bz_firingMapAvg.m

[dlevenstein]

Hey guys - I'm trying to use bz_firingMapAvg.m and am missing a function KalmanVel... can someone add this to the repo?

[dlevenstein]

@valegarman maybe?

[samamckenzie]

this is my old function pulled from the web, maybe it was modified for the repo

On Tue, Jul 28, 2020 at 3:16 PM Dan Levenstein notifications@github.com wrote:

@valegarman https://github.com/valegarman maybe?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/buzsakilab/buzcode/issues/391#issuecomment-665287527, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADM57AAG57EXS3ELUURKFR3R545Z3ANCNFSM4PK5YWKA .

function [t,x,y,vx,vy,ax,ay] = KalmanVel(posx,posy,post,order,Q,R) % root.KalmanVel(x, y, t, order); % % Code adapted from Sturla Molden (see below) to work within CMBHOME % framework. Returns the velocity estimation using the Kalman Filter on % recorded position. % % Kalman filter for obtaining an appriximate Bayesian MAP estimate to the rat's % trajectory from raw video tracker data. % % The trajectory model is the set of Taylor series expansions: % % x(t) = x(a) + x'(a)(t-a) + 1/2 x''(a)(t-a)^2 + o(h) % x'(t) = x'(a) + x''(a)(t-a) + o(h)
% x''(t) = x''(a) + o(h) % % The prediction step vill approximate the state variables [x(t), x'(t), x''(t)] % by expanding around a = t-1. The correction step will use the observation % at time t and the estimated state to create a corrected ("filtered") estimate % of the state at time t. The corresponding state space model is: %
% state: x(t+1) = A x(t) + w, with w ~ N(0,Q)
% observation: z(t) = H x(t) + v, with v ~ N(0,R) % % % Mandatory input arguments to the routine: % % posx, posy, post -- tracker raw data and time stamps % % order -- order of approximation (Taylor series) to the trajectory % 0: ignore all derivatives (locally constant approximation)
% 1: include first derivatile (locally linear approximation) % 2: include first and 2nd derivative (locally quadratic approximation) % % NB! It looks like the quadratic approximation is the better method, at % least for recordings where the rat swims in circle(s). Note that circular % velocity and acceleration are not included in the state model, we might % get a better filter for these data by including these parameters.
% % Optional arguments:
% % Q -- a priori specified system noise covariance matrix, rank (2+2order) x (2+2order) % default value: 0.1 eye(2 + 2order)
% % R -- a priori specified measurement noise covariance matrix, rank 2 x 2 % default value: eye(2) % % Output arguments from the Kalman filter: % % t(k) -- time stamps for filter output % % [x(k), y(k)] -- approximately the most probable location at time t(k) conditional % on the observed [posx,posy] in the period [t(1),t(k)], the a priori specified % Q and R matrices, and the prior state variable. % % [vx(k), vy(k)] -- the most probable velocity at time t(k) conditional on the % observed [posx,posy] in the period [t(1),t(k)] and the a priori specified Q and % R matrices, and the prior state variable.
% % [ax(k), ay(k)] -- the most probable acceleration at time t(k) conditional on the % observed [posx,posy] in the period [t(1),t(k)], the a priori specified Q and % R matrices, and the prior state variable.
% % Missing positions indicated by the value NaN for posx and posy are fitted using % the EM algorithm of Dempster et al. (1977). % % % Copyright (C) 2004 Sturla Molden % Centre for the Biology of Memory % Norwegian University of Science and Technology % %

% Default values. These are manually tuned for good performance if (nargin < 5) Q = 0.1 eye(2 + 2order); end if (nargin < 6) R = eye(2); end % Chop off any missing data in the start of session n = length(posx); lastmissing = min(find(isfinite(posx))) - 1; posx = posx(lastmissing+1:end); posy = posy(lastmissing+1:end); post = post(lastmissing+1:end); % Run Kalman filter on the remaining samples missing = zeros(n,1); missing(isnan(posx)) = 1; if (sum(missing)) % Missing data, use EM algorithm to get MAP estimators (Dempster et al. 1977) % Find the missing data we want to augment, initially augment % with Kalman predicted positions, then augment with Kalman filtered % positions. Iterate ten times to allow the augmented data to converge. missing_index = find(missing); [x,y,vx,vy,ax,ay] = kfilter(posx,posy,post,order,Q,R,1,missing); for i = 1:10 posx(missing_index) = x(missing_index); posy(missing_index) = y(missing_index); [x,y,vx,vy,ax,ay] = kfilter(posx,posy,post,order,Q,R,0); end else % No missing data, get the MAP estimates from a single pass [x,y,vx,vy,ax,ay,mm] = kfilter(posx,posy,post,order,Q,R,0); end t = post;

% This is the actual Kalman filter function [x,y,vx,vy,ax,ay,mm] = kfilter(posx,posy,post,order,Q,R,firstrun,missing) % allocate memory for return values n = length(posx); x = zeros(n,1); y = zeros(n,1); vx = zeros(n,1); vy = zeros(n,1); ax = zeros(n,1); ay = zeros(n,1); mm = zeros(n,1); % initialise return values and filtered state estimate x(1) = posx(1); y(1) = posy(1); vx(1) = 0; vy(1) = 0; ax(1) = 0; ay(1) = 0; switch (order) case {0} cX = [posx(1) posy(1)]'; case {1} cX = [posx(1) posy(1) 0 0]'; case {2} cX = [posx(1) posy(1) 0 0 0 0]'; end cP = 0.1eye(2 + 2order); I = eye(2+2order); outlier = 0; for k = 2:n % compute A and H from the time lag T = post(k) - post(k-1); switch(order) case {0} A = [1 0; ... 0 1]; H = [1 0; ... 0 1]; case {1} A = [1 0 T 0; ... 0 1 0 T; ... 0 0 1 0; ... 0 0 0 1]; H = [1 0 0 0; ... 0 1 0 0]; ...
case {2} A = [1 0 T 0 0.5TT 0; ... 0 1 0 T 0 0.5TT; ... 0 0 1 0 T 0; ... 0 0 0 1 0 T; ... 0 0 0 0 1 0; ... 0 0 0 0 0 1;];
H = [1 0 0 0 0 0; ... 0 1 0 0 0 0]; end if (firstrun & missing(k)) % missing data, only predict % in the next EM steps they will be augmented with their MAP estimates pX = A cX; pP = A cP A' + Q;
% the equations are obtained by setting the Kalman gain to zero cX = pX;
cP = pP;
else % data not missing, predict and correct % prediction step
pX = A cX; pP = A cP A' + Q; % observation z = [posx(k); posy(k)]; residual = z - HpX; % validation gate for robustifying against extreme outliers chisq = [1000, 1000, 1000]; % just use a ridicilous threshold invS = (HpPH' + R)^-1; % measurement prediction covariance mahalanobis = residual' invS residual; mm(k) = mahalanobis; if ((outlier>5) | (mahalanobis < chisq(order+1))) % within validation gate -- perform correction step with % the new measurement (i.e. non-zero Kalman gain) K = pP H' invS; cX = pX + Kresidual; cP = (I - KH)*pP; outlier = 0; else % outlier -- ignore this measurement
% the equations are obtained by setting the Kalman gain to zero cX = pX;
cP = pP;
outlier = outlier + 1; end
end % save Kalman filtered states (cX) x(k) = cX(1); y(k) = cX(2); if (order > 0) vx(k) = cX(3); vy(k) = cX(4); end if (order > 1) ax(k) = cX(5); ay(k) = cX(6); end end

[AntonioFR8]

I will upload it now. Let me know if the pf function works well for you. I think ipshita also made a version for trials, not sure is uploaded

On Tue, Jul 28, 2020 at 5:16 PM Dan Levenstein notifications@github.com wrote:

@valegarman https://github.com/valegarman maybe?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/buzsakilab/buzcode/issues/391#issuecomment-665287527, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADHSQQ3RS6OI66G2DVXC4ZLR545Z3ANCNFSM4PK5YWKA .

-- Antonio Fernandez-Ruiz, PhD Sir Henry Wellcome Post-doctoral fellow Buzsaki Lab. NYU Neuroscience Institute New York University, Langone Medical Center East River Science Park, 450 East 29th Street, 9th Floor New York, NY 10016

[dlevenstein]

I've hit/fixed a few bugs so far. Will upload fixes once I get it to run through

[dlevenstein]

Not sure why or if it matters but this code seems to systematically under-calculate the firing rate in place fields. Maybe in the smoothing step? The black line is from a basic histogram, blue line is from bz_findPlaceFieldStats

[dlevenstein]

ah, yeah - it's from the smoothing parameter... as I increase my bin overlap it becomes closer

[AntonioFR8]

which function is bz_findPlaceFieldStats? I can't find it

On Tue, Jul 28, 2020 at 6:14 PM Dan Levenstein notifications@github.com wrote:

ah, yeah - it's from the smoothing parameter... as I increase my bin overlap it becomes closer

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/buzsakilab/buzcode/issues/391#issuecomment-665311021, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADHSQQZHU5Z3CUULF5RMDOTR55ETBANCNFSM4PK5YWKA .

-- Antonio Fernandez-Ruiz, PhD Sir Henry Wellcome Post-doctoral fellow Buzsaki Lab. NYU Neuroscience Institute New York University, Langone Medical Center East River Science Park, 450 East 29th Street, 9th Floor New York, NY 10016

[dlevenstein]

sorry, I mean bz_firingMapAvg