Hotspots of dendritic spine turnover facilitates new spines and NN sparsity (Frank et al 2018)

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Accession:227087
Model for the following publication: Adam C. Frank, Shan Huang, Miou Zhou, Amos Gdalyahu, George Kastellakis, Panayiota Poirazi, Tawnie K. Silva, Ximiao Wen, Joshua T. Trachtenberg, and Alcino J. Silva Hotspots of Dendritic Spine Turnover Facilitate Learning-related Clustered Spine Addition and Network Sparsity
Reference:
1 . Frank AC, Huang S, Zhou M, Gdalyahu A, Kastellakis G, Silva TK, Lu E, Wen X, Poirazi P, Trachtenberg JT, Silva AJ (2018) Hotspots of dendritic spine turnover facilitate clustered spine addition and learning and memory. Nat Commun 9:422 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Connectionist Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron with dendritic subunits;
Channel(s):
Gap Junctions:
Receptor(s): NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; MATLAB;
Model Concept(s): Active Dendrites; Synaptic Plasticity;
Implementer(s): Kastellakis, George [gkastel at gmail.com];
Search NeuronDB for information about:  NMDA;
/
tomodel
exportfig
.ignore
README.md *
.gitignore *
append_pdfs.m *
copyfig.m *
crop_borders.m *
eps2pdf.m *
export_fig.m *
fix_lines.m *
ghostscript.m *
im2gif.m *
isolate_axes.m *
LICENSE *
pdf2eps.m *
pdftops.m *
print2array.m *
print2eps.m *
read_write_entire_textfile.m *
user_string.m *
using_hg2.m *
                            
%EXPORT_FIG  Exports figures suitable for publication
%
% Examples:
%   im = export_fig
%   [im alpha] = export_fig
%   export_fig filename
%   export_fig filename -format1 -format2
%   export_fig ... -nocrop
%   export_fig ... -transparent
%   export_fig ... -native
%   export_fig ... -m<val>
%   export_fig ... -r<val>
%   export_fig ... -a<val>
%   export_fig ... -q<val>
%   export_fig ... -p<val>
%   export_fig ... -<renderer>
%   export_fig ... -<colorspace>
%   export_fig ... -append
%   export_fig ... -bookmark
%   export_fig(..., handle)
%
% This function saves a figure or single axes to one or more vector and/or
% bitmap file formats, and/or outputs a rasterized version to the
% workspace, with the following properties:
%   - Figure/axes reproduced as it appears on screen
%   - Cropped borders (optional)
%   - Embedded fonts (vector formats)
%   - Improved line and grid line styles
%   - Anti-aliased graphics (bitmap formats)
%   - Render images at native resolution (optional for bitmap formats)
%   - Transparent background supported (pdf, eps, png)
%   - Semi-transparent patch objects supported (png only)
%   - RGB, CMYK or grayscale output (CMYK only with pdf, eps, tiff)
%   - Variable image compression, including lossless (pdf, eps, jpg)
%   - Optionally append to file (pdf, tiff)
%   - Vector formats: pdf, eps
%   - Bitmap formats: png, tiff, jpg, bmp, export to workspace 
%   
% This function is especially suited to exporting figures for use in
% publications and presentations, because of the high quality and
% portability of media produced.
%
% Note that the background color and figure dimensions are reproduced
% (the latter approximately, and ignoring cropping & magnification) in the
% output file. For transparent background (and semi-transparent patch
% objects), use the -transparent option or set the figure 'Color' property
% to 'none'. To make axes transparent set the axes 'Color' property to
% 'none'. Pdf, eps and png are the only file formats to support a
% transparent background, whilst the png format alone supports transparency
% of patch objects.
%
% The choice of renderer (opengl, zbuffer or painters) has a large impact
% on the quality of output. Whilst the default value (opengl for bitmaps,
% painters for vector formats) generally gives good results, if you aren't
% satisfied then try another renderer.  Notes: 1) For vector formats (eps,
% pdf), only painters generates vector graphics. 2) For bitmaps, only
% opengl can render transparent patch objects correctly. 3) For bitmaps,
% only painters will correctly scale line dash and dot lengths when
% magnifying or anti-aliasing. 4) Fonts may be substitued with Courier when
% using painters.
%
% When exporting to vector format (pdf & eps) and bitmap format using the
% painters renderer, this function requires that ghostscript is installed
% on your system. You can download this from:
%   http://www.ghostscript.com
% When exporting to eps it additionally requires pdftops, from the Xpdf
% suite of functions. You can download this from:
%   http://www.foolabs.com/xpdf
%
%IN:
%   filename - string containing the name (optionally including full or
%              relative path) of the file the figure is to be saved as. If
%              a path is not specified, the figure is saved in the current
%              directory. If no name and no output arguments are specified,
%              the default name, 'export_fig_out', is used. If neither a
%              file extension nor a format are specified, a ".png" is added
%              and the figure saved in that format.
%   -format1, -format2, etc. - strings containing the extensions of the
%                              file formats the figure is to be saved as.
%                              Valid options are: '-pdf', '-eps', '-png',
%                              '-tif', '-jpg' and '-bmp'. All combinations
%                              of formats are valid.
%   -nocrop - option indicating that the borders of the output are not to
%             be cropped.
%   -transparent - option indicating that the figure background is to be
%                  made transparent (png, pdf and eps output only).
%   -m<val> - option where val indicates the factor to magnify the
%             on-screen figure pixel dimensions by when generating bitmap
%             outputs. Default: '-m1'.
%   -r<val> - option val indicates the resolution (in pixels per inch) to
%             export bitmap and vector outputs at, keeping the dimensions
%             of the on-screen figure. Default: '-r864' (for vector output
%             only). Note that the -m option overides the -r option for
%             bitmap outputs only.
%   -native - option indicating that the output resolution (when outputting
%             a bitmap format) should be such that the vertical resolution
%             of the first suitable image found in the figure is at the
%             native resolution of that image. To specify a particular
%             image to use, give it the tag 'export_fig_native'. Notes:
%             This overrides any value set with the -m and -r options. It
%             also assumes that the image is displayed front-to-parallel
%             with the screen. The output resolution is approximate and
%             should not be relied upon. Anti-aliasing can have adverse
%             effects on image quality (disable with the -a1 option).
%   -a1, -a2, -a3, -a4 - option indicating the amount of anti-aliasing to
%                        use for bitmap outputs. '-a1' means no anti-
%                        aliasing; '-a4' is the maximum amount (default).
%   -<renderer> - option to force a particular renderer (painters, opengl
%                 or zbuffer) to be used over the default: opengl for
%                 bitmaps; painters for vector formats.
%   -<colorspace> - option indicating which colorspace color figures should
%                   be saved in: RGB (default), CMYK or gray. CMYK is only
%                   supported in pdf, eps and tiff output.
%   -q<val> - option to vary bitmap image quality (in pdf, eps and jpg
%             files only).  Larger val, in the range 0-100, gives higher
%             quality/lower compression. val > 100 gives lossless
%             compression. Default: '-q95' for jpg, ghostscript prepress
%             default for pdf & eps. Note: lossless compression can
%             sometimes give a smaller file size than the default lossy
%             compression, depending on the type of images.
%   -p<val> - option to add a border of width val to eps and pdf files,
%             where val is in units of the intermediate eps file. Default:
%             0 (i.e. no padding).
%   -append - option indicating that if the file (pdfs only) already
%             exists, the figure is to be appended as a new page, instead
%             of being overwritten (default).
%   -bookmark - option to indicate that a bookmark with the name of the
%               figure is to be created in the output file (pdf only).
%   handle - The handle of the figure, axes or uipanels (can be an array of
%            handles, but the objects must be in the same figure) to be
%            saved. Default: gcf.
%
%OUT:
%   im - MxNxC uint8 image array of the figure.
%   alpha - MxN single array of alphamatte values in range [0,1], for the
%           case when the background is transparent.
%
%   Some helpful examples and tips can be found at:
%      https://github.com/ojwoodford/export_fig
%
%   See also PRINT, SAVEAS.

% Copyright (C) Oliver Woodford 2008-2014

% The idea of using ghostscript is inspired by Peder Axensten's SAVEFIG
% (fex id: 10889) which is itself inspired by EPS2PDF (fex id: 5782).
% The idea for using pdftops came from the MATLAB newsgroup (id: 168171).
% The idea of editing the EPS file to change line styles comes from Jiro
% Doke's FIXPSLINESTYLE (fex id: 17928).
% The idea of changing dash length with line width came from comments on
% fex id: 5743, but the implementation is mine :)
% The idea of anti-aliasing bitmaps came from Anders Brun's MYAA (fex id:
% 20979).
% The idea of appending figures in pdfs came from Matt C in comments on the
% FEX (id: 23629)

% Thanks to Roland Martin for pointing out the colour MATLAB
% bug/feature with colorbar axes and transparent backgrounds.
% Thanks also to Andrew Matthews for describing a bug to do with the figure
% size changing in -nodisplay mode. I couldn't reproduce it, but included a
% fix anyway.
% Thanks to Tammy Threadgill for reporting a bug where an axes is not
% isolated from gui objects.

% 23/02/12: Ensure that axes limits don't change during printing
% 14/03/12: Fix bug in fixing the axes limits (thanks to Tobias Lamour for
%           reporting it).
% 02/05/12: Incorporate patch of Petr Nechaev (many thanks), enabling
%           bookmarking of figures in pdf files.
% 09/05/12: Incorporate patch of Arcelia Arrieta (many thanks), to keep
%           tick marks fixed.
% 12/12/12: Add support for isolating uipanels. Thanks to michael for
%           suggesting it.
% 25/09/13: Add support for changing resolution in vector formats. Thanks
%           to Jan Jaap Meijer for suggesting it.
% 07/05/14: Add support for '~' at start of path. Thanks to Sally Warner
%           for suggesting it.

function [im, alpha] = export_fig(varargin)
% Make sure the figure is rendered correctly _now_ so that properties like
% axes limits are up-to-date.
drawnow;
% Parse the input arguments
[fig, options] = parse_args(nargout, varargin{:});
% Isolate the subplot, if it is one
cls = all(ismember(get(fig, 'Type'), {'axes', 'uipanel'}));
if cls
    % Given handles of one or more axes, so isolate them from the rest
    fig = isolate_axes(fig);
else
    % Check we have a figure
    if ~isequal(get(fig, 'Type'), 'figure');
        error('Handle must be that of a figure, axes or uipanel');
    end
    % Get the old InvertHardcopy mode
    old_mode = get(fig, 'InvertHardcopy');
end
% Hack the font units where necessary (due to a font rendering bug in
% print?). This may not work perfectly in all cases. Also it can change the
% figure layout if reverted, so use a copy.
magnify = options.magnify * options.aa_factor;
if isbitmap(options) && magnify ~= 1
    fontu = findobj(fig, 'FontUnits', 'normalized');
    if ~isempty(fontu)
        % Some normalized font units found
        if ~cls
            fig = copyfig(fig);
            set(fig, 'Visible', 'off');
            fontu = findobj(fig, 'FontUnits', 'normalized');
            cls = true;
        end
        set(fontu, 'FontUnits', 'points');
    end
end
% MATLAB "feature": axes limits and tick marks can change when printing
Hlims = findall(fig, 'Type', 'axes');
if ~cls
    % Record the old axes limit and tick modes
    Xlims = make_cell(get(Hlims, 'XLimMode'));
    Ylims = make_cell(get(Hlims, 'YLimMode'));
    Zlims = make_cell(get(Hlims, 'ZLimMode'));
    Xtick = make_cell(get(Hlims, 'XTickMode'));
    Ytick = make_cell(get(Hlims, 'YTickMode'));
    Ztick = make_cell(get(Hlims, 'ZTickMode'));
end
% Set all axes limit and tick modes to manual, so the limits and ticks can't change
set(Hlims, 'XLimMode', 'manual', 'YLimMode', 'manual', 'ZLimMode', 'manual');
set_tick_mode(Hlims, 'X');
set_tick_mode(Hlims, 'Y');
set_tick_mode(Hlims, 'Z');
% Set to print exactly what is there
set(fig, 'InvertHardcopy', 'off');
% Set the renderer
switch options.renderer
    case 1
        renderer = '-opengl';
    case 2
        renderer = '-zbuffer';
    case 3
        renderer = '-painters';
    otherwise
        renderer = '-opengl'; % Default for bitmaps
end
% Do the bitmap formats first
if isbitmap(options)
    % Get the background colour
    if options.transparent && (options.png || options.alpha)
        % Get out an alpha channel
        % MATLAB "feature": black colorbar axes can change to white and vice versa!
        hCB = findobj(fig, 'Type', 'axes', 'Tag', 'Colorbar');
        if isempty(hCB)
            yCol = [];
            xCol = [];
        else
            yCol = get(hCB, 'YColor');
            xCol = get(hCB, 'XColor');
            if iscell(yCol)
                yCol = cell2mat(yCol);
                xCol = cell2mat(xCol);
            end
            yCol = sum(yCol, 2);
            xCol = sum(xCol, 2);
        end
        % MATLAB "feature": apparently figure size can change when changing
        % colour in -nodisplay mode
        pos = get(fig, 'Position');
        % Set the background colour to black, and set size in case it was
        % changed internally
        tcol = get(fig, 'Color');
        set(fig, 'Color', 'k', 'Position', pos);
        % Correct the colorbar axes colours
        set(hCB(yCol==0), 'YColor', [0 0 0]);
        set(hCB(xCol==0), 'XColor', [0 0 0]);
        % Print large version to array
        B = print2array(fig, magnify, renderer);
        % Downscale the image
        B = downsize(single(B), options.aa_factor);
        % Set background to white (and set size)
        set(fig, 'Color', 'w', 'Position', pos);
        % Correct the colorbar axes colours
        set(hCB(yCol==3), 'YColor', [1 1 1]);
        set(hCB(xCol==3), 'XColor', [1 1 1]);
        % Print large version to array
        A = print2array(fig, magnify, renderer);
        % Downscale the image
        A = downsize(single(A), options.aa_factor);
        % Set the background colour (and size) back to normal
        set(fig, 'Color', tcol, 'Position', pos);
        % Compute the alpha map
        alpha = round(sum(B - A, 3)) / (255 * 3) + 1;
        A = alpha;
        A(A==0) = 1;
        A = B ./ A(:,:,[1 1 1]);
        clear B
        % Convert to greyscale
        if options.colourspace == 2
            A = rgb2grey(A);
        end
        A = uint8(A);
        % Crop the background
        if options.crop
            [alpha, v] = crop_borders(alpha, 0, 1);
            A = A(v(1):v(2),v(3):v(4),:);
        end
        if options.png
            % Compute the resolution
            res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3;
            % Save the png
            imwrite(A, [options.name '.png'], 'Alpha', double(alpha), 'ResolutionUnit', 'meter', 'XResolution', res, 'YResolution', res);
            % Clear the png bit
            options.png = false;
        end
        % Return only one channel for greyscale
        if isbitmap(options)
            A = check_greyscale(A);
        end
        if options.alpha
            % Store the image
            im = A;
            % Clear the alpha bit
            options.alpha = false;
        end
        % Get the non-alpha image
        if isbitmap(options)
            alph = alpha(:,:,ones(1, size(A, 3)));
            A = uint8(single(A) .* alph + 255 * (1 - alph));
            clear alph
        end
        if options.im
            % Store the new image
            im = A;
        end
    else
        % Print large version to array
        if options.transparent
            % MATLAB "feature": apparently figure size can change when changing
            % colour in -nodisplay mode
            pos = get(fig, 'Position');
            tcol = get(fig, 'Color');
            set(fig, 'Color', 'w', 'Position', pos);
            A = print2array(fig, magnify, renderer);
            set(fig, 'Color', tcol, 'Position', pos);
            tcol = 255;
        else
            [A, tcol] = print2array(fig, magnify, renderer);
        end
        % Crop the background
        if options.crop
            A = crop_borders(A, tcol, 1);
        end
        % Downscale the image
        A = downsize(A, options.aa_factor);
        if options.colourspace == 2
            % Convert to greyscale
            A = rgb2grey(A);
        else
            % Return only one channel for greyscale
            A = check_greyscale(A);
        end
        % Outputs
        if options.im
            im = A;
        end
        if options.alpha
            im = A;
            alpha = zeros(size(A, 1), size(A, 2), 'single');
        end
    end
    % Save the images
    if options.png
        res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3;
        imwrite(A, [options.name '.png'], 'ResolutionUnit', 'meter', 'XResolution', res, 'YResolution', res);
    end
    if options.bmp
        imwrite(A, [options.name '.bmp']);
    end
    % Save jpeg with given quality
    if options.jpg
        quality = options.quality;
        if isempty(quality)
            quality = 95;
        end
        if quality > 100
            imwrite(A, [options.name '.jpg'], 'Mode', 'lossless');
        else
            imwrite(A, [options.name '.jpg'], 'Quality', quality);
        end
    end
    % Save tif images in cmyk if wanted (and possible)
    if options.tif
        if options.colourspace == 1 && size(A, 3) == 3
            A = double(255 - A);
            K = min(A, [], 3);
            K_ = 255 ./ max(255 - K, 1);
            C = (A(:,:,1) - K) .* K_;
            M = (A(:,:,2) - K) .* K_;
            Y = (A(:,:,3) - K) .* K_;
            A = uint8(cat(3, C, M, Y, K));
            clear C M Y K K_
        end
        append_mode = {'overwrite', 'append'};
        imwrite(A, [options.name '.tif'], 'Resolution', options.magnify*get(0, 'ScreenPixelsPerInch'), 'WriteMode', append_mode{options.append+1});
    end
end
% Now do the vector formats
if isvector(options)
    % Set the default renderer to painters
    if ~options.renderer
        renderer = '-painters';
    end
    % Generate some filenames
    tmp_nam = [tempname '.eps'];
    if options.pdf
        pdf_nam = [options.name '.pdf'];
    else
        pdf_nam = [tempname '.pdf'];
    end
    % Generate the options for print
    p2eArgs = {renderer, sprintf('-r%d', options.resolution)};
    if options.colourspace == 1
        p2eArgs = [p2eArgs {'-cmyk'}];
    end
    if ~options.crop
        p2eArgs = [p2eArgs {'-loose'}];
    end
    try
        % Generate an eps
        print2eps(tmp_nam, fig, options.bb_padding, p2eArgs{:});
        % Remove the background, if desired
        if options.transparent && ~isequal(get(fig, 'Color'), 'none')
            eps_remove_background(tmp_nam, 1 + using_hg2(fig));
        end
        % Add a bookmark to the PDF if desired
        if options.bookmark
            fig_nam = get(fig, 'Name');
            if isempty(fig_nam)
                warning('export_fig:EmptyBookmark', 'Bookmark requested for figure with no name. Bookmark will be empty.');
            end
            add_bookmark(tmp_nam, fig_nam);
        end
        % Generate a pdf
        eps2pdf(tmp_nam, pdf_nam, 1, options.append, options.colourspace==2, options.quality);
    catch ex
        % Delete the eps
        delete(tmp_nam);
        rethrow(ex);
    end
    % Delete the eps
    delete(tmp_nam);
    if options.eps
        try
            % Generate an eps from the pdf
            pdf2eps(pdf_nam, [options.name '.eps']);
        catch ex
            if ~options.pdf
                % Delete the pdf
                delete(pdf_nam);
            end
            rethrow(ex);
        end
        if ~options.pdf
            % Delete the pdf
            delete(pdf_nam);
        end
    end
end
if cls
    % Close the created figure
    close(fig);
else
    % Reset the hardcopy mode
    set(fig, 'InvertHardcopy', old_mode);
    % Reset the axes limit and tick modes
    for a = 1:numel(Hlims)
        set(Hlims(a), 'XLimMode', Xlims{a}, 'YLimMode', Ylims{a}, 'ZLimMode', Zlims{a}, 'XTickMode', Xtick{a}, 'YTickMode', Ytick{a}, 'ZTickMode', Ztick{a});
    end
end
end

function [fig, options] = parse_args(nout, varargin)
% Parse the input arguments
% Set the defaults
fig = get(0, 'CurrentFigure');
options = struct('name', 'export_fig_out', ...
                 'crop', true, ...
                 'transparent', false, ...
                 'renderer', 0, ... % 0: default, 1: OpenGL, 2: ZBuffer, 3: Painters
                 'pdf', false, ...
                 'eps', false, ...
                 'png', false, ...
                 'tif', false, ...
                 'jpg', false, ...
                 'bmp', false, ...
                 'colourspace', 0, ... % 0: RGB/gray, 1: CMYK, 2: gray
                 'append', false, ...
                 'im', nout == 1, ...
                 'alpha', nout == 2, ...
                 'aa_factor', 0, ...
                 'bb_padding', 0, ...
                 'magnify', [], ...
                 'resolution', [], ...
                 'bookmark', false, ...
                 'quality', []);
native = false; % Set resolution to native of an image

% Go through the other arguments
for a = 1:nargin-1
    if all(ishandle(varargin{a}))
        fig = varargin{a};
    elseif ischar(varargin{a}) && ~isempty(varargin{a})
        if varargin{a}(1) == '-'
            switch lower(varargin{a}(2:end))
                case 'nocrop'
                    options.crop = false;
                case {'trans', 'transparent'}
                    options.transparent = true;
                case 'opengl'
                    options.renderer = 1;
                case 'zbuffer'
                    options.renderer = 2;
                case 'painters'
                    options.renderer = 3;
                case 'pdf'
                    options.pdf = true;
                case 'eps'
                    options.eps = true;
                case 'png'
                    options.png = true;
                case {'tif', 'tiff'}
                    options.tif = true;
                case {'jpg', 'jpeg'}
                    options.jpg = true;
                case 'bmp'
                    options.bmp = true;
                case 'rgb'
                    options.colourspace = 0;
                case 'cmyk'
                    options.colourspace = 1;
                case {'gray', 'grey'}
                    options.colourspace = 2;
                case {'a1', 'a2', 'a3', 'a4'}
                    options.aa_factor = str2double(varargin{a}(3));
                case 'append'
                    options.append = true;
                case 'bookmark'
                    options.bookmark = true;
                case 'native'
                    native = true;
                otherwise
                    val = str2double(regexp(varargin{a}, '(?<=-(m|M|r|R|q|Q|p|P))-?\d*.?\d+', 'match'));
                    if ~isscalar(val)
                        error('option %s not recognised', varargin{a});
                    end
                    switch lower(varargin{a}(2))
                        case 'm'
                            options.magnify = val;
                        case 'r'
                            options.resolution = val;
                        case 'q'
                            options.quality = max(val, 0);
                        case 'p'
                            options.bb_padding = val;
                    end
            end
        else
            [p, options.name, ext] = fileparts(varargin{a});
            if ~isempty(p)
                options.name = [p filesep options.name];
            end
            switch lower(ext)
                case {'.tif', '.tiff'}
                    options.tif = true;
                case {'.jpg', '.jpeg'}
                    options.jpg = true;
                case '.png'
                    options.png = true;
                case '.bmp'
                    options.bmp = true;
                case '.eps'
                    options.eps = true;
                case '.pdf'
                    options.pdf = true;
                otherwise
                    options.name = varargin{a};
            end
        end
    end
end

% Set default anti-aliasing now we know the renderer
if options.aa_factor == 0
    options.aa_factor = 1 + 2 * (~(using_hg2(fig) && strcmp(get(ancestor(fig, 'figure'), 'GraphicsSmoothing'), 'on')) | (options.renderer == 3));
end

% Convert user dir '~' to full path
if numel(options.name) > 2 && options.name(1) == '~' && (options.name(2) == '/' || options.name(2) == '\')
    options.name = fullfile(char(java.lang.System.getProperty('user.home')), options.name(2:end));
end

% Compute the magnification and resolution
if isempty(options.magnify)
    if isempty(options.resolution)
        options.magnify = 1;
        options.resolution = 864;
    else
        options.magnify = options.resolution ./ get(0, 'ScreenPixelsPerInch');
    end
elseif isempty(options.resolution)
    options.resolution = 864;
end  

% Check we have a figure handle
if isempty(fig)
    error('No figure found');
end

% Set the default format
if ~isvector(options) && ~isbitmap(options)
    options.png = true;
end

% Check whether transparent background is wanted (old way)
if isequal(get(ancestor(fig(1), 'figure'), 'Color'), 'none')
    options.transparent = true;
end

% If requested, set the resolution to the native vertical resolution of the
% first suitable image found
if native && isbitmap(options)
    % Find a suitable image
    list = findobj(fig, 'Type', 'image', 'Tag', 'export_fig_native');
    if isempty(list)
        list = findobj(fig, 'Type', 'image', 'Visible', 'on');
    end
    for hIm = list(:)'
        % Check height is >= 2
        height = size(get(hIm, 'CData'), 1);
        if height < 2
            continue
        end
        % Account for the image filling only part of the axes, or vice
        % versa
        yl = get(hIm, 'YData');
        if isscalar(yl)
            yl = [yl(1)-0.5 yl(1)+height+0.5];
        else
            if ~diff(yl)
                continue
            end
            yl = yl + [-0.5 0.5] * (diff(yl) / (height - 1));
        end
        hAx = get(hIm, 'Parent');
        yl2 = get(hAx, 'YLim');
        % Find the pixel height of the axes
        oldUnits = get(hAx, 'Units');
        set(hAx, 'Units', 'pixels');
        pos = get(hAx, 'Position');
        set(hAx, 'Units', oldUnits);
        if ~pos(4)
            continue
        end
        % Found a suitable image
        % Account for stretch-to-fill being disabled
        pbar = get(hAx, 'PlotBoxAspectRatio');
        pos = min(pos(4), pbar(2)*pos(3)/pbar(1));
        % Set the magnification to give native resolution
        options.magnify = (height * diff(yl2)) / (pos * diff(yl));
        break
    end
end
end

function A = downsize(A, factor)
% Downsample an image
if factor == 1
    % Nothing to do
    return
end
try
    % Faster, but requires image processing toolbox
    A = imresize(A, 1/factor, 'bilinear');
catch
    % No image processing toolbox - resize manually
    % Lowpass filter - use Gaussian as is separable, so faster
    % Compute the 1d Gaussian filter
    filt = (-factor-1:factor+1) / (factor * 0.6);
    filt = exp(-filt .* filt);
    % Normalize the filter
    filt = single(filt / sum(filt));
    % Filter the image
    padding = floor(numel(filt) / 2);
    for a = 1:size(A, 3)
        A(:,:,a) = conv2(filt, filt', single(A([ones(1, padding) 1:end repmat(end, 1, padding)],[ones(1, padding) 1:end repmat(end, 1, padding)],a)), 'valid');
    end
    % Subsample
    A = A(1+floor(mod(end-1, factor)/2):factor:end,1+floor(mod(end-1, factor)/2):factor:end,:);
end
end

function A = rgb2grey(A)
A = cast(reshape(reshape(single(A), [], 3) * single([0.299; 0.587; 0.114]), size(A, 1), size(A, 2)), class(A));
end

function A = check_greyscale(A)
% Check if the image is greyscale
if size(A, 3) == 3 && ...
        all(reshape(A(:,:,1) == A(:,:,2), [], 1)) && ...
        all(reshape(A(:,:,2) == A(:,:,3), [], 1))
    A = A(:,:,1); % Save only one channel for 8-bit output
end
end

function eps_remove_background(fname, count)
% Remove the background of an eps file
% Open the file
fh = fopen(fname, 'r+');
if fh == -1
    error('Not able to open file %s.', fname);
end
% Read the file line by line
while count
    % Get the next line
    l = fgets(fh);
    if isequal(l, -1)
        break; % Quit, no rectangle found
    end
    % Check if the line contains the background rectangle
    if isequal(regexp(l, ' *0 +0 +\d+ +\d+ +r[fe] *[\n\r]+', 'start'), 1)
        % Set the line to whitespace and quit
        l(1:regexp(l, '[\n\r]', 'start', 'once')-1) = ' ';
        fseek(fh, -numel(l), 0);
        fprintf(fh, l);
        % Reduce the count
        count = count - 1;
    end
end
% Close the file
fclose(fh);
end

function b = isvector(options)
b = options.pdf || options.eps;
end

function b = isbitmap(options)
b = options.png || options.tif || options.jpg || options.bmp || options.im || options.alpha;
end

% Helper function
function A = make_cell(A)
if ~iscell(A)
    A = {A};
end
end

function add_bookmark(fname, bookmark_text)
% Adds a bookmark to the temporary EPS file after %%EndPageSetup
% Read in the file
fh = fopen(fname, 'r');
if fh == -1
    error('File %s not found.', fname);
end
try
    fstrm = fread(fh, '*char')';
catch ex
    fclose(fh);
    rethrow(ex);
end
fclose(fh);

% Include standard pdfmark prolog to maximize compatibility
fstrm = strrep(fstrm, '%%BeginProlog', sprintf('%%%%BeginProlog\n/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse'));
% Add page bookmark
fstrm = strrep(fstrm, '%%EndPageSetup', sprintf('%%%%EndPageSetup\n[ /Title (%s) /OUT pdfmark',bookmark_text));

% Write out the updated file
fh = fopen(fname, 'w');
if fh == -1
    error('Unable to open %s for writing.', fname);
end
try
    fwrite(fh, fstrm, 'char*1');
catch ex
    fclose(fh);
    rethrow(ex);
end
fclose(fh);
end

function set_tick_mode(Hlims, ax)
% Set the tick mode of linear axes to manual
% Leave log axes alone as these are tricky
M = get(Hlims, [ax 'Scale']);
if ~iscell(M)
    M = {M};
end
M = cellfun(@(c) strcmp(c, 'linear'), M);
set(Hlims(M), [ax 'TickMode'], 'manual');
end

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