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Fast access/concatenation of large array structure

Asked by D. Plotnick on 13 Apr 2017
Latest activity Commented on by Matt J
on 19 Apr 2017
I have a large structure array (500K+ items), and I wish to access certain fields of the that array and concatenate the results. Below is a placeholder example.
A{1}.time = 1500
A{1}.data.temp = 70;
A{1}.data.humidity = 20;
A{2}.time = 1501
A{2}.data.temp = 73;
A{2}.data.humidity = 19;
etc. Till we have 500,000 of these. (I have made it a cell array since the actual entries differ in my data, and I have other code that will go through and just grab the cells we want.)
Now, I want to access e.g. all of the 'data' and concatenate it so that I have a simple vector I can plot. Currently this is done using a loop, but that is very slow. Is there a faster way to do this than some version of the below:
fieldNames = fields(A{1}.data);
for ii = 1:length(fieldNames)
out.(fieldNames{ii}) = ...
cat(1,cellfun(@(x) getField(x,'data',fieldNames{ii}), A));
end
where
function out = getField(in, fieldname1,fieldname2)
out = in.(fieldname1).(fieldname2);
end
Again, this certainly works but for extremely large datasets with lots of fields it becomes very very slow. I bet that there is a much more efficient way of gathering all of the data contained in the fields and subfields of a large data set like above. Any help is appreciated.
Thanks, -Dan
An additional discovery: Matlab is somehow storing the field names for each sub-structure individually. In the above example, it has memory allocated for the fieldnames data.temp and data.humidity TWICE (once for each copy). This is why it is so slow. A 50 Mbyte set of data has grown to 3 GB because of this organization scheme. I am going to make a separate post about this (is the memory issue resolved if each entry is a known class? That way the field names aren't stored once for each copy?).

  5 Comments

@Daniel Plotnick: storing your data in a cell arry of structure is less efficient than storing your data in a simple structure array (aka a non-scalar structure). If yous stored the data in a structure array then accessing that data would be much simpler, as you can use constructs like:
[S.f1]
{S(idx).f2}
and other neat and simple ways to access the data.
But then you should also keep in mind that in general you should keep data together as much as possible, not split in into lots of separate scalar values on their own. When data is stored in simple numeric vectors/matrices/arrays, then working with that data is faster and easier. Then you can unleash the real power of MATLAB!
After all, the name MATLAB come from MATrix LABoratory, and not from "lets split the data up into millions of scalar values".
Thank you. Yes, I am actually doing this as a struct array (mostly) now, as I realized I could use this method sometime after I posted.
However, while I absolutely agree with your in general statement above, the data is output in that format by Matlab's memmapfile function. I am reading in a byte stream of messages in the form [header | payload]. The header must be read in using memmapfile as the originator has written it in mixed format (uint32, double, int16, etc.). memmapfile itself returns a structure array. For a 50 MB file it corresponds to a 600K+ length array, and the core issue is how to then quickly read in the headers, determine the payload format, parse the payload, and return the payload contents.
memmapfile is convenient but not mandatory: you can use a bunch of fread() instead.

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1 Answer

Answer by Matt J
on 14 Apr 2017
Edited by Matt J
on 14 Apr 2017
 Accepted Answer

I don't quite understand why you are using a cell array and not a struct array. Your example will not work unless all A{i} have the same field names so a struct array should have been sufficient.
In any case, you should be able to create a struct array and do faster concatenations with it as follows,
structArray=[A{:}];
dataArray=[structArray.data];
Now you can concatenate individual fields of dataArray in a similar way, e.g.,
out.temp=[dataArray.temp];
You can loop over the field names of dataArray, similar to what you are doing now, to repeat this kind of concatenation for all fields.
I feel obliged to mention, though, that your data organization looks like it is bound for trouble. It is inefficient, in general, to store large amounts of data scattered across structs and cell arrays. Cells and structs do not use contiguous memory, and so are not efficient storage-wise or built for fast access. Nesting them in sub-structs makes the problem worse. You should really be storing all your temp, humidity, etc... data in their own vectors to begin with. Or at least, you should be doing so if the data is going to get large and speed is a priority.

  6 Comments

I have done so at your suggestion. Thanks.
As to Matt's comment, I have implemented your suggestion. I am still ending up re-inserting afterwards (into a custom class hierarchy now) , but that is due to data-product requirements as opposed to my own desire for speed. Thanks.
If you really want these results re-inserted back into a struct array ... then you must use a for-loop
My comment here wasn't really very precise. There are alternatives to for-loops, but they will not be faster, e.g,
header1Cell=num2cell( swapbytes([example.header1]) );
[example.header1]= deal(header1Cell{:});

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