giveROI.m

function varargout = giveROI(action,varargin)
% Returns features for a region-of-interest (ROI)
% giveROI(action)
%  action - particular operation relating to a ROI ('define')
%
% roi = giveROI('define',shape)
% Defines a region of interest
%   roi - structure of roi properties 
%   shape - string indicating the shape of the roi ('circular')
%
% roi = giveROI('define','circular',num_pts,r)
%   num_pts - number of points for bounding the roi
%   r - radius of circular roi
%   Centroid - structure definining the center coordinates for the roi
%
% roi = giveROI('define','circular',num_pts,r,xC,yC)
%   xC - roi x-center
%   yC - roi y-center
%
% im_roi = giveROI('unstabilized',im,roi,dSample)
% returns roi image, without rotation correction
%   im - full frame image
%   roi - structure with stats on roi
%   dSample - logical that indicates whether to downsample the roi image
%
% im_roi = giveROI('stabilized',im,roi,dSample,tform,imMean)
% returns roi image, WITH rotation correction
%   tform - rotation matrix for current frame 
%   imMean - (optional) mean image, used for image subtraction
%
%[im_roi,bw_mask,roi_rect,bw_roi_mask,imStable] = giveROI(...
%   im_roi - image within the roi (downsampled, if dSampling==1)
%   bw_mask - binary image for the roi with dimensions of im
%   roi_rect - [x y width height] of the roi bounding box
%   bw_roi_mask - binary of mask in roi
%   imStable - image stablized against rotation
%
% Developed by McHenryLab at UC Irvine


%% Translate inputs 

if strcmp(action,'define')
    
    roi.shape       = varargin{1};
    num_pts         = varargin{2};
    roi.r           = varargin{3};
    
    % Define center points
    if nargin>4
        roi.xCntr = varargin{4};
        roi.yCntr = varargin{5};
    else
        roi.xCntr = 0;
        roi.yCntr = 0;
    end
    
    
elseif strcmp(action,'unstabilized')
    
    im      = varargin{1};
    roi     = varargin{2};
    dSample = varargin{3};
    
    if nargin > 4
        imMean  = varargin{4};
    else
        imMean  = [];
    end
        
elseif strcmp(action,'stabilized')
    
    im      = varargin{1};
    roi     = varargin{2};
    dSample = varargin{3};
    tform   = varargin{4};
    
    if nargin > 5
        imMean  = varargin{5};
    else
        imMean  = [];
    end
    
elseif strcmp(action,'tform stabilized')
    
    im      = varargin{1};
    roi     = varargin{2};
    dSample = varargin{3};
    tform   = varargin{4};
    
    if nargin > 5
        imMean  = varargin{5};
    else
        imMean  = [];
    end
       
else
    error('Do not recognize action')
end


%% Parameters

if strcmp(action,'define')
    
    % Angular coordinates for circular roi
    roi.theta = linspace(0,2*pi,num_pts);
    
    % Circular coordinates for new roi in image FOR
    roi.xPerimG  = round(floor(roi.r-1).*cos(roi.theta) + roi.xCntr);
    roi.yPerimG  = round(floor(roi.r-1).*sin(roi.theta) + roi.yCntr);
    
    % Circular coordinates for new roi in roi FOR
    roi.xPerimL    = round(floor(roi.r-1).*cos(roi.theta) + roi.r);
    roi.yPerimL    = round(floor(roi.r-1).*sin(roi.theta) + roi.r);
    
    % Bounding rectange for the roi
    roi.rect = [round(roi.xCntr-roi.r) round(roi.yCntr-roi.r) ceil(roi.r*2) ceil(roi.r*2)];

else
    
    % Maximum size of an image dimension (for downsampling)
    maxSize = 250;
    
end


%% Create images

if ~strcmp(action,'define')
    
    pixval = 255;
    
    % Pad image to the left, if needed
    if roi.rect(1)<1
        n  = abs(roi.rect(1))+1;
        im = [ones(size(im,1),n).*pixval im];
        roi.rect(1) = 1;
    end
     
    % Pad image to the top, if needed
    if roi.rect(2)<1
        n           = abs(roi.rect(2))+1;
        im          = [ones(n,size(im,2)).*pixval; im];
        roi.rect(2) = 1;
    end
        
    % Pad image to the right, if needed
    if (roi.rect(1)+roi.rect(3)+1)>=size(im,2)
        n = ceil(roi.rect(1)+roi.rect(3)+2 - size(im,2));
        im = [im ones(size(im,1),n).*pixval];     
    end
    
    % Pad image to the bottom, if needed
    if (roi.rect(2)+roi.rect(4)+1)>=size(im,1)
        n = ceil(roi.rect(2)+roi.rect(4)+2 - size(im,1));
        im = [im; ones(n, size(im,2)).*pixval];     
    end
    
   clear n
        
    % Binary mask in image im    
    bw_mask = roipoly(size(im,1),size(im,2),...
        [roi.rect(1) roi.rect(1)+roi.rect(3)+1 ...
         roi.rect(1)+roi.rect(3)+1 roi.rect(1) ...
         roi.rect(1)],...
        [roi.rect(2) roi.rect(2) ...
         roi.rect(2)+roi.rect(4)+1 roi.rect(2)+roi.rect(4)+1 ...
         roi.rect(2)]);
    
    % Translate image (for tform stabilized mode)
    if strcmp(action,'tform stabilized')
        
        % Get angular rotation from tform
        %tformInv = invert(tform);
        
        % Translate image
        im = imtranslate(im,tform.T(3,1:2));
    end
     
    % Crop image
    im_roi  = imcrop(im,roi.rect);
    
    % Check that roi is square
    if size(im_roi,1)~=size(im_roi,2)
        error('Image not square and needs to be');
    end
    
    if ~isempty(imMean)
        im_roi = imadjust(imcomplement(imsubtract(imMean,im_roi)));
    end
    
    % White out pixels outside of circular roi
    %bw_roi_mask = roipoly(size(im_roi,1),size(im_roi,2),yCirc_roi,xCirc_roi);
    bw_roi_mask = roipoly(size(im_roi,1),size(im_roi,2),roi.yPerimL,roi.xPerimL);
    
    % White out area around roi
    im_roi(~bw_roi_mask) = 255;
    
    % Reduce size (helps speed up image registration)
    if dSample && (length(im)>maxSize)
        
        % Factor by which to resize
        imFactor = maxSize/length(im);
        
        % Downsample image
        im_roi = imresize(im_roi,imFactor);
        
        bw_roi_mask = imresize(bw_roi_mask,imFactor);
        % White out pixels outside of circular roi
        %bw_roi = roipoly(size(im_roi,1),size(im_roi,2),round(yC*imFactor),round(xC*imFactor));
    end

    
    if strcmp(action,'stabilized')
        
        if length(tform)>1 && isfield(tform,'T') && isempty(tform.T)
            error('You need to provide tform if you want imStable');
        end
        
        % If tform exists, calculate angle . . .
        if isprop(tform,'T')       
            % Get angular rotation from tform
            tformInv = invert(tform);
            rot_ang  = atan2(tformInv.T(2,1),tformInv.T(1,1))*180/pi;
            
        % Rotation angle passed as tform . . .
        elseif length(tform)==1
            rot_ang = tform;

        end
        
        imStable = imrotate(im_roi,-rot_ang,'bilinear','crop');
        
%         % Coordinate system for im_roi
%         R = imref2d(size(im_roi));
%         
%         % Adjust WorldLimits to restrict transformation to just rotation
%         % around center
%         R.XWorldLimits = R.XWorldLimits-mean(R.XWorldLimits);
%         R.YWorldLimits = R.YWorldLimits-mean(R.YWorldLimits);
% %         R.XIntrinsicLimits = R.XWorldLimits;
% %         R.YIntrinsicLimits = R.YWorldLimits;
%         
%         
%         % Stablize image
%         imStable = imwarp(im_roi,R,tform,'OutputView',R,...
%             'FillValues',255,'SmoothEdges',true);
        
        % White out beyond roi
        imStable(~bw_roi_mask) = 255;
        
        % Deliver imStable
        im_roi = imStable;
        
    elseif strcmp(action,'tform stabilized')
        

        
        rot_ang  = atan2(tform.T(2,1),tform.T(1,1))*180/pi;
        
        
        imStable = imrotate(im_roi,rot_ang,'bilinear','crop');
        

        % White out beyond roi
        imStable(~bw_roi_mask) = 255;
        
        % Deliver imStable
        im_roi = imStable;
        
        
    end
end


%% Define output

% If defining roi . . .
if strcmp(action,'define')
    
    varargout{1} = roi;
    
% Otherwise . . .
else
    
    varargout{1} = im_roi;
    
    if nargout>1
        varargout{2} = bw_mask;
        
        if nargout>2
            varargout{3} = bw_roi_mask;
            
        end
    end
end