Coverting Timetable to Column Vector

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Sam
Sam on 16 Nov 2022
Commented: Sam on 1 Dec 2022
Hi everyone,
I am working with .edf files and am using edfread, which is giving me a timetable output, when I would like a column vector.
We are recording voltage data in 1-hour increments at a sampling frequency of 1 KHz with 6 channels, each channel is unique.
I am using the option 'DataRecordOutputType' set to 'vector', which just makes this weirder.
Here's the code:
data = edfread('filename.edf','DataRecordOutputType' ,'vector');
and the output is:
I can solve this via doing the following:
data = edfread('filename.edf','DataRecordOutputType' ,'vector');
abf_like = [];
new_data = cell2mat(data{1,1});
abf_like = new_data;
for i = 2:size(data, 1)
new_data = cell2mat(data{i,1});
abf_like = vertcat(abf_like, new_data);
end
Which outputs my desired array (3600500 x 1). But this takes forever (understandably so), and there are 6 channels per edf file and many files. What am I missing with edfread, or what can I do to speed this up?
Thanks for any insight you can offer.
edit: here's something that works for what I need. Still would like some alternatives, if there are any:
clear all; close all; clc
edf = edfread('filename.edf');
abf_like = edf_to_abf(edf);
function out = edf_to_abf(edf)
edf = timetable2table(edf); edf = table2cell(edf);
edf = edf(:, 2:end);
abf_like = zeros(3600500,1);
abf_like = table(abf_like);
for j = 1:6
single_data = edf(:,j);
abf_like{:,j} = unpacker(single_data);
clear single_data
end
out = table2array(abf_like);
end
function out = unpacker(data)
abf_like(:,1) = cell2mat(data(1,1));
r = 501;
for i = 2:size(data, 1)
abf_like(r:r+499,1) = cell2mat(data(i,1));
r = r + 500;
end
out = abf_like;
end

Accepted Answer

Peter Perkins
Peter Perkins on 30 Nov 2022
Sam, it looks like you are ending up with a 7201x6 timetable whose variables are cell arrays, and each cell contains a 500x1 double vector. And it sounds like you want six (or one?) 7201*500x1 vector.I can't speak to how you are ending up with that timetable without seeing the file, but getting that should not take a long time:
>> tt = timetable(Size=[7201 2],VariableTypes=repmat("cell",1,2),StartTime=seconds(0),TimeStep=seconds(.5));
>> tt{:,:} = {rand(500,1)}
tt =
7201×2 timetable
Time Var1 Var2
__________ ______________ ______________
0 sec {500×1 double} {500×1 double}
0.5 sec {500×1 double} {500×1 double}
1 sec {500×1 double} {500×1 double}
1.5 sec {500×1 double} {500×1 double}
2 sec {500×1 double} {500×1 double}
2.5 sec {500×1 double} {500×1 double}
: : :
3597.5 sec {500×1 double} {500×1 double}
3598 sec {500×1 double} {500×1 double}
3598.5 sec {500×1 double} {500×1 double}
3599 sec {500×1 double} {500×1 double}
3599.5 sec {500×1 double} {500×1 double}
3600 sec {500×1 double} {500×1 double}
Display all 7201 rows.
>> tic, var1 = vertcat(tt.Var1{:}); toc
Elapsed time is 0.030527 seconds.
>> size(var1)
ans =
3600500 1
  3 Comments
Sam
Sam on 1 Dec 2022
@Peter Perkins You are absolutely amazing! Thank you very much. I never would have figured that out.

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