Why is my array definition ignoring all columns except the first?

I have created multiple arrays of 5 cells that each contain a 1200x3 double with the code below. (I know this isn't the best way to deal with a bunch of variables, but I just can't write out all 510 variables I have constantly within my time limit for this assignment)

for i = 1:5
    E.Time{:,i} = RD.Empty_Time(:,i);
    E.Toe{:,i} = [RD.Empty_Toe_X(:,i), RD.Empty_Toe_Y(:,i), RD.Empty_Toe_Z(:,i)];
    E.Med_Ankle{:,i} = [RD.Empty_Med_Ankle_X(:,i), RD.Empty_Med_Ankle_Y(:,i), RD.Empty_Med_Ankle_Z(:,i)];
    E.Lat_Ankle{:,i} = [RD.Empty_Lat_Ankle_X(:,i), RD.Empty_Lat_Ankle_Y(:,i), RD.Empty_Lat_Ankle_Z(:,i)];
    E.Shank{:,i} = [RD.Empty_Shank_X(:,i), RD.Empty_Shank_Y(:,i), RD.Empty_Shank_Z(:,i)];
    E.Med_Knee{:,i} = [RD.Empty_Med_Knee_X(:,i), RD.Empty_Med_Knee_Y(:,i), RD.Empty_Med_Knee_Z(:,i)];
    E.Lat_Knee{:,i} = [RD.Empty_Lat_Knee_X(:,i), RD.Empty_Lat_Knee_Y(:,i), RD.Empty_Lat_Knee_Z(:,i)];
    E.Hip{:,i} = [RD.Empty_Hip_X(:,i), RD.Empty_Hip_Y(:,i), RD.Empty_Hip_Z(:,i)];
end

example result: E.Toe = 1200x3 double 1200x3 double 1200x3 double 1200x3 double 1200x3 double

I then find all NAN entries from three variables that might potentially have them (all the others are complete) with the code below

for i = 1:5
    E.Hgoodvals{:,i} = find(E.Hip{i}(:,1));
    E.LKgoodvals{:,i} = find(E.Lat_Knee{i}(:,1));
    E.MKgoodvals{:,i} = find(E.Med_Knee{i}(:,1));
    E.goodvals{:,i} = intersect(E.Hgoodvals{:,i},E.LKgoodvals{:,i});
    E.goodvals{:,i} = intersect(E.goodvals{:,i},E.MKgoodvals{:,i});
    E.Time{:,i} = E.Time{:,i}(E.goodvals{:,i});
    E.Index{:,i} = length(E.goodvals{:,i}); %Not relevant for this question
    E.D_Time{:,i} = E.Time{:,i}(2:E.Index{:,i}) - E.Time{:,i}(1:E.Index{:,i}-1); %Not relevant for this question
end

The result from this relevant to this question is E.goodvals = 1007x1 double 941x1 double 956x1 double 903x1 double 967x1 double

I then try to create vectors of the necessary sections (eg from Toe to Ankle) and then only include the good values

for i = 1:5
    E.Toe_Ankle{:,i} = [E.Toe{:,i}(:,1)-E.Lat_Ankle{:,i}(:,1), E.Toe{:,i}(:,2)-E.Lat_Ankle{:,i}(:,2), E.Toe{:,i}(:,3)-E.Lat_Ankle{:,i}(:,3)];
    E.Toe_Ankle{:,i} = E.Toe_Ankle{:,i}(E.goodvals{:,i});
    E.Ankle_Knee{:,i} = [E.Lat_Ankle{:,i}(:,1)-E.Lat_Knee{:,i}(:,1), E.Lat_Ankle{:,i}(:,2)-E.Lat_Knee{:,i}(:,2), E.Lat_Ankle{:,i}(:,3)-E.Lat_Knee{:,i}(:,3)];
    E.Ankle_Knee{:,i} = E.Ankle_Knee{:,i}(E.goodvals{:,i});
    E.Knee_Ankle{:,i} = [E.Lat_Knee{:,1}(:,1)-E.Lat_Ankle{:,i}(:,1), E.Lat_Knee{:,i}(:,2)-E.Lat_Ankle{:,i}(:,2), E.Lat_Knee{:,i}(:,3)-E.Lat_Ankle{:,i}(:,3)];
    E.Knee_Ankle{:,i} = E.Knee_Ankle{:,i}(E.goodvals{:,i});
    E.Hip_Knee{:,i} = [E.Hip{:,i}(:,1)-E.Lat_Knee{:,i}(:,1), E.Hip{:,i}(:,2)-E.Lat_Knee{:,i}(:,2), E.Hip{:,i}(:,3)-E.Lat_Knee{:,i}(:,3)];
    E.Hip_Knee{:,i} = E.Hip_Knee{:,i}(E.goodvals{:,i});
end

Which I believe should create 4 different cell arrays each with 5 columns and each cell contains a different amount of rows by 3 column doubles. However the result from this is for example E.Toe_Ankle = 1007x1 double 941x1 double 956x1 double 903x1 double 967x1 double. And the column in all these doubles is just the first column (eg taking only E.Toe{:,i}(:,1)-E.Lat_Ankle{:,i}(:,1) and nothing after the comma).

I am trying to get for example E.Toe_Ankle = 1007x3 double 941x3 double 956x3 double 903x3 double 967x3 double

Is there something wrong with this that I am not seeing?

I can upload files if it is needed to see the actual data.

[Stephen23]

Rather than nesting lots of identically-sized cell arrays inside one scalar structure, it looks like one non-scalar structure array would fit your data better:

https://www.mathworks.com/help/matlab/matlab_prog/access-multiple-elements-of-a-nonscalar-struct-array.html

Answer 1

[Joshua Lucas Ewert]

Nevermind all, I figured out the answer myself. The code

for i = 1:5
    E.Toe_Ankle{:,i} = [E.Toe{:,i}(:,1)-E.Lat_Ankle{:,i}(:,1), E.Toe{:,i}(:,2)-E.Lat_Ankle{:,i}(:,2), E.Toe{:,i}(:,3)-E.Lat_Ankle{:,i}(:,3)];
    E.Toe_Ankle{:,i} = E.Toe_Ankle{:,i}(E.goodvals{:,i});
    E.Ankle_Knee{:,i} = [E.Lat_Ankle{:,i}(:,1)-E.Lat_Knee{:,i}(:,1), E.Lat_Ankle{:,i}(:,2)-E.Lat_Knee{:,i}(:,2), E.Lat_Ankle{:,i}(:,3)-E.Lat_Knee{:,i}(:,3)];
    E.Ankle_Knee{:,i} = E.Ankle_Knee{:,i}(E.goodvals{:,i});
    E.Knee_Ankle{:,i} = [E.Lat_Knee{:,1}(:,1)-E.Lat_Ankle{:,i}(:,1), E.Lat_Knee{:,i}(:,2)-E.Lat_Ankle{:,i}(:,2), E.Lat_Knee{:,i}(:,3)-E.Lat_Ankle{:,i}(:,3)];
    E.Knee_Ankle{:,i} = E.Knee_Ankle{:,i}(E.goodvals{:,i});
    E.Hip_Knee{:,i} = [E.Hip{:,i}(:,1)-E.Lat_Knee{:,i}(:,1), E.Hip{:,i}(:,2)-E.Lat_Knee{:,i}(:,2), E.Hip{:,i}(:,3)-E.Lat_Knee{:,i}(:,3)];
    E.Hip_Knee{:,i} = E.Hip_Knee{:,i}(E.goodvals{:,i});
end

needs to be this

for i = 1:5
    for j = 1:3
    E.Toe_Ankle{:,i} = [E.Toe{:,i}(:,1)-E.Lat_Ankle{:,i}(:,1), E.Toe{:,i}(:,2)-E.Lat_Ankle{:,i}(:,2), E.Toe{:,i}(:,3)-E.Lat_Ankle{:,i}(:,3)];
    E.Toe_Ankle{:,i} = E.Toe_Ankle{:,i}(E.goodvals{:,i},:);
    E.Ankle_Knee{:,i} = [E.Lat_Ankle{:,i}(:,1)-E.Lat_Knee{:,i}(:,1), E.Lat_Ankle{:,i}(:,2)-E.Lat_Knee{:,i}(:,2), E.Lat_Ankle{:,i}(:,3)-E.Lat_Knee{:,i}(:,3)];
    E.Ankle_Knee{:,i} = E.Ankle_Knee{:,i}(E.goodvals{:,i},:);
    E.Knee_Ankle{:,i} = [E.Lat_Knee{:,1}(:,1)-E.Lat_Ankle{:,i}(:,1), E.Lat_Knee{:,i}(:,2)-E.Lat_Ankle{:,i}(:,2), E.Lat_Knee{:,i}(:,3)-E.Lat_Ankle{:,i}(:,3)];
    E.Knee_Ankle{:,i} = E.Knee_Ankle{:,i}(E.goodvals{:,i},:);
    E.Hip_Knee{:,i} = [E.Hip{:,i}(:,1)-E.Lat_Knee{:,i}(:,1), E.Hip{:,i}(:,2)-E.Lat_Knee{:,i}(:,2), E.Hip{:,i}(:,3)-E.Lat_Knee{:,i}(:,3)];
    E.Hip_Knee{:,i} = E.Hip_Knee{:,i}(E.goodvals{:,i},:);
    end
end

Just a couple more colons needed added