Extract Data from Structure and Transfer it into Cell Array

Hello everybody,

I am quite new to Matlab and can't come up with a solution to the following problem:

From a single particle tracking program that uses Matlab (uTrack, to be precise) I get the tracking results as a structure. Inside this strucutre, the tracks of every particle is stored within a cell array. In this cell array, the tracks can then be found as a matrix (two other matrices are also there with other information) in the following way:

    x coord / y coord / z coord / Amplitude / dx / dy / dz / dA ...

This would be the first time point. Then it starts again with x coord, y coord, and so on for the second time point until the end.

For further evaluation, I only need the x and the y coordinates in a cell array in the following form

    [t1 x1 y1;
     t2 x2 y2;
     t3 x3 y3;
     ...]

with on element in the cell array for each particle.

Therefore, I need to somehow extract the x and y coordinates, transfer them and add the time information in the first column with the correct lenght.

I have already tried to convert the data to a matrix, but the problem here is that the tracks have of course not all the same lengths. I get then a lot of NaN which cause problems in the following steps...

Any help would be very much appreciated!

[Guillaume]

I don't really understand the whole details of your structure, could you show an example?

Similarly it's not very clear what you want out of it? A cell array of matrices (one per particle)? Again an example would help.

[LM]

Thank you for your answer! I have attached the output-file (outputstruct.mat) of the tracking program. The data I need is inside the structure "tracksFinal". If you open it, you will find inside a Nx1 structure, N standing for the number of tracks - in this example 855. Inside each of these structures are three doubles. The double "tracksCoordAmpCG" contains the relevant information in the form I worte above:

   x coord / y coord / z coord / Amplitude / dx / dy / dz / dA ...

Therefore, it is just one row with 8 elements per time point. Relevant are only the x and y coords.

I have also attached another type of output - it is the same data, but in a matrix style (outputmatrix.mat). I don't know what is easier to deal with. In the matrix there are a lot of NaNs which may cause problems...

The infromation about the time is not written the output, this would be 0.05 s/frame - so 0/0.05/0.1/0.15 etc. This would be added seperately.

In the end, I need the following: A cell array with one element for each track like this:

<TL1x3 double>
<TL2x3 double>
<TL3x3 double> and so on

TL stands for the track length and the 3 originiates from the three columns of each track: One for the time, one for the x and one for the y coord, so every element looks like this:

t1   x1   y1
t2   x2   y2
t3   x3   y3    and so on

As I mentioned, no NaNs may appear in the coords. +

Again, thank your very much for your help!

Answer 1

[Guillaume]

First, a point of terminology:

tracksFinal is the Nx1 structure, there is no structure inside. It consists of three fields (not doubles), tracksCoordAmpCG is one of the field and it contains a row vector consisting of repeats of sequence of 8 elements where each element is as you've described.

I'm still not entirely clear on what exactly you want the output to look like, so first, I'll show you a few things:

To convert the values of one field of a structure array into a cell array of those value:

tcampCG = {tracksFinal(:).tracksCoordAmpCG}

To convert a row vector of 8 repeating elements into an Mx8 matrix, use reshape:

 tcampCG1 = reshape(tracksFinal(1).tracksCoordAmpCG, 8, [])'

In the end, I think the following may be what you want:

tcampCG = {tracksFinal(:).tracksCoordAmpCG}; %transform field into cell array
for trackindex = 1:numel(tcampCG) %iterates over the elements of the cell array
   tcampCGi = reshape(tcampCG{trackindex}, 8, [])'; %reshape element to 8 columns
   tracktimes = (0:size(tcampCGi, 1)-1) * 0.05; %calculate time 
   tcampCG{trackindex} = [ tracktimes', tcampCGi(:, [1 2])]; %concatenate time with column 1 and 2 and put back into cell array
end