_root,fold_num,curr_subject,curr_Y_pred,curr_Y_true,curr_selected_feats,num_predictions,test_subject_indices,unique_subjects,data_source) % this function simply saves key data from each training fold to file % to enable parallelization of folds during training...
88cc8eb7789ad6a957c8a5215ba340af3ee0bac6fe77ca3a3b7ce643e24b829a
MATLAB
589
44
function plotFigure_MASTER_rev(~) load('Neurovascular_development_Figures_Data.mat'); %% Fig 1 generatePanels_Fig01(Fig01) %% Fig 2 %% Fig 3 generatePanels_Fig03(Fig03) %% Fig 4 generatePanels_Fig04(Fig04) %% Fig 5 generatePanels_Fig05(Fig05) %% Fig 6 generatePanels_Fig06_rev(Fig06) %% SUPPLE...
f4ef6f0c6ca7fd5fed35236013ddaa6420eb4616531e157775a221a09b6ffe4e
MATLAB
589
23
% Fast evaluation of psychometric function for gap detection experiments % Author: Lasse Osterhagen % Unselect practice trials fh = @(x) x.ID > 0; % Evaluate log files fsa = FileStatsAccumulator('Duration', fh); [out_mean, group] = funcByGroup(fsa.dPrime, fsa.header, @mean); % Draw plots subjectNo = fsa.files.name{...
58f3230961d8de02f7438cfdddcffdf229a150ebb41a8bdc290a1db3215bc5fc
MATLAB
590
26
function Csoa = visIDX_Csoa_fromAUTO(sdf,info) SDFmax = max(sdf,[],'all'); TM = info.TM; Csoa = figure; condNum = [9,10,11,12]; for i = 1:4 subplot(4,1,i) plot(TM,sdf(condNum(i),:),'-k','LineWidth',2);hold on; title({info.conditNameForCC{condNum(i)},strcat('TrlNum=',string(info.CondTria...
bd5736e69c9be626624ec9e96c75ca0212ba7a24581813053d600b61ba0104a7
MATLAB
590
22
function val = get(comp,prop_name) % GET Get ETIME_comp property from the specified object % and return the value. Property names are: % Name,Sig_comp,Swp_on,Seq_on,Static_value,Sweep,Seq_values. global ETIME_COMP_DEFAULT; if isa(prop_name,'char') switch prop_name case 'Sig_comp' val = comp.Sig...
1fcdf2f410d8be06d37b2c4766c254d367f59876e817c2574a01e3022ecd3aff
MATLAB
591
16
function info_line = get_signal_info(sig) % GET_SIGNAL_INFO extract information about the given Signal object. % info_line = GET_SIGNAL_INFO(SIG) returns a character array that hold % information on the given Signal object. % The content of the information includes name of the Signal and % information about each co...
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MATLAB
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function samp_points=synth(sig,samp_rate,trial_dur,varargin) % SYNTH is PULSE synth function. % SAMP_POINTS=SYNTH(SIG,SAMP_RATE,TRIAL_DUR,VARARGIN) Samples the signal % according to the givan SAMP_RATE and TRIAL_DUR. Returns the sampled % points. % varargin should be empty. switch nargin case 4 params=var...
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MATLAB
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function cm = com(A,d1,d2,d3) % center of mass calculation % inputs: % A: d X nr matrix, each column in the spatial footprint of a neuron % d1, d2, d3: the dimensions of the 2-d (or 3-d) field of view % output: % cm: nr x 2 (or 3) matrix, with the center of mass coordinates if nargin < 4 d3 = 1; end if d3 == 1 ...
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MATLAB
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function [succeeded,err]=halt(rx8) dev_num=get(rx8,'Device_num'); err=''; actx_cntrl=get(rx8,'Controler'); if (invoke(actx_cntrl,'Halt')==0) err_msg = invoke(actx_cntrl,'GetError'); if length(err_msg) > 0 err=err_msg; end succeeded=0; str=['%Error Halting RX8_',num2str(dev_num)]; else su...
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MATLAB
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% conduct svm analysis with given cross-validation # (crossN) and % repetition # (repeatN) function [auc, acc, spec, sens, xxs, yys] = SampleNsvm (x, y, crossN, repeatN) auc = []; acc = []; spec = []; sens = []; xxs={}; yys={}; k=0; for r = 1:repeatN [aucs, xs, ys, tf] = svmAUC (x,y, crossN); ...
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MATLAB
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function [CH] = calcCH(obj,clusters,useChans,maxDimension) %calcCH CalinskiHarabasz cluster quality % clusters = Integer indices identifying clusters % useChans (optional) = logical array of channels to use % maxDimension (optional) = Use all dimensions from the second to this % dimension; if omitted, use ...
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MATLAB
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% get point, channel information for initial figure display function [display_point, channel_index, channel_name, channel_counts] = retrieve_view_data_info(handles, pipeline_data) point_index = get(handles.point_list, 'value'); point_list = get(handles.point_list, 'string'); point_name = point_list{poi...
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MATLAB
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% function that sets all ranges in a parameters controls, i.e. change one changes all function set_gui_mask_values(src, slider_handle, text_handle, min, value, max) if strcmp(src, 'range') if value > max; value = max; end if value < min; value = min; end elseif strcmp(src, 'slide') %pa...
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MATLAB
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% Test monocular trials %% Initial settings clear close all PostSetup('BrockWork') flag_SaveFigs = false; % load session data penetration = '151221_E_eD_LFP.mat'; sdfwin = [-0.150 .5]; % Assign preferences X.DE = 2; X.NDE = 3; X.PS = 0; X.NS = 90; IDX = singleSessionID...
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MATLAB
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function [succeeded,err]=run(rx8) dev_num=get(rx8,'Device_num'); err=''; actx_cntrl=get(rx8,'Controler'); if (invoke(actx_cntrl,'Run')==0) err_msg = invoke(actx_cntrl,'GetError'); if length(err_msg) > 0 err=err_msg; end succeeded=0; str=['%Error Running RX8_',num2str(dev_num)]; else succe...
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MATLAB
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function Simult = visIDX_Simult_fromAUTO(sdf,info) SDFmax = max(sdf,[],'all'); TM = info.TM; Simult = figure; condNum = [5,6,7,8]; for i = 1:4 subplot(4,1,i) plot(TM,sdf(condNum(i),:),'-k','LineWidth',2);hold on; title({info.conditNameForCC{condNum(i)},strcat('TrlNum=',string(info.CondT...
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MATLAB
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function [] = tcp_client() h_maestro = tcpip('132.64.105.163', 81, 'NetworkRole', 'client'); fopen(h_maestro); pause(0.5); % t_get = tcpip('132.64.61.62',88,'NetworkRole','server'); % % Wait for connection % t_get.InputBufferSize = 512; % disp('Waiting for connection'); % fopen(t_get); ...
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MATLAB
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function countsNoBg = gui_MibiRemoveBackgroundByMaskAllChannels_graded(countsAllSFiltCRSum,mask,gains) channelNum = size(countsAllSFiltCRSum,3); mask3d = repmat(mask,1,1,channelNum); countsNoBg = countsAllSFiltCRSum; if ~exist('gains') countsNoBg(mask3d) = 0; else for layer=1:size(co...
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MATLAB
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function new_sig=NEW_SIGNAL(varargin) % NEW_SIGNAL class constructor. switch nargin case 0 % if no input arguments, create a default object m_sig=Main_signal('NEW_SIGNAL'); new_sig.num_of_comps=5;%assuming NEW_SIGNAL have 1 more unique component beside the basic 4. new_sig=class(new_sig,'NEW_SIGNAL',m_...
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MATLAB
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function ICsoa = visIDX_ICsoa_fromAUTO(sdf,info) SDFmax = max(sdf,[],'all'); TM = info.TM; ICsoa = figure; condNum = [13,14,15,16]; for i = 1:4 subplot(4,1,i) plot(TM,sdf(condNum(i),:),'-k','LineWidth',2);hold on; title({info.conditNameForCC{condNum(i)},strcat('TrlNum=',string(info.Cond...
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MATLAB
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function output=ASLInterleaveControlTag(CTRL,TAG) % ClinicalASL toolbox 2023, JCWSiero % interleave CTRL and TAG data; CTRL1..TAG1..CTRL2..TAG2.. CTRLTAG=[]; dims = size(CTRL);% xdim y xim zdim tdim asl_label odd_index=2*(1:dims(4)) - 1; even_index=2*(1:dims(4)); if(nargin == 1) data=CTRL; if lengt...
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MATLAB
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function [ f ] = DataDensityPlot( x, y, levels ) %DATADENSITYPLOT Plot the data density % Makes a contour map of data density % x, y - data x and y coordinates % levels - number of contours to show % % By Malcolm Mclean % map = dataDensity(x, y, 256, 256); map = map - min(min(map)); map = f...
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MATLAB
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function [IDX, closestDvecBA] = gui_MibiGetClosestDDoubleCountPeaks(markerApeaks,markerBpeaks,K) % function MibiGetClosestDDoubleCountPeaks(dataA,dataB,K) % function calculates for dataA and dataB the distance to the K closest % neighbours. Peaks with value above 1 get counted several times [xA yA]=find(markerApeaks);...
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MATLAB
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function reps_data = get_data_reps(swp) % reps_data =GET_DATA_REPS(swp) returns an array of values that would be generated for % this Sweep object . % The values are generated according to it's STEP,range(SDATA,EDATA),NUM_DATA and REPS. % Each data will appear reps times in the array returned (total of % reps*num_data...
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MATLAB
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function out= FS_Get_background() mov_listing=dir(fullfile(pwd,'*.mat')); mov_listing={mov_listing(:).name}; filenames=mov_listing; for i=1:length(mov_listing) load(fullfile(pwd,mov_listing{i}),'video'); sig_noise = squeeze(video.frames(:,:,2,:)); % green channel noise = squeeze(video.frames(:,:,3,:)); % blue c...
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MATLAB
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function behaviorTbl = fillBehaviorTbl(behaviorTbl, area, IA, type, state) oldBT = behaviorTbl; switch state case 'go' response = 'reward'; case 'no' response = 'nothing'; case 'punish' response = 'punishment'; end switch type case 1 type = 'food'; case 2 type...
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MATLAB
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function sig= change_seq_values_by_index(sig,comp_index,arr,str_arr) % CHANGE_SEQ_VALUES changes the sequenced-values of the given component. % SIG=CHANGE_SEQ_VALUES(SIG,COMP,ARR,STR_ARR) changes the signal component's sequenced % values to the given arr and it's string representation to str_arr. % Returns the Signal a...
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MATLAB
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function pa5=PA5(varargin) switch nargin case 0 % if no input arguments, create a default object pa5.device_num=1; pa5.controler=actxcontrol('PA5.x',[5 5 26 26]); pa5.atten=0; pa5=class(pa5,'PA5'); case 1 if (isa(varargin{1},'PA5')) pa5 = varargin{1}; else % treat_error('Inp...
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MATLAB
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function x = baseMto10(sigma, M) %------------------------------------------------------------------------------------------------- % PURPOSE: convert base M to base 10 % % INPUTS: % sigma: base M value % M: base % % OUTPUTS: % x: decimal value %--------------------------------------------------------------------...
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MATLAB
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classdef (Abstract) AudioObjectGenerator < handle %AUDIOOBJECTGENERATOR - interface for the generation of AudioObjects. % This is an iterator interface that must be implemeted by classes that % provide new AudioObjects. % Author: Lasse Osterhagen methods function append(~) % Append an AudioObject to ...
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MATLAB
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function [response] = uploadTIFF(auth_token, url, filepath) % filepath needs to be a path to a properly-formatted multipage TIFF url_response = httpGET(auth_token, [url, '/upload_mibitiff/sign_tiff_url/']); % we're going to use url_response.Body.Data.url url = url_response.Body.Data.url; fid = fopen...
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MATLAB
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clear all clc %% group_name={'group_1' 'group_2'}; dir = 'dir\'; save_dir = 'save_dir\'; ext = '.txt'; %% for a=5:1:10 for j=1:1:6 filename = [char(group_name(a)) num2str(j)]; savename = [char(save_name(a)) num2str(j)]; A=importdata([dir, filename ext]); pixel_number=400; frame_number=100; for i=1:...
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MATLAB
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function [Result] = AO_ClearChannelData(); %% This function will clear the buffers for colecting data used for both comand AO_GetAlignedData,AO_GetChannelData % Result is an integer result of the AO_ClearChannelData, 0 = no function errors Result=MexFileEthernetStandAlone(27); %% Copyright (C) 2011 AlphaLabSnR ...
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MATLAB
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25
function [x] = imtranslatetrail(x, offset) x = imtt(x, [offset(1),0]); x = imtt(x, [0,offset(2)]); end function [y] = imtt(x, offset) y = imtranslate(x, offset, 'FillValue', NaN); if offset(1)>0 y(:,1:offset(1)) = repmat(x(:,1),1,abs(offset(1))); elseif offset(1)<0 y(:,(end+of...
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MATLAB
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%% % Plots all main figures for Handy and Borisyuk. Investigating the % ability of astrocytes to drive neural network synchrony. 2023 % % See the individual files for additional details %% clear; close all; clc; % DiRT simulations plotFig1; % Non-spatial, one population plotFig3and4; % Non-spatial, two population...
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MATLAB
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function x = baseMto10_table(sigma, pow_vec) %------------------------------------------------------------------------------------------------- % PURPOSE: convert base M to base 10 % % INPUTS: % sigma: base M value % M: base % % OUTPUTS: % x: decimal value %--------------------------------------------------------...
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MATLAB
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'tesitning is AO_StartConnection function'; DSPMAC='3c:2d:b7:41:17:80';%this have to be the mac address of your system (dsp) PCMac='3c:2d:55:12:34:FE';%mac address of the pc which run this matlab Activeadapte=-1; %the number of the connection you are using %-1 tell will search for the ...
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MATLAB
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function db2LFP = PCP_U_NormalizeLFP(db2LFP, inSampleRate, varargin) % Utility meant to normalize the LFP and make sure that it is independant % of the inpendance of contacts % Handles variable argument if nargin > 2, in1ChanSel = varargin{1}; else, in1ChanSel = 1:size(db2LFP, 1); end % Selects the channels d...
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MATLAB
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function info_line = get_info(s_coord) % GET_INFO returns information on the Signal Coordinator. % INFO_LINE=GET_INFO(S_COORD) returns information on the Signal Coordinator. signal=get(s_coord,'Main_signal'); num_envs=get(signal,'Num_of_env'); str_line=get_signal_info(signal); if num_envs==0 str_line=strvcat(str_li...
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MATLAB
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%% Save all the figs function saveAllTheFigs(figNameList,FolderName) % Example inputs % % figNameList = {'Lam_Sus','Lam_Trans','TransVsSus','allContactLine','Lam_Line'}; % % FolderName = strcat(OUTDIR_PLOT,'figsFrom-visWithGramm_IOT\'); % Your destination folder % cd(FolderName) FigList = findobj(allchild(0), 'flat'...
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MATLAB
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paths = uigetdiles('/Users/raymondbaranski/GitHub/MIBIAnalysis/'); waitfig = waitbar(0, 'Converting TIFF organization...'); for point=1:numel(paths) readPath = paths{point}; writePath = strsplit(readPath, filesep); writePath{end-1} = [writePath{end-1}, '_convert']; writeDir = writePath; writeDir(end) = ...
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MATLAB
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32
function total_area=computeSurfArea(verts,edges,selection) edge_vec=reshape(edges,3,size(edges,1)/3); total_area=0; for e=1:size(edge_vec,2) vert_inds=abs(edge_vec(:,e)); %check if all inds are in selection if(any(selection(vert_inds)==0)) continue end vi=verts(abs...
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MATLAB
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function val=find_crid_in_signal(signal,crid) % FIND_CRID_IN_SIGNAL search for a component in the signal with % the given coordination-index(crid).Returns 1 if found, 0 otherwise. % VAL=FIND_CRID_IN_SIGNAL(SIGNAL,CRID) search for a component in % the given signal with the given coordination-index(crid). Returns 1 ...
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MATLAB
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function beam_ind = CheckInputBeams() s = daq.createSession('ni'); addDigitalChannel(s,'Dev1','Port0/Line0:3','InputOnly') %1 2 3 4 addDigitalChannel(s,'Dev1','Port2/Line0:3','InputOnly') %5 6 7 8 addDigitalChannel(s,'Dev1','Port4/Line0:3','InputOnly') %9 10 11 12 startBackground(s); lh = addlistener(s,'DataAvaila...
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MATLAB
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function val = get(comp,prop_name) % GET Get STIME_comp property from the specified object % and return the value. Property names are: % Name,Sig_comp,Swp_on,Seq_on,Static_value,Sweep,Seq_values. global FILE_COMP_DEFAULT; if isa(prop_name,'char') switch prop_name case 'Sig_comp' val = comp.Stri...
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MATLAB
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21
function min_stime=get_least_stimet(line) signal_list=get(line,'Chan_signals'); synth=get(line,'Synth_chan'); min_stime=-1; if ~isempty(signal_list) for k=1:4 signal=signal_list{k}; if ((~isempty(signal)) && synth(k)) main_sig=get(signal,'Main_signal'); stime_comp=get_comp_by...
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MATLAB
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function val = get_comp_by_index(env,comp_index) % GET_COMP_BY_INDEX gets env's component according to the specified index. % VAL=GET_COMP_BY_INDEX(ENV,COMP_INDEX) Gets The given Envelope % component according to the specified component index. % Index Range may include :1,2,3,or 4 (as the maximum number of Envelope com...
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MATLAB
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function [succeeded,err]=soft_trigger(rx8,num_trig) dev_num=get(rx8,'Device_num'); err=''; actx_cntrl=get(rx8,'Controler'); if (invoke(actx_cntrl,'SoftTrg',num_trig)==0) err_msg = invoke(actx_cntrl,'GetError'); if length(err_msg) > 0 err=err_msg; succeeded=0; end str=['%Error Soft-Triggering R...
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MATLAB
647
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function list=get_comp_list(line) % GET_COMP_LIST returns the list of components of a Basic_line object. % LIST=GET_COMP_LIST(LINE) returns the list of components of the given % Basic_line object - that is all components that construct it's signals % on the 4 channels including components that are part of it's Envelop...
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MATLAB
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classdef StoppedState < LogbookState %STOPPEDSTATED happens when an experiment has been stopped. % Author: Lasse Osterhagen properties (SetAccess = private) stopTimes end methods function this = StoppedState(evaluator) this@LogbookState(evaluator) end function evaluate(this, event) ...
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MATLAB
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function def=get_default(env,index) % GET_DEFAULT returns Envelope default value for the relevant component. % DEF=GET_DEFAULT(ENV,INDEX) returns Envelope default value for the % relevant component (according to the given index). num_comps=get(env,'Num_of_comps'); index_opt=(1:1:num_comps); if num_comps>0 if (~isint(...
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MATLAB
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classdef ExperimentState < handle % Base class for all experiment states. % Author: Lasse Osterhagen properties (Access = protected) % experimentController functions as context experimentController end methods function this = ExperimentState(experimentController) ...
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MATLAB
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function s_comp= update_input_method(s_comp,input_method,varargin) % UPDATE_INPUT_METHOD changes the input method of this signal component. % There are one input method possible: 'STRING'. % (future one: STRING_LIST) % switch input_method case 'STRING' if ((nargin==4) && (length(varargin)==2)) s_co...