PhoRigidAlignmentCompute.m

% Pho Rigid Alignment Computation Script: Pipeline Stage 0
% Pho Hale, November 10, 2020
% Given the specified dateStrings, computes the translations required to align all registered .tif files in a date folder with the "reference" date folder (the first one in the cell array).
% Produces a series of offsets, which are saved into an output file 'output.mat'.
addpath(genpath('helpers'));

dateStrings = {'20200117','20200120','20200124'}; % Strings representing each date.
[rawOutpaths, registeredOutpaths] = fnBuildPaths(dateStrings);

numberOfDays = length(registeredOutpaths);
numberOfOffsets = numberOfDays-1;
% Allocate output structures:
outputRegistrationCorrections.translation_offset_first_to_second = zeros(numberOfOffsets,2);

refIndicies = ones(numberOfOffsets,1); % All index 1
nextIndicies = 2:numberOfDays;

for i = 1:numberOfOffsets
    % Load first and second days:
    prevIndex = refIndicies(i);
    nextIndex = nextIndicies(i);

    % Get the tif paths for each
    registeredTifFolder_prev = registeredOutpaths{prevIndex}.tifFolder;
    registeredTifFolder_next = registeredOutpaths{nextIndex}.tifFolder;

    %% Main Loading:
    [registered_imageInfo_prev, registered_imageInfo_next] = fnLoadRelevantImages(registeredTifFolder_prev, registeredTifFolder_next);

    %% Main Computation:
    [offset_first_to_second, debugStructures] = fnPhoComputeRegistrationOffset(registered_imageInfo_prev.currRegisteredImage, registered_imageInfo_next.currRegisteredImage);
    outputRegistrationCorrections.translation_offset_first_to_second(i,:) = offset_first_to_second;

    % Shows simple offset:
    Rfixed = imref2d(size(registered_imageInfo_next.currRegisteredImage));
    registered = imwarp(registered_imageInfo_next.currRegisteredImage, debugStructures.tform, 'OutputView', Rfixed);

    figure(2)
    subplot(1,2,1)
    imshowpair(registered_imageInfo_prev.currRegisteredImage, registered_imageInfo_next.currRegisteredImage)
    title('Original Offsets')
    subplot(1,2,2)
    imshowpair(registered_imageInfo_prev.currRegisteredImage, registered)
    title('Fixed Offsets')
    disp('done.')
    
end

% Save the results if needed:
save('output.mat','dateStrings','outputRegistrationCorrections','-mat')

function [registered_imageInfo_prev, registered_imageInfo_next] = fnLoadRelevantImages(registeredTifFolder_prev, registeredTifFolder_next)
    % Set the datasources
    imds.registered_prev.ReadFcn = @fnCustomTifStackReader;
    imds.registered_next.ReadFcn = @fnCustomTifStackReader;

    % Load the datasources
    imds.registered_prev = imageDatastore(registeredTifFolder_prev,'IncludeSubfolders',false,'FileExtensions','.tif','LabelSource','foldernames');
    imds.registered_next = imageDatastore(registeredTifFolder_next,'IncludeSubfolders',false,'FileExtensions','.tif','LabelSource','foldernames');

    % Extract information from the loaded datastores
    registered_imageInfo_prev.count = size(imds.registered_prev.Files, 1);
    registered_imageInfo_next.count = size(imds.registered_next.Files, 1);

    % Get prev/next index:
    registered_imageInfo_prev.last_index = registered_imageInfo_prev.count;
    registered_imageInfo_next.first_index = 1;

    % Load the current data:
    registered_imageInfo_prev.fileName = imds.registered_prev.Files{registered_imageInfo_prev.last_index}; % Get the last index of the previous one
    registered_imageInfo_prev.currLoadedData = bfOpen3DVolume(registered_imageInfo_prev.fileName);
    registered_imageInfo_prev.currLoadedImgStack = registered_imageInfo_prev.currLoadedData{1,1}{1,1}; % Produces the desired 512x512x2000 (2000 frames per .tif) output
    registered_imageInfo_prev.imgStackSize.numberOfFrames = size(registered_imageInfo_prev.currLoadedImgStack,3);

    registered_imageInfo_next.fileName = imds.registered_next.Files{registered_imageInfo_next.first_index}; % Get the first index of the next one
    registered_imageInfo_next.currLoadedData = bfOpen3DVolume(registered_imageInfo_next.fileName);
    registered_imageInfo_next.currLoadedImgStack = registered_imageInfo_next.currLoadedData{1,1}{1,1}; % Produces the desired 512x512x2000 (2000 frames per .tif) output
    registered_imageInfo_next.imgStackSize.numberOfFrames = size(registered_imageInfo_next.currLoadedImgStack,3);

    %% Individual Frame Level
    % Load the last frame of the prev day and the first frame of the next day
    registered_imageInfo_prev.currRegisteredImage = registered_imageInfo_prev.currLoadedImgStack(:,:,registered_imageInfo_prev.imgStackSize.numberOfFrames); % Get the last from the first prev stack
    registered_imageInfo_next.currRegisteredImage = registered_imageInfo_next.currLoadedImgStack(:,:,1); % Get first frame from the next stack

    % imshow(registered_imageInfo_prev.currRegisteredImage)
    % imshow(registered_imageInfo_next.currRegisteredImage)

    fnPhoMatrixPlot(registered_imageInfo_prev.currRegisteredImage);
    fnPhoMatrixPlot(registered_imageInfo_next.currRegisteredImage);

    % registered_imageInfo_prev.currRegisteredImage = imds.registered_prev.readimage(registered_imageInfo_prev.imgStackSize.numberOfFrames); % Get the last from the first prev stack
    % registered_imageInfo_next.currRegisteredImage = imds.registered_next.readimage(1); % Get first frame from the next stack

    % Original Offset:
    figure
    imshowpair(registered_imageInfo_prev.currRegisteredImage, registered_imageInfo_next.currRegisteredImage)
    title('Original Offsets')
end