How to extract data from a 3D Array?

I have a large (500x5x79039) 3D array, which is mostly filled with zeros. Now I want to extract the slices with content into a smaller array and save them. I’ve already tried the solution from this Article, but then I get the same page repeated multiple times, resulting in too many entries and duplicates.

Ideally, I would like to extract the pages exactly as they were saved, provided there is data on those pages.

[Jonas]

so a slice is a 2d matrix for me, into which direction do you want to slice? if i understood correctly, you only want those 2d slices, in whch at least one entry is not zero?

[Simon Schirk]

Yes, exactly.

[Harald]

Jonas inquired about the direction of indexing. In other words, you can get

a) a n x 5 x 79039 array with n < 500

b) a 500 x n x 79039 array with n < 5

c) a 500 x 5 x n array with n < 79039

Each can be done, but it would be great to know which of the three you are looking for.

[Simon Schirk]

Sorry, my bad. I'm looking for c). The Data I'm looking for should be displayed as 500 x 5 x n, like the pages in my existing array.

Answer 1

[Dyuman Joshi]

Use logical indexing -

%Sample data
p = 5;
q = 6;
r = 4;

y = rand(p,q,r)-1;

y(:, :, [2 r+1]) = zeros(p,q,2)

y = 
y(:,:,1) =

   -0.7285   -0.6881   -0.6747   -0.3796   -0.1672   -0.6574
   -0.9762   -0.6068   -0.9793   -0.0795   -0.9972   -0.5266
   -0.7477   -0.1073   -0.9397   -0.5630   -0.9243   -0.7642
   -0.2448   -0.1465   -0.7908   -0.8282   -0.3473   -0.0134
   -0.3137   -0.4403   -0.8926   -0.5689   -0.2770   -0.4045


y(:,:,2) =

     0     0     0     0     0     0
     0     0     0     0     0     0
     0     0     0     0     0     0
     0     0     0     0     0     0
     0     0     0     0     0     0


y(:,:,3) =

   -0.0481   -0.3703   -0.8937   -0.2620   -0.6424   -0.1590
   -0.3590   -0.7458   -0.8042   -0.6762   -0.5639   -0.4337
   -0.4247   -0.3759   -0.6399   -0.7271   -0.9687   -0.0107
   -0.3895   -0.5470   -0.2762   -0.8224   -0.4897   -0.7164
   -0.5377   -0.7156   -0.8387   -0.6348   -0.3393   -0.1025


y(:,:,4) =

   -0.7409   -0.3158   -0.9468   -0.7263   -0.4370   -0.7029
   -0.3200   -0.8704   -0.2631   -0.8824   -0.4113   -0.4293
   -0.5657   -0.7926   -0.9319   -0.6440   -0.1914   -0.1186
   -0.0940   -0.8801   -0.3449   -0.3131   -0.0717   -0.8211
   -0.6848   -0.8336   -0.2107   -0.4389   -0.7302   -0.3056


y(:,:,5) =

     0     0     0     0     0     0
     0     0     0     0     0     0
     0     0     0     0     0     0
     0     0     0     0     0     0
     0     0     0     0     0     0

%Check if there is any non-zero element in a page
idx = any(y, [1 2])

idx = 1x1x5 logical array
idx(:,:,1) =

   1


idx(:,:,2) =

   0


idx(:,:,3) =

   1


idx(:,:,4) =

   1


idx(:,:,5) =

   0

%Use the (logical) index to get the corresponding data
out = y(:, :, idx)

out = 
out(:,:,1) =

   -0.7285   -0.6881   -0.6747   -0.3796   -0.1672   -0.6574
   -0.9762   -0.6068   -0.9793   -0.0795   -0.9972   -0.5266
   -0.7477   -0.1073   -0.9397   -0.5630   -0.9243   -0.7642
   -0.2448   -0.1465   -0.7908   -0.8282   -0.3473   -0.0134
   -0.3137   -0.4403   -0.8926   -0.5689   -0.2770   -0.4045


out(:,:,2) =

   -0.0481   -0.3703   -0.8937   -0.2620   -0.6424   -0.1590
   -0.3590   -0.7458   -0.8042   -0.6762   -0.5639   -0.4337
   -0.4247   -0.3759   -0.6399   -0.7271   -0.9687   -0.0107
   -0.3895   -0.5470   -0.2762   -0.8224   -0.4897   -0.7164
   -0.5377   -0.7156   -0.8387   -0.6348   -0.3393   -0.1025


out(:,:,3) =

   -0.7409   -0.3158   -0.9468   -0.7263   -0.4370   -0.7029
   -0.3200   -0.8704   -0.2631   -0.8824   -0.4113   -0.4293
   -0.5657   -0.7926   -0.9319   -0.6440   -0.1914   -0.1186
   -0.0940   -0.8801   -0.3449   -0.3131   -0.0717   -0.8211
   -0.6848   -0.8336   -0.2107   -0.4389   -0.7302   -0.3056