I would like help setting up my code

Hi,

I have an array (31003x1), made up of -1’s, 0’s, and 1’s, that represents neural data. The data was down-sampled from 24.414 KHz to 1 KHz.

I want to see how many times UP initiation takes place.

UP initiation is defined as:

A suppressed state (0), followed by a transition period (random 0’s, +1’s, and -1’s), and then an UP (+1) state. The suppressed state needs to last 90 ms (or 90 data points); the transition period should last 10 ms (or 10 data points); and the UP state needs to last 100 ms (or 100 data points).

OR [defined as]

A DOWN state (-1), followed by a transition period, and then an UP state (+1). Like above, the DOWN state needs to last 90 ms, the transition 10 ms, and the UP state 100 ms.

For the same array, I want to also see how many times UP termination takes place.

UP termination is defined as:

An UP state (+1), followed by a transition phase, and then a suppressed state (-1). The UP state needs to last 100 ms; the transition period 20 ms; and the suppressed state 80 ms.

OR

An UP state (+1), that is followed by a period of transition, and then a DOWN state (-1). Similarly, the UP state needs to last 100 ms; the transition period 20 ms; and the DOWN state 80 ms.

I’m having trouble getting started with this, and would any appreciate your help or guidance.

Thank you.

[Jan]

Convert the definitions to an abstract representation, which can be expressed as Matlab code.

"An UP state (+1), followed by a transition phase, and then a suppressed state (-1). The UP state needs to last 100 ms; the transition period 20 ms; and the suppressed state 80 ms."

This is less useful for the readers. Convert this as far as possible to expressions about elements of a vector. How man elements must have which value?

What does the "OR" parts of the definitions mean? Are their two different definitions or does the definition contain an Either/Or part?

"The data was down-sampled from 24.414 KHz to 1 KHz" - does this detail matter?

[NA]

Hi Jan,

Thanks for getting back to me.

"An UP state (+1), followed by a transition phase, and then a suppressed state (-1). The UP state needs to last 100 ms; the transition period 20 ms; and the suppressed state 80 ms."

For this statement (UP termination), I have created the below expressions:

%UP termination templates
U=ones(100,1); %up state
trans=20; %transition is 20 data points
S=zeros(80,1); %suppressed state

I am not sure how to use these templates to run them through the array, and count the number of times UP termination takes place. I tried the following:

%con is the array (31003x1), made up of -1's, 0's, and 1's.

isequal(con,[U; con+trans; S]);

I know it's wrong. Can you please give me more pointers.

Thanks

[Jan]

Please post one or some relevant examples of how an "UP state" looks like.

Are you searching for subvectors with this value: [ones(100, 1); zeros(80, 1)]? Then:

strfind(con.',  [ones(100, 1); zeros(80, 1)].')

strfind replies the indices of the matching subvectors. It operates on double vectors also inspite of its name. It needs row vectors as input.

[NA]

Hi Jan, thanks for getting back to me.

An UP state is: [ones(100, 1); TRANSITION; zeros(80, 1)];

The TRANSITION period is a segment of 20 datapoints that I would like to overlook because it is made up of random 0's, 1's and -1's.

Is there a way of searching through con accounting for this transition period?

Many thanks

[Jan]

Then the states cannot be uniquely identified. See this example with a shorter pattern

UP = [1,1,1,x,x,x,x,0,0,0]  % Pattern: 3*1, 4 transitions, 3*0
signal = [1,1,1,1,0,0,0,0,0,0]
UP 1:     ^ ^ ^ x x x ^ ^ ^ 
UP 2:       ^ ^ ^ x x x ^ ^ ^

Which one should be chosen?

Answer 1

[Jan]

up1 = strfind(con.', ones(1, 100));
up2 = strfind(con.', zeros(1, 80));
up  = intersect(up1, up2 - 21);

Cleanup detections with a too short distance:

upc = zeros(size(up));
t = -Inf;
c = 0;
for k = 1:numel(up)
    if up(k) - t > 201
        c      = c + 1;
        upc(c) = up(k);
    end
end
up = upc(1:c);

There might be a nicer version.