function RemoveFramesFunction(movName,removeCornersFlag,removeEdgesFlag)
% RemoveFramesFunction_v3_flycap loads the movie, plays it so the user can find the frames to keep,
% and crops the rest of the frames.
%
% WARNING: the original movie is overwritten! Please keep all originals in a separate place.
%
%%%%%%% Arguments:
% movName [string]: name of movie to crop
% removeCornersFlag ['y' or 'n'];
    % 'y' means ignore corners of frames (connected components in frames that have a pixel in a corner).
    % 'n' means analyze frames "as is".
% removeCornersFlag ['y' or 'n'];
    % 'y' means ignore corners of frames (connected components in frames that have a pixel in a corner).
    % 'n' means analyze frames "as is".
% removeEdgesFlag ['y' or 'n'];
    % 'y' means remove all black pixels connected to edges (connected components in frames that have a pixel within
    % 3 pixels of the edge).
    % 'n' means analyze frames "as is".
%%%%%% Instructions:
% The movie is "shown" in 25 frame blocks. Record the FIRST frame to keep and the LAST frame to keep. 0 is ignored.
% For example: if right side does not need to be cut, setting the LAST frame to keep to 0 (or any number greater
% than numFrames) means that the right side will not get cut. Similarly for the left side.
% You will get a chance to see the movie as many times as you want to confirm. After choosing the 
% first and last frame, the movie will be cropped appropriately and overwrite the existing file. 
% WARNING AGAIN: IT IS IMPORTANT TO KEEP THE ORIGINAL MOVIE IN A DIFFERENT FOLDER AS THE MOVIE IS OVERWRITTEN!


workingDir = tempname;
mkdir(workingDir);
mkdir(workingDir,'images');

close

% Load Original Movie And Create Sorted Images From Frames
movOriginal = VideoReader(movName);
numFrames = movOriginal.NumberOfFrames; %#ok<*VIDREAD>
movHeight = movOriginal.Height;
movWidth = movOriginal.Width;

for i = 1:numFrames
    img = read(movOriginal,i);
    img = img(:,:,2); % take only green channel (camera was set to process in "green-scale")
    imwrite(img,fullfile(workingDir,'images',sprintf('img%d.jpg',i)));
end

imageNames = dir(fullfile(workingDir,'images','*.jpg'));
imageNames = {imageNames.name}';

imageStrings = regexp([imageNames{:}],'(\d*)','match');
imageNumbers = str2double(imageStrings);

[~,sortedIndices] = sort(imageNumbers);
sortedImageNames = imageNames(sortedIndices);


for n = 1:ceil(numFrames/25)
    close
    figure('units','normalized','outerposition',[0 0 1 1])
    for i = 1+25*(n-1):min(25*n,numFrames)
        subplot(5,5,mod(i-1,25)+1)
        img = imread(fullfile(workingDir,'images',sortedImageNames{i}));
        imshow(img)
        title(['Frame = ',num2str(i)])
        if mod(i+1,25) == 1                
            pause
        end
        imshow(img)
        title(['Frame = ',num2str(i)])
    end
end


% Ask for frame boundaries
    % cut before left frame, after right frame, 0 gets ignored - e.g. if you want to crop before a certain frame only)
movReplayAnswer = 'y';
leftFrameCut = 0; % defaults - movie unchanged
rightFrameCut = 0;  % defaults - movie unchanged
framesToRemoveLeft = [];
framesToRemoveRight = [];
while not(isequal(movReplayAnswer,'n'))
    movieReplayPrompt = 'Show movie again? (y/n)';
    movReplayAnswer = inputdlg(movieReplayPrompt,'Movie Replay?');
    
    if isequal(movReplayAnswer,{}) % cancel is pressed
        break
    else
        movReplayAnswer = movReplayAnswer{1}; % take entry
    end
    
    if isequal(movReplayAnswer,'y')
        close
        figure('units','normalized','outerposition',[0 0 1 1])
        for n = 1:ceil(numFrames/25)
            close
            figure
            for i = 1+25*(n-1):min(25*n,numFrames)
                subplot(5,5,mod(i-1,25)+1)
                img = imread(fullfile(workingDir,'images',sortedImageNames{i}));
                imshow(img)
                title(['Frame = ',num2str(i)])
                if mod(i+1,25) == 1                
                    pause
                end

                imshow(img)
                title(['Frame = ',num2str(i)])
            end
        end
    elseif isequal(movReplayAnswer,'n')
        dlgTitle = 'Input first and last frames to keep. Use 0 to ignore that side.';
        promptLeftCut = 'First frame to keep (0 to ignore):';
        promptRightCut = 'Last frame to keep (0 to ignore):';
        num_lines = 1;
        inputPrompts = {promptLeftCut,promptRightCut};
        dlgDefaults = {'0','0'};
        frameCells = inputdlg(inputPrompts,dlgTitle,num_lines,dlgDefaults);
        if not(isequal(frameCells,{})) % cancel not pressed
            leftFrameCut = str2num(frameCells{1}); %#ok<*ST2NM>
            rightFrameCut = str2num(frameCells{2});
        end
    else
        display('Unrecognized Key')
    end
end


if leftFrameCut ~= 0 && not(isempty(leftFrameCut))
    leftFrameCut = round(leftFrameCut);
    framesToRemoveLeft = 1:leftFrameCut-1;
end

if rightFrameCut ~= 0 && not(isempty(rightFrameCut))
    framesToRemoveRight = rightFrameCut+1:numFrames;
end

framesToRemove = union(framesToRemoveLeft,framesToRemoveRight);

% Crop Movie

for i = framesToRemove
    delete(fullfile(workingDir,'images',sortedImageNames{i})) % BE CAREFUL, AS DELETE DOES NOT GIVE ANY WARNINGS WHEN REMOVING FILES
end

imageNames = dir(fullfile(workingDir,'images','*.jpg'));
imageNames = {imageNames.name}';

imageStrings = regexp([imageNames{:}],'(\d*)','match');
imageNumbers = str2double(imageStrings);

[~,sortedIndices] = sort(imageNumbers);
sortedImageNames = imageNames(sortedIndices);

numFrames = length(sortedImageNames);


if isequal(removeCornersFlag,'y')
    cornerIdx = [sub2ind([movHeight movWidth],1:7,1:7),...
        sub2ind([movHeight movWidth],movHeight:-1:(movHeight-6),1:7),...
        sub2ind([movHeight movWidth],1:7,movWidth:-1:(movWidth-6)),...
        sub2ind([movHeight movWidth],movHeight:-1:(movHeight-6),movWidth:-1:(movWidth-6))];
    for i = 1:numFrames
        img = imread(fullfile(workingDir,'images',sortedImageNames{i}));
        imgForCornerRemoval = im2bw(img,.3); % hard code low threshold to really get corners
        connectedComponentsForCornerRemoval = bwconncomp(~imgForCornerRemoval,4);
        connectedComponentsForCornerRemoval = connectedComponentsForCornerRemoval.PixelIdxList;
        for j = 1:length(connectedComponentsForCornerRemoval)
            if not(isempty(intersect(connectedComponentsForCornerRemoval{j},cornerIdx)))
                img(connectedComponentsForCornerRemoval{j}) = 256; % set to be WHITE in original image (since fly is black)
                    % remember: white is 256 (this is a greyscale image)
                imshow(img)
            end
        end
        imwrite(img,fullfile(workingDir,'images',sprintf('img%d.jpg',i)));
    end
    
    imageNames = dir(fullfile(workingDir,'images','*.jpg'));
    imageNames = {imageNames.name}';

    imageStrings = regexp([imageNames{:}],'(\d*)','match');
    imageNumbers = str2double(imageStrings);

    [~,sortedIndices] = sort(imageNumbers);
    sortedImageNames = imageNames(sortedIndices);

    numFrames = length(sortedImageNames);    
end


if isequal(removeEdgesFlag,'y')
    edgeIdx = [sub2ind([movHeight movWidth],1:movHeight,1*ones(1,movHeight)),...
        sub2ind([movHeight movWidth],1:movHeight,movWidth*ones(1,movHeight)),...
        sub2ind([movHeight movWidth],movHeight*ones(1,movWidth),1:movWidth),...
        sub2ind([movHeight movWidth],1*ones(1,movWidth),1:movWidth)];
    for i = 1:numFrames
        img = imread(fullfile(workingDir,'images',sortedImageNames{i}));
        imgForEdgeRemoval = im2bw(img,.6); % hard code reasonably high threshold to really get all dark pixels
            % that form edges. NOTE: this will ALSO remove the fly if even a leg touches an edge
            % pixel or anything close to that - it will be visible in the
            % frames to remove.

        connectedComponentsForEdgeRemoval= bwconncomp(~imgForEdgeRemoval,4);
        connectedComponentsForEdgeRemoval = connectedComponentsForEdgeRemoval.PixelIdxList;
        for j = 1:length(connectedComponentsForEdgeRemoval)
            if not(isempty(intersect(connectedComponentsForEdgeRemoval{j},edgeIdx)))
                img(connectedComponentsForEdgeRemoval{j}) = 256;
                imshow(img)
            end
        end
        imwrite(img,fullfile(workingDir,'images',sprintf('img%d.jpg',i)));
    end
    
    imageNames = dir(fullfile(workingDir,'images','*.jpg'));
    imageNames = {imageNames.name}';

    imageStrings = regexp([imageNames{:}],'(\d*)','match');
    imageNumbers = str2double(imageStrings);

    [~,sortedIndices] = sort(imageNumbers);
    sortedImageNames = imageNames(sortedIndices);

    numFrames = length(sortedImageNames);    
end



outputCroppedMovie = VideoWriter(movName);
outputCroppedMovie.FrameRate = movOriginal.FrameRate;
open(outputCroppedMovie);
for i = 1:numFrames
    img = imread(fullfile(workingDir,'images',sortedImageNames{i}));
    writeVideo(outputCroppedMovie,img);
end
close(outputCroppedMovie);

end