forwardModelDemo_Summer2021.asv

% forwardModelDemo: Illustrate the principle of inverted encoding models
%
% Implementation for 3D motion perception
% by Bas Rokers (rokers@nyu.edu)
% Based on demo of forward model for estimating
% tuning functions (TFs)
% js: 9.9.2014, (jserences@ucsd.edu)

% Relevant papers:
% Brouwer & Heeger, 2009 - http://www.jneurosci.org/content/jneuro/29/44/13992.full.pdf
% Kok, Brouwer et al, 2013 - http://www.jneurosci.org/content/jneuro/33/41/16275.full.pdf
% Sprague, Ester, Serences, 2014 - https://www.sciencedirect.com/science/article/pii/S096098221400935X

% Requirements:
% Matlab deep learning toolbox (plotconfusion)
% Circular statistics toolbox - https://github.com/circstat/circstat-matlab

restoredefaultpath
circstat_path = '~/Documents/GitHub/circstat-matlab';
if exist(circstat_path,'dir')
    addpath(genpath('~/Documents/GitHub/circstat-matlab')); % Add Circular Statistics toolbox
else
    error('Please install the Circular statistics toolbox - https://github.com/circstat/circstat-matlab')
end
set(0, 'DefaultLineLineWidth', 2); % Set figure linewidth default

clear all;
close all;

%% Section 0: Parameters

% Encoding model
nChans      = 8; % number of channels in your model (does not have to match # stim features).
basis       = 'cosine'; %'von_mises'; %'delta'; %'cosine', 'von_mises'

% Data
nDirections = 8; % number of stimulus directions in your study
nRepeats    = 20; % number repeats of each motion direction for the simulation
nTrials     = nRepeats * nDirections; % number of trials in your experiment.

nFolds = 250; % n-fold cross-validation

%% Section 1: Build encoding model

% design the basis function for estimating the channel weights in each voxel
% basis function is nChannels x nDirections
xs = linspace(0, 360-360/nDirections, nDirections);
channel_peaks = linspace(0, 360-360/nChans, nChans);
switch basis
    case 'delta'
        bf = eye(nChans); % delta functions
    case 'cosine'
        exponent = 5;
        for ii = 1:nChans
            bf(ii,:) = cosd(channel_peaks(ii)-xs).^exponent; % cosine
        end
    case 'von_mises'
        kappa = 5; % concentration parameter, like 1/sigma
        for ii = 1:nChans
            bf(ii,:) = circ_vmpdf(pi.*xs./180, pi*xs(ii)./180, kappa); % von mises (to fix)
        end
    otherwise
        error('Unknown basis function')
end

% Lowell wants to explore bimodal gaussians
% Lowell: Can you provide some motivation?

bf = max(0,bf); % rectify
% bf = bf./max(bf); % norm to unit height

%% Plot model
figure(1); hold on
ph = plot([xs 360],[bf, bf(:,1)]); % repeat 0 deg data at 360
xlabel({' ','Motion Direction (deg)'})
ylabel({' ','Channel Response',' '});
title('Encoding model')
axis([0 360 0 1]);
xticks(0:45:360);
yticks(0:.25:1);

%% Section 2: Load data

% TAFKAP_Decode(data, params);
% data is nTrials x nVoxels

sub = 'sub-0201';
ses = {'01'}; %,'02'};
run = 1:10; %[[1:10]'];%,[1:10]'];
roi =  {'V2'};
% roi =  {'V1','V2','hMT','IPS0'};
%roiname =  {'V1','V2','V3','V3A','hV4','LO','hMT','MST','IPS'};
% roiname = {'V1','V2','V3','V3A','V3B','hV4','LO1','LO2','hMT','MST','IPS0','IPS1','IPS2','IPS3','IPS4','IPS5','VO1','VO2','SPL1','PHC1','PHC2','FEF'};
projectDir = '~/Dropbox (RVL)/MRI/Decoding/';
DATA = loadmydata(sub,ses,run,projectDir,roi);

gg = [5:-1:1 8:-1:6 4:8 1:3]'; % true trial design matrix across all runs %lh
g = repmat(gg,10,1);

% This demo contains V1, MT and IPS data for one participant (br)
% 3D motion stimuli are presented in 8 labeled directions, where
% 1: rightward, 3: towards, 5:leftward, and 7: away.
% Intermediate values reflect intermediate directions moving directly
% towards or away from one of the eyes

% Heads up TAFKAP does:
% normalize per TR over voxels. Check if that matters
% Also, make sure to pull TAFKAP again

% load('workspace.mat') % fft detrended, z-scored data
% load('workspace_pct.mat'); % percent BOLD change data
% load('workspace_pct_poly.mat'); % percent BOLD change data, 1st order polynomial detrend
% load('workspace_poly_z.mat'); % polynomial detrend, z-scored
% load('workspace_sub-205-poly-0_z.mat'); % sub-205, polynomial detrend, z-scored
% load('workspace_sub-205-poly-3_z_roi-all.mat'); % sub-205, polynomial detrend, z-scored

% % load data directly
% for ii = 1 %1:20
%     % load fmriprepped data
%     nii{ii} = niftiread('~/Dropbox (RVL)/MRI/Decoding/derivatives/fmriprep/sub-0201/ses-01/func/sub-0201_ses-01_task-3dmotion_run-1_space-T1w_desc-preproc_bold.nii.gz');
%
%     % apply mask
%     mask = niftiread('~/Dropbox (RVL)/MRI/Decoding/derivatives/fmriprep/sub-0201/ses-01/anat/rois/sub-0201_space-T1w_downsampled_V1.nii.gz');
%     mask = repmat(mask,[1,1,1,250]);
%
%     nii_masked{ii} = nii{ii}(mask);
%
%     % extract timeseries in mask
%     masked_nii{ii} = cosmo_slice
%
%
%     % detrend, normalize and average
% end

% _pct data has some outliers (>500% signal change) in V1 that affect the
% results
% Contains rois (roi names), new_p (parameters),
% and masked_ds (trials x voxels dataset organized by roi)

for whichRoi = 1:length(roi)
    % whichRoi = 1; % V1 - 1, hMT - 2, IPS - 3

    % take average of every 2 TRs
    data = (DATA{whichRoi}(1:2:end-1,:) + DATA{whichRoi}(2:2:end,:)) ./2;

    % average every 8 datapoints (if wanted)
    % data = squeeze(mean(reshape(data,15,8,[])));

    % data = masked_ds{whichRoi}.samples;

    g = repmat(1:8,1,15)';
    % g = round(new_p.stimval./22.5); % ground truth, convert back to labels 1-8
    % block = new_p.runNs; % block/scan indices

    % data = DATA{whichRoi};

    % zero-meaning seems to result in weird behavior, rank-deficiency errors
    % and strange channel response reconstruction
    % at least for non-delta basis functions
    % BR thinks it has something to do with:
    % If the channels peak exactly on or halfway between the stimuli you sampled,
    % then the problem is underspecified, as the two channels on either side
    % of each sampled stimulus value make the same prediction for the response at that stimulus value.

    % Inspect data
    figure(2)
    imagesc(data)
    title('Measured voxel response')
    xlabel('Voxel #')
    ylabel('Trial #')

    % % Old (UW data)
    % load('myData_br_V1.mat')
    % load('myData_br_MT.mat') % contains trials x nVoxels
    % % load('myData_br_IPS.mat')
    %
    % % data is trials x voxels
    % data = [traindat; testdat]; % reconstitute. Data was originally 50/50 split
    % g = [Truth; Truth]; % presented direction on each trial
    % block = sort(repmat((1:nRepeats)', nDirections, 1));

    %% STEP 3: Hold one block out and solve for channel weights: 'Forward model'

    chan = []; chan_tstg = []; totpred_direction

    for ff=1:nFolds % Hold one fold out at a time
        fprintf('Computing iteration %d out of %d\n', ff, nFolds);

        % stratify by scan and motion direction
        % sometimes shows weird reconstructed channel responses
        % c.training = (block ~= (rem(ff,20)+1));   % set training data
        % c.test = ~c.training;                     % data from training scans (all but one scan)

        % Hold one out cross validation
        c = cvpartition(g, 'Holdout', 0.2);                 % stratify by motion direction, but not scan
        trn = data(c.training,:);                   % training data
        tst = data(c.test,:);                       % test data

        trng = g(c.training);                       % trial labels for training data.
        tstg = g(c.test);                           % trial labels for test data.

        % create the design matrix for computing channel weights in each voxel
        X = zeros(size(trn,1), nChans); % initialize predicted channel responses

        % Define presented directions
        % presented_dir = [0 80 90 100 180 260 270 280]; % 24.0063% in MT, delta function
        % presented_dir = [0 70 90 110 180 250 270 290]; % 24.6938% in MT
        % presented_dir = [0 60 90 120 180 240 270 300]; % 28.3938% in MT
        % presented_dir = [0 55 90 125 180 235 270 305]; % 29.325% in MT
        % presented_dir = [0 50 90 130 180 230 270 310]; % 29.175% in MT
        % presented_dir = linspace(0, 360-360/nChans, nChans); % 29.2188% in MT
        % presented_dir = [0 30 90 150 180 210 270 330]; % 28.8813% in MT - better l/r decoding, worse t/a

        for ii=1:size(trn,1)
            % populate predicted channel responses
            % Retinal motion channel responses
            X(ii,:) = bf(:,trng(ii)); % rows: observations (trials), columns: predicted response of each orientation channel
            % Or use channel responses closer to world motion Oblique
            % trajectories are closer to toward/away trajectories, so would
            % produce more similar channel responses
            % will not work correctly for delta basis function, as it will just
            % rescale relative amplitude of basis functions
            % X(ii,:) = fshift(bf(1,:),presented_dir(trng(ii))*4/180); % rows: observations (trials), columns: predicted response of each orientation channel

        end

        % use a GLM to compute weight of each channel in each
        % voxel, based on data from the training set.
        w = X\trn; % channel weights matrix - or inv(X'*X)*X'*trn;
        
        % Optional - regularize (shrink weights)
        % TODO 

        % then invert and apply to test data ...
        % basically, you solved for the weights using the
        % training data, now you have some observed data from the test set, and
        % you want to infer the channel response profile (tuning function) that
        % best maps the known selectivity of each voxel (w) to the test data
        x = (w'\tst')';  % reconstructed channel responses - or (inv(w*w')*w*tst')'

        % stack up the channel responses from each iteration of holding
        % one fold out... chan contains blocks by directions (20x8) by channels (8)
        %chan((ff-1)*nDirections+1:ff*nDirections,:) = x;
        chan = [chan; x];
        chan_tstg = [chan_tstg; tstg];


        % Compute predicted motion direction
        pred_direction = [];
        for ii = 1:length(tstg)
            pred_direction(ii) = mod(rad2deg(circ_mean(deg2rad(channel_peaks),x(ii,:))),360);
        end
        total_pred_direction = [total_pred_direction; pred_direction];
    end

    %% Visualize Results %%
    nplot = ceil(sqrt(length(roi)));

    %% Plot channel weights (w) for a sample voxel
    figure(3); hold on
    title('Channel weights (w) for a sample voxel')
    subplot(nplot,nplot,whichRoi)
    whichVoxel = 10; % Pick a sample voxel
    bar(w(:,whichVoxel))
    xlabel('Channel (deg)')
    ylabel('Weight')
    title(['Channel weights (voxel ' num2str(whichVoxel) ')'])
    xlim([.5 nChans+.5])
    set(gca,'xticklabel', xs)
    title(roi(whichRoi))

    %% Plot combined channel response for test data

    figure(5), hold on
    subplot(nplot,nplot,whichRoi)
    meanchan = grpstats(chan,chan_tstg)'; % calculate mean per channel
    ph = plot([xs 360], [meanchan meanchan(:,1)],'o-'); % tuning each direction
    % plot([0 360],[mean(mean(chan)) mean(mean(chan))],'k:'); % mean response

    % format figure
    if whichRoi == length(roi)
        lh = legend(cellfun(@num2str,num2cell(xs), 'UniformOutput',false));
        set(lh, 'Location', 'northeastoutside')
    end

    title(lh,'Presented direction')

    title([roi(whichRoi) 'Mean Reconstructed channel response'])
    xlabel('Direction Channel (deg)')
    ylabel('Estimated Response')
    xticks([0:45:360])
    xlim([0 360])

    % % Compute average reconstructed channel response
    % for ii = 1:nDirections
    %     mean_chan(ii,:) = mean(chan(ii:nDirections:nTrials,:));
    % end
    %
    % figure; hold on
    % plot([xs 360],[mean_chan mean_chan(:,1)])
    % title('Mean channel response (averaged over hold-outs)')
    % xlabel('Direction (deg)')
    % ylabel('Channel response')
    % xticks([0:45:360])
    % xlim([0 360])
    % lh = legend(cellfun(@num2str,num2cell(xs), 'UniformOutput',false));
    % set(lh, 'Location', 'northeastoutside')
    % title(lh,'Presented direction')

    %% Plot combined channel response for test data
    % Response as a function of presented direction, grouped by stimulus 
    % x - reconstructed channel response
    % tstg - presented direction label
    figure(9)
    hold on
    for ii = 1:length(tstg)
        plot(xs,sum(x(ii,:)'.*bf))
    end
    legend(num2str(tstg))
    % plot()
    xlabel('Direction (deg)')
    ylabel('Combined Channel Response')

    %% Make predictions (based on weighted sum of channel responses
    for ii = 1:length(tstg)
        pred_direction(ii) = mod(rad2deg(circ_mean(deg2rad(channel_peaks),x(ii,:))),360);
    end
    figure(20)
    subplot(nplot,nplot,whichRoi)
    scatter(xs(tstg),pred_direction)
    lsline
    xlabel('Presented direction label')
    ylabel('Predicted direction label')
    xlim([0 360])
    ylim([0 360])
    title(roi(whichRoi))

    %% Make predictions (based on correlation between observed and predicted
    % reconstruction)

    %% Plot confusion matrix (presented vs reconstructed (max x) over iterations

    % compute predicted motion direction
    for ii = 1:size(chan_tstg)
        [~, pred(ii)] = max(chan(ii,:)); % This is wrong as it predominantly produces estimates that align with the peak of a channel
    end

    % Instead either
    % (1) compute a weighted circular sum of the channel weights and its basis
    % function peak
    % (2) generate predicted channel responses for stimuli on 0:360 in 1 deg
    % increments, and pick the stimulus direction where the resulting curve
    % correlates best with the observed combined weighted channel response

    % figure; hold on
    % plotconfusion(categorical(g),categorical(pred'),'Test')

    % or alternatively, fit von mises to chan and read off mean

    % or do it yourself
    conmat = confusionmat(categorical(chan_tstg),categorical(floor(pred_direction/45))');
    conmat = conmat.*nDirections./length(chan_tstg);

    figure(6); hold on;
    subplot(nplot,nplot,whichRoi)
    conmat = [conmat; conmat(1,:)]; % wrap matrix
    conmat = [conmat, conmat(:,1)];
    imagesc(conmat);
    % clim = [0 .5]; % upper, lower limits
    % imagesc(conmat, clim);

    xlabel('Presented direction')
    ylabel('Decoded direction')

    xticks([1:9])
    xticklabels(cellstr([{char(8594)} {char(8599)} {char(8593)} {char(8598)} {char(8592)} {char(8601)} {char(8595)} {char(8600)} {char(8594)}]))

    yticks([1:9])
    yticklabels(cellstr([{char(8594)} {char(8599)} {char(8593)} {char(8598)} {char(8592)} {char(8601)} {char(8595)} {char(8600)} {char(8594)}]))

    axis tight
    title(roi(whichRoi))

    if whichRoi == length(roi)
        cb = colorbar;
    end
    cb.Label.String = 'Classification performance (%)';

    % % Todo: Make blue/white/red colorbar, with white = chance performance
    % % Or maybe red -> blue with transparency?
    % T = [255,   0,   0          %// red
    %      255, 255,  255         %// white
    %      255, 255,  255         %// white
    %      0, 0, 255]./255; %// blue again  -> note that this means values between 161 and 255 will be indistinguishable
    % x = [0; 50; 100; 255];
    % mymap = interp1(x/255,T,linspace(0,1,255));
    %
    % colormap(mymap)
    % % use caxis

    %% Extra stuff follows below

    %% Plot average tuning function for each cross-validated test stimulus

    % Shift the rows (tf on each trial) so that the channel corresponding to the stimulus on
    % each trial is in the middle column

    for ii=1:size(chan,1)
        schan(ii,:) = circshift(chan(ii,:), -chan_tstg(ii)+5); % center on 0 deg channel
    end

    figure(7), hold on
    plot([-180:360/nChans:180], [mean(schan), mean(schan(:,1))],'o-')
    % plot([-180 180],[mean(mean(schan)) mean(mean(schan))],'k:'); % mean response
    xlabel('Distance from Preferred Direction (deg)')
    ylabel('Estimated Response')
    title('Mean Tuning/Channel Response Function')
    xlim([-180 180])
    xticks([-180:45:360])
    if whichRoi == length(roi)
        legend(roi)
    end

    %% Or as a matrix
    % figure
    % imagesc(meanchan)
    % xlabel('Channels');
    % ylabel('Stimuli');
    % colorbar
    % axis xy

    %% How well did we do on the test set?
    disp(['Overall accuracy: ' num2str(100.*mean(chan_tstg == pred')) '%'])

end