Transparency violation error. Using 'eval' in a 'parfor' loop

Question

Giridhar sai pavan kumar Konduru 2021-5-12

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/828485-transparency-violation-error-using-eval-in-a-parfor-loop

评论： Giridhar sai pavan kumar Konduru 2021-5-15

采纳的回答： Jan

在 MATLAB Online 中打开

Hello,

I am new to coding

I am trying to speed up the processing of my code by suing parfor loop however there are 2 eval functions in it

Here's the complete code;

tic
EventName = 'Hypopnea';
CHN = 'ECG';
fre = 200;
Felist = 'signal_tsallisEntropy';
Nor = 'Normalize_Whole_signal'; % Normalize_Whole_signal
Dset = 'visit1'; % visit3
Mpath = 'F:\Dataset';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 osp1 = '2_Features';
 sp1 = 'MAT files';
 sec = 30;
 level = 5;
 sp2 = strcat(Mpath,'\',sp1,'\',Dset);
 load([sp2,'\RST.mat'])
 load(['Event_List.mat'])
 Ledf = RST.(CHN).(['fre_',num2str(fre)]);
 TSNor = '';
 if strcmp(Nor,'Normalize_Whole_signal')
     TSNor = '_Normalize';
 end
% Xfeat = table;
parfor i = 1:size(Ledf,1)    
     Cname = char(Ledf(i,1));
     
     LP1 = strcat(sp2,'\',Cname,'_info.mat');
     LP2 = strcat(sp2,'\',Cname,'_rec.mat');
     CR_info = load(LP1);
     CR_data = load(LP2); %%%%%
     [id1,id2] = ismember(CHN,CR_info.hdr.label); 
       
     SleepEpochs = size(CR_info.y.SleepStages,2); % available sleep epochs
     EVstruct = CR_info.y.ScoredEvents; % 1 by n : struct || Events
     szREC = size(CR_data.record,2); % record size
     MaxFre = max(CR_info.hdr.frequency); % max available frequency
     REpoch = min(SleepEpochs,szREC/MaxFre/sec);
     REC = CR_data.record(id2,1:(REpoch*sec*fre));
     if strcmp(Nor,'Normalize_Whole_signal')
         REC = Z_score_mat(REC);
     end
     REC = reshape(REC,(sec*fre),REpoch)';
     LRST = Event_label(sec,REpoch,EVstruct,TE,TE_U);
     Label = cell(LRST.Total,1);
     Label(:,1) = {'Normal'};
     eval(['Label(LRST.',EventName,',1) = {EventName};']);
     eval(['[tpl1,tpl2] = ismember(LRST.',EventName,',LRST.ALL_Event);'])
     USls = LRST.ALL_Event; 
     USls(tpl2,:) = [];
                 
     REC(USls,:) = [];
     Label(USls,:) = [];
                
     sp3 = strcat(Mpath,'\',osp1,'\',Dset,'\',EventName,'\',CHN,...
         '_fre_',num2str(fre),TSNor,'\',Cname);
     if isfolder(sp3) == 0
         mkdir(sp3)
     end
     feat_mat = WDecBi_1(REC,level,Felist,i);
     MTab = table(feat_mat,Label);
     mysave([sp3,'\',Felist,'.mat'],MTab)
              
%      YC = load([sp3,'\',Felist,'.mat']);
%      Xfeat = cat(1,Xfeat,YC.MTab);
    clc
    disp(i)
    toc
end
function mysave1(fName, MTab)
  save(fName,'MTab');
end

Can anybody please find an alternative to eval function in parfor loop

I'd be glad to receive any help

Thank you.

2 个评论
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Jonas 2021-5-12

在 MATLAB Online 中打开

use real code instead of eval function. smth like

Label(LRST.(EventName),1)=...

similarly in the other case. it is possible to use the dot expression with a variable, but you have to put parenthesis around the variable behin the dot like

varname='firstThing';
myStruct.(varname)

Stephen23 2021-5-12

"I am new to coding ... however there are 2 eval functions in it"

Avoid eval for trivial code like this:

https://www.mathworks.com/help/matlab/matlab_prog/generate-field-names-from-variables.html

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Answer 1

Jan 2021-5-12

3
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/828485-transparency-violation-error-using-eval-in-a-parfor-loop#answer_698445

在 MATLAB Online 中打开

Some general hints:

load() without catching its output to a variable creates variables dynamically in the workspace. This impedes Matlab's JIT acceleration. In consequence loops can need up to 100 times more processing time. Another effect is that it impedes the debugging. I cannot guess, which variables are contained in the files. Therefore it is much harder to deside if some calls are functions or indexed variables.

 load([sp2,'\RST.mat'])    % RST = load(fullfile(sp2,'RST.mat'))
 load(['Event_List.mat'])  % Event = load('Event_List.mat'); 

Use fullfile() instead of strcat, because it is safer and cares about the operating system automatically.

sp2 = fullfile(Mpath, sp1, Dset); % strcat(Mpath,'\',sp1,'\',Dset);

Use braces instead of CHAR to get a char from a cell string:

Cname = Ledf{i}; % char(Ledf(i,1))

ISMEMBER is an overkill for comparing a single char vector:

id2 = find(strcmp(CHN, CR_info.hdr.label));

Avoid EVAL like hell. It makes the debugging horrible and slows down the processing massively again by craeting variables dynamically:

% eval(['Label(LRST.',EventName,',1) = {EventName};']);
Label{LRST.(EventName), 1} = EventName;
% eval(['[tpl1,tpl2] = ismember(LRST.',EventName,',LRST.ALL_Event);'])
[tpl1, tpl2] = ismember(LRST.(EventName), LRST.ALL_Event);
% I cannot test this, but this should be enough to demonstrate how to avoid
% EVAL.