twinTreeTM/plot_ConnectedGrains.m at main · MONSTERgroup/twinTreeTM · GitHub

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function plot_ConnectedGrains(grainsVar, mergedGrains, connectedGrains, allNeighTwins, connComponents, varargin)
    % Plotting ConnectedGrains and More

    if ~isempty(varargin{1})
        allTwinBoundaries = varargin{1};
    end

    imgSampPath = evalin('base', 'imgSampPath');
    samp_name = evalin('base', 'samp_name');
    methodName = evalin('base', 'methodName');

    phaseName = evalin('base', 'phaseName');
    if length(grainsVar.mineralList) > 1
        grainsVar = grainsVar(phaseName);
    end

    figure;
    plot(grainsVar, grainsVar.meanOrientation)
    hold on
    plot(grainsVar.boundary, 'linecolor', 'k', 'linewidth', 1)
    plot(mergedGrains.boundary, 'linecolor', 'r', 'linewidth', 1.5, 'linestyle', '-', ...
        'displayName', 'merged grains')
    plot(connectedGrains.boundary, 'linecolor', 'k', 'linewidth', 2, 'linestyle', '-', ...
        'displayName', 'connected grains')
    hold off
    export_fig(char(fullfile(imgSampPath, sprintf('%s_connCompGBs_%s.png', samp_name, methodName))), '-m2');
    close

    if ~isempty(allTwinBoundaries)
        figure;
        plot(grainsVar, grainsVar.meanOrientation)
        hold on
        plot(grainsVar.boundary, 'linecolor', 'k', 'linewidth', 1)
        plot(allTwinBoundaries, allTwinBoundaries.prop.twinOrder, 'linewidth', 1.5)
        hold on
        plot(connectedGrains.boundary, 'linecolor', 'k', 'linewidth', 2, 'linestyle', '-') % ,'displayName', 'connected grains')
        hold off
        colormap(jet(6));
        setColorRange([0.5 6.5])
        mtexColorbar('title', 'twin order of twin boundaries');
        export_fig(char(fullfile(imgSampPath, sprintf('%s_connCompGBs_wTBs_%s.png', samp_name, methodName))), '-m2');
        close
    end

    numComponents = max(connComponents);
    cmap = lines(numComponents);
    componentColors = cmap(connComponents, :);

    figure;
    plot(grainsVar, componentColors)
    hold on
    plot(grainsVar.boundary, 'linecolor', 'k', 'linewidth', 1)
    plot(connectedGrains.boundary, 'linecolor', 'w', 'linewidth', 2, 'linestyle', '-') %,'displayName', 'connected grains')
    % title(sprintf('Connected Components (%d clusters)', numComponents))
    hold off
    export_fig(char(fullfile(imgSampPath, sprintf('%s_connComps_IDcolored_%s.png', samp_name, methodName))), '-m2');
    close

    % Plot connections within each component, colored by twin order
    figure;
    plot(grainsVar, grainsVar.meanOrientation)
    hold on
    plot(grainsVar.boundary, 'linewidth', 1)
    hold on
    plot(connectedGrains.boundary, 'linecolor', 'w', 'linewidth', 2, 'linestyle', '-')

    for i = 1:length(allNeighTwins)
        matrix = allNeighTwins{i};
        if isempty(matrix) || size(matrix, 2) < 2
            continue;
        end
        twinMask = matrix(:,2) ~= 0;
        if ~any(twinMask)
            continue;
        end
        neighbors = matrix(twinMask, 1);
        orders = matrix(twinMask, 2);
        centroid1 = grainsVar(i).centroid;
        for j = 1:length(neighbors)
            neighborId = neighbors(j);
            twinOrder = orders(j);
            if connComponents(i) == connComponents(neighborId)
                centroid2 = grainsVar(neighborId).centroid;
                cmap = jet(6);
                if twinOrder >= 1 && twinOrder <= 6
                    edgeColor = cmap(twinOrder, :);
                else
                    edgeColor = [0.5 0.5 0.5];
                end
                h = plot([centroid1(1), centroid2(1)], [centroid1(2), centroid2(2)], ...
                    'Color', edgeColor, 'LineWidth', 1.75);
                h.Color(4) = 0.45; % Set alpha to 0.5 (50% opacity), adjust between 0-1
            end
        end
    end

    title('Twin Connections within Connected Components');
    colormap(jet(6));
    setColorRange([0.5 6.5])
    mtexColorbar('title', 'twin order')
    hold off
    export_fig(char(fullfile(imgSampPath, sprintf('%s_connCompGBs_twinNetwork_%s.png', samp_name, methodName))), '-m2');
    close
end