Saving parts of Matlab cell array - arrays

Question

I am using Matlab for some data collection, and I want to save the data after each trial (just in case something goes wrong). The data is organized as a cell array of cell arrays, basically in the format
data{target}{trial} = zeros(1000,19)
But the actual data gets up to >150 MB by the end of the collection, so saving everything after each trial becomes prohibitively slow.
So now I am looking at opting for the matfile approach (http://www.mathworks.de/de/help/matlab/ref/matfile.html), which would allow me to only save parts of the data. The problem: this doesn't support cells of cell arrays, which means I couldn't change/update the data for a single trial; I would have to re-save the entire target's data (100 trials).
So, my question:
Is there another different method I can use to save parts of the cell array to speed up saving?
(OR)
Is there a better way to format my data that would work with this saving process?

Answer 1

A not very elegant but possibly effective solution is to use trial as part of the variable name. That is, use not a cell array of cell arrays (data{target}{trial}), but just different cell arrays such as data_1{target}, data_2{target}, where 1, 2 are the values of the trial counter.
You could do that with eval: for example
trial = 1; % change this value in a for lopp
eval([ 'data_' num2str(trial) '{target} = zeros(1000,19);']); % fill data_1{target}
You can then save the data for each trial in a different file. For example, this
eval([ 'save temp_save_file_' num2str(trial) ' data_' num2str(trial)])
saves data_1 in file temp_save_file_1, etc.

Answer 2

Update:
Actually it does appear to be possible to index into cell arrays, just not iside cell arrays. Hence, if you store your data slightly differently it seems like you can use matfile to update only part of it. See this example:
x = cell(3,4);
save x;
matObj = matfile('x.mat','writable',true);
matObj.x(3,4) = {eye(10)};
Note that this gives me a version warning, but it seems to work.
Hope this does the trick. However, still look into the next part of my answer as it may help you even more.
For calculations it is usually not required to save to disk after every iteration. An easy way to get a speedup (at the cost of a little more risk) is to save only after every n trials.
Like this for example:
maxTrial = 99;
saveEvery = 10;
for trial = 1:maxTrial
myFun; %Do your calculations here
if trial == maxTrial || mod(trial, saveEvery) == 0
save %Put your save command here
end
end
If your data is always at (or within) a certain size, you can also choose to store your data in a matrix rather than a cell array, then you can use indexing to save only part of the file.

Answer 3

In response to #Luis I will post an other way to deal with the situation.
It is indeed an option to save data in named variables or files, but to save a named variable in a named file seems too much.
If you only change the name of the file, you can save everything without using eval:
assuming you are dealing with trial 't':
filename = ['temp_save_file_' + num2str(t)];
If you really want, you can use print commands to write it as 001 for example.
Now you can simply use this:
save(filename, myData)
To use this, construct the filename again and so something like this:
totalData = {}; %Initialize your total data
And then read them as you wrote them (inside a loop):
load(filename)
totalData{t} = myData