paths = {'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\a\',...
    'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\b\',...
    'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\c\',...
    'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\a_alt\',...
    'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\a\',...
    'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\b\',...
    'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\c\',...
    'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\d\'};

fontSize = 18;%font size in figs
lineWidth = 3;%line widths in figs (if you have lines
aspectRatio = 1;%aspect ratio of figs (may be irrelevant with zratio below)
zratio = 150;%aspect ratio of z axis to others (typically nm, while others um, so quite high)

lightStyle = 'gouraud';%the FaceLighting option in surf to use

%%% To change colormap of 2D plots, find line 'colormap jet' and change
%%% 'jet' to whatever you like

viewEl = [45:5:55];%list of view elevations to save for each image
viewAz = [45:5:55];%similar for azimuth

zLimits = [-2000,100];%typical values for surface plot z limits, 2um deep, allow 100nm above surface

cropIms = {5,0,643,543,'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\a\profile2.png','S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\a\pow4pol2.asc';...
    5,0,721,492,'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\b\profile4.png','S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\b\pow4pol4.asc';...
    5,0,706,498,'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\c\profile6.png','S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\c\pow4pol6.asc';...
    5,0,725,462,'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\a_alt\profile8.png','S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 4\a_alt\pow4pol8.asc';...
    5,0.96,661,528,'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\a\profile60.png','S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\a\zescope\inv60.asc';...
    5,0.96,692,525,'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\b\profile50.png','S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\b\zescope\trench50.asc';...
    5,0,683,538,'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\c\profile17.png','S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\c\zescope\bowl17.asc';...
    5,0,648,533,'S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\d\profile17.png','S:\private\djh2v07\Other stuff\My papers\masters grayscale\figures\figure 3\d\zescope\cone17Pow3_2.asc'};

if ~isempty(cropIms)
    pathiInds = cell2mat(cropIms(:,1));
    jInds = cell2mat(cropIms(:,2));
else
    pathiInds = [];
    jInds = [];
end

rescaleVal = 1.40;%how much bigger need to make ideal im to equal size at sample
% for pathi = 7:size(cropIms,1)
for pathi = 6:8
    
    path = cropIms{pathi,6};
    writePath = cropIms{pathi,5};
    endpath = strfind(path,'\');
    writeEndPath = strfind(writePath,'\');
    currfile = path(endpath(end)+1:end);
    
    %     folderconts = dir(path);
    
    % path = 'S:\private\djh2v07\Other stuff\results\20170731 nickel greyscale zemaps\';
    
    %     numfiles = size(folderconts,1);
    
    %     for j = 1:numfiles
    %         currfile = folderconts(j).name;
    %         if length(currfile)<=3 || ~strcmp(currfile(end-2:end),'asc')
    %             continue;
    %         end
    %     currIm = imread([path,currfile]);
    currIm = flipud(dlmread([path],'	',[15,0,15+1039,1391]));
    currIm = currIm - median(currIm(:));
    currIm = currIm/1000;%get to µm
    %     currIm = currIm/max(currIm(:));
    %     imwrite(currIm,[path,'result',num2str(j),'.bmp']);
    %     currImEn = imadjust(currIm);
    %     imwrite(currImEn,[path,'resultEnhanced',num2str(j),'.bmp']);
    %     figure(1);
    
    fid = fopen([path]);
    
    for ti = 1:7
        tline = fgets(fid);
        if ti==6
            xmax = tline;
            xmax = strrep(xmax,'# x-length = ','');
            xmax = str2num(xmax);
            xmax = xmax/1000;%get to um
        end
        if ti==7
            ymax = tline;
            ymax = strrep(ymax,'# y-length = ','');
            ymax = str2num(ymax);
            ymax = ymax/1000;%get to um
        end
    end
    
    pixX = xmax/size(currIm,2);
    
    %         if ismember(pathi,pathiInds) && ismember(j,jInds)
    %             cropImsI = find(pathiInds==pathi & jInds==j);
    cropImsI = pathi;
    
    currIm2 = circshift(currIm,[size(currIm,1)/2 - cropIms{cropImsI,4},size(currIm,2)/2 - cropIms{cropImsI,3}]);
    idealIm = double(imread(cropIms{cropImsI,5}));
    
    %             xCropMin = cropIms{cropImsI,3};
    %             xCropMax = cropIms{cropImsI,4};
    %             yCropMin = cropIms{cropImsI,5};
    %             yCropMax = cropIms{cropImsI,6};
    %         else
    %             xCropMin = 1;
    %             xCropMax = size(currIm,2);
    %             yCropMin = 1;
    %             yCropMax = size(currIm,1);
    %         end
    
    if cropImsI > 4%saved ideal ims differently for stuff in figure 4 than figure 3 for some reason, quicker to do this hack than track down where fig 4 ims were generated and make consistent
        idealIm = -idealIm;
    else
        idealIm = idealIm - max(idealIm(size(idealIm,1)/2,:));
    end
    
    idealIm2 = imresize(idealIm,rescaleVal*size(idealIm),'nearest');
    idealIm3 = PasteCentre(idealIm2,zeros(size(currIm)));
    idealIm5 = idealIm3;
    imVals = unique(idealIm3);
    for g = -1:1
        for h = -1:1
            
            idealIm4 = zeros(size(idealIm3));
            currIm3 = circshift(currIm2,[g,h]);
            if cropIms{cropImsI,2}~=0
                rotCurrIm = imrotate(currIm3,cropIms{cropImsI,2},'crop');
            else
                rotCurrIm = currIm3;
            end
            %                 for k = 1:359
            %                     rotCurrIm = rotCurrIm + imrotate(currIm3,k,'bilinear','crop');
            %                 end
            %                 rotCurrIm = rotCurrIm/360;
            
            for m = 1:length(imVals)
                idealIm4(idealIm3 == imVals(m)) = mean(rotCurrIm(idealIm3 == imVals(m)));
            end
            
            %             aveLineProf = mean(rotCurrIm(floor(size(rotCurrIm,1)/2)-cropIms{cropImsI,1}:floor(size(rotCurrIm,1)/2)+cropIms{cropImsI,1}-1,:));
            aveLineProf = idealIm4(floor(size(idealIm4,1)/2),:);
%             if strcmp(currfile,'bowl17.asc')
%                 idealIm2 = idealIm5/min(idealIm(size(idealIm,1)/2,:))*(-0.560);
%             else
                idealIm2 = idealIm5/min(idealIm(size(idealIm,1)/2,:))*min(medfilt1(aveLineProf,10));
%             end
            %             plot(1:size(rotCurrIm,2),aveLineProf,linspace(95,size(rotCurrIm,2)-96,size(idealIm,2)),idealIm(size(idealIm,1)/2,:))
            %             plot((1:size(rotCurrIm,2))*pixX,aveLineProf,linspace(44,size(rotCurrIm,2)-44,size(idealIm2,2))*pixX,idealIm2(size(idealIm2,1)/2,:));%pixel ratio from measuring features is 1.45 asc image to ideal image, ideal image is 900 wide, asc is 1392 wide, thus want idealIm to cover 900*1.45=1305 pixels centrally, 87 pixels difference between this and width of asc, so take about 44 off either side, looks like good fit
            plot((1:size(rotCurrIm,2))*pixX,aveLineProf,(1:size(rotCurrIm,2))*pixX,idealIm2(size(idealIm2,1)/2,:));%pixel ratio from measuring features is 1.45 asc image to ideal image, ideal image is 900 wide, asc is 1392 wide, thus want idealIm to cover 900*1.45=1305 pixels centrally, 87 pixels difference between this and width of asc, so take about 44 off either side, looks like good fit
            
            imagePath = [writePath(1:writeEndPath(end)-1),'\lineProfiles\result',num2str(pathi),'AsIdealProfile',currfile,'OffsetX',num2str(h),'OffsetY',num2str(g),'.png'];
            
            legend('Machined','Ideal','Location','northeast')
            
            xlabel('x /µm');
            xlim([20,70]);
            ylabel('z /µm');
            yLims = ylim;
            ylim([yLims(1) - (yLims(2)-yLims(1))/10,yLims(2) + (yLims(2)-yLims(1))/10]);%10% space top and bottom
            make_figure_setSizes(1,18,3,1);
            
            
            saveas(gcf,imagePath);
        end
    end
    
    %         xVals = linspace(1,xmax,size(currIm,2));
    %         yVals = linspace(1,ymax,size(currIm,1));
    
    %         imagesc(xVals(1:xCropMax-xCropMin+1),yVals(1:yCropMax-yCropMin+1),currIm(yCropMin:yCropMax,xCropMin:xCropMax));colorbar;
    %         imagePath = [path,'result',num2str(j),'AsLineProfile',currfile,'.png'];
    %         make_figure_setSizes(1,18,3,1);
    %         pause(0.00001);
    %         frame_h = get(handle(gcf),'JavaFrame');
    %         set(frame_h,'Maximized',1);
    % set(frame_h,'PaperPositionMode','auto')
    %         colormap jet;
    %         axis image;
    %         xlabel('x /µm');
    %         ylabel('y /µm');
    %         saveas(gcf,imagePath);
    
    %plot in 3D
    
    %         [X,Y] = meshgrid(xVals,yVals);
    %
    %         for vE = viewEl
    %             for vA = viewAz
    %
    %                 %         viewEl = 40;
    %                 %         viewAz = 55;
    %                 figure(1);
    %                 surf(X(1:yCropMax-yCropMin+1,1:xCropMax-xCropMin+1),Y(1:yCropMax-yCropMin+1,1:xCropMax-xCropMin+1),currIm(yCropMin:yCropMax,xCropMin:xCropMax),'EdgeColor','none','FaceLighting',lightStyle);
    %                 make_figure_setSizes(1,fontSize,lineWidth,aspectRatio);
    %                 view(vA,vE);
    %                 daspect([1,1,zratio])
    %                 lightangle(-45,30)
    %                 colormap hot
    %                 xlabel('x /µm');
    %                 ylabel('y /µm');
    %                 zlabel('z /nm');
    % %                 zlim(zLimits);
    %                 frame_h = get(handle(gcf),'JavaFrame');
    %                 set(frame_h,'Maximized',1);
    %                 imagePath = [path,'variousAngles\result',num2str(j),'AsFig3D',currfile(1:end-4),'ViewEl',num2str(vE),'ViewAz',num2str(vA),'.png'];
    %                 saveas(gcf,imagePath);
    %             end
    %         end
    
    %     end
end