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create_pngs.m
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function create_pngs(thres_string)
% channel_no = current_path;
% disp(channel_no);
% handles.channel_no = strcat('channel',extractAfter(channel_no, string('channel')));
handles.modification_tracker = [];
channel_path = cd('./oSort/');
folder_name = dir();
% saved_identifier = folder_name(length(folder_name)).name;
cd(strcat(thres_string, '/sort/')); % cd(strcat('detect1Thresh6kern18', '/sort/'));
folder_name = dir();
cd(folder_name(length(folder_name)).name);
mat_name_d = dir('*_sorted_new.mat');
mat_name = {mat_name_d.name};
handles.spikes_data = load(mat_name{1}); % 'P1_sorted_new.mat'
cd(channel_path);
title = ['pngs_', thres_string];
mkdir(title);
cd(title);
disp(handles.spikes_data.nrAssigned);
sieved = NaN(length(handles.spikes_data.assignedNegative), 64, length(handles.spikes_data.nrAssigned(:,1)));
counter_list = ones(1,length(handles.spikes_data.nrAssigned(:,1)));
max_arr = NaN(1, length(handles.spikes_data.assignedNegative));
min_arr = NaN(1, length(handles.spikes_data.assignedNegative));
new_counter = 1;
for i = 1:length(handles.spikes_data.assignedNegative)
for j = 1:length(handles.spikes_data.nrAssigned(:,1))
if handles.spikes_data.assignedNegative(i) == handles.spikes_data.nrAssigned(j,1)
for k = 1:length(handles.spikes_data.nrAssigned(:,1))
if handles.spikes_data.nrAssigned(k,1) == handles.spikes_data.nrAssigned(j,1)
sieved(counter_list(k),:,k) = downsample(handles.spikes_data.newSpikesNegative(i,:),4,2);
max_arr(new_counter) = max(sieved(counter_list(k),:,k));
min_arr(new_counter) = min(sieved(counter_list(k),:,k));
% if max(sieved(counter_list(k),:,k)) > max_max
% max_max = max(sieved(counter_list(k),:,k));
% end
% if min(sieved(counter_list(k),:,k)) < min_min
% min_min = min(sieved(counter_list(k),:,k));
% end
new_counter = new_counter + 1;
counter_list(k) = counter_list(k) + 1;
break;
end
end
end
end
end
for i = 1:length(counter_list)
counter_list(i) = counter_list(i) - 1;
end
max_arr = max_arr(1:new_counter-1);
min_arr = min_arr(1:new_counter-1);
max_max = prctile(max_arr, 97.5) + 50;
min_min = prctile(min_arr, 2.5) - 50;
sieved_means = nanmean(sieved, 1);
meandata = cell(4, length(handles.spikes_data.nrAssigned(:,1)));
for i = 1:length(handles.spikes_data.nrAssigned(:,1))
meandata{1,i} = sieved_means(1,:,i);
meandata{2,i} = counter_list(i);
end
meandata{3,1} = min_min;
meandata{4,1} = max_max;
save('meandata.mat', 'meandata');
fig1 = figure();
ax1 = axes('Parent', fig1);
for i = 1:length(counter_list)
disp(size(counter_list));
disp(size(sieved));
disp(i);
cluster1 = plot(ax1, 1:64, sieved(1:counter_list(i),:,i), '-', 'Color', [0 0 0 0.05]);
hold(ax1,'on');
cluster2 = plot(ax1, [0 64], [0 0], '-.', 'Color', [0 0 0], 'LineWidth', 3);
hold(ax1,'off');
xlim([0 64]);
ylim([min_min max_max]);
grid on
set(ax1,'XTickLabel',[], 'YTickLabel', []);
set(ax1, 'Color', 'None');
ax = gca;
if i == 1
outerpos = ax.OuterPosition;
ti = ax.TightInset;
left = outerpos(1) + ti(1);
bottom = outerpos(2) + ti(2);
ax_width = outerpos(3) - ti(1) - ti(3);
ax_height = outerpos(4) - ti(2) - ti(4);
ax.Position = [left bottom ax_width ax_height];
end
ax.LineWidth = 3;
ax.YTick = round(min_min/50)*50:50:max_max;
ax.XTick = [10 20 30 40 50 60];
set(ax, 'Color', 'None');
file_name = char(strcat('cluster',string(handles.spikes_data.nrAssigned(i,1)),'.png'));
file_name2 = char(strcat('cluster',string(handles.spikes_data.nrAssigned(i,1)),'.fig'));
file_name2
%saveas(gcf,file_name);
export_fig(file_name, '-transparent', '-png');
%savefig(gcf, file_name2);
end
% stitched on autocorr-noise processing here %
handles.distinct_plots = handles.spikes_data.nrAssigned(:,1);
handles.noise_status3 = zeros(1, length(handles.spikes_data.nrAssigned(:,1)));
for k = 1:length(handles.noise_status3)
curr_times_spike_train = NaN(1,length(handles.spikes_data.assignedNegative));
count = 1;
for i = 1:length(handles.spikes_data.assignedNegative)
if handles.spikes_data.assignedNegative(i) == handles.distinct_plots(k)
curr_times_spike_train(1,count) = handles.spikes_data.newTimestampsNegative(i);
count = count + 1;
end
end
curr_times_spike_train = curr_times_spike_train(1,1:count-1);
spike_train = convertToSpiketrain(curr_times_spike_train, 1);
[~,~,~,Cxx] = psautospk(spike_train, 1);
Cxx(1) = [];
Cxx = Cxx(floor(length(Cxx)/2):length(Cxx));
Cxx = Cxx(15:100);
[~, ~, ~, p] = findpeaks(Cxx);
thres = median(p) + 3*std(p);
[~, identified] = findpeaks(Cxx, 'MinPeakProminence', thres);
diff_c = diff(identified);
median_c = median(diff_c);
counter_c = 0;
for i = 1:length(diff_c)
if abs(diff_c(i) - median_c) < 2
counter_c = counter_c + 1;
end
end
if counter_c/length(diff_c) >= 0.7 && length(diff_c) > 1
handles.noise_status3(k) = 1;
end
end
tosave = handles.noise_status3;
save('autocorr_noise.mat', 'tosave');
cd(channel_path);
end
function [f,Pxxn,tvect,Cxx] = psautospk(spk,tstep,nfft,window,noverlap,dflag)
if ( (nargin ~= 6) & (nargin ~= 2) )
disp(' ');
disp('usage1: psautospk(spk,tstep) ');
disp(' ');
disp('usage2: psautospk(spk,tstep,nfft,window,noverlap,dflag) ');
disp(' ');
disp(' for more information type "help psautospk" in the main');
disp(' matlab window');
disp(' ');
return;
end;
if ( nargin == 2 )
nfft = 2048;
window = bartlett(nfft);
noverlap = 1024;
dflag = 'none';
end;
%computes the sampling frequency in Hz
tstep_s = tstep*1e-3; %converts to sec
Fs = 1/tstep_s; %in Hz
%computes and subtracts the mean firing rate
spk = spk(:); %convertes to column vector if necessary
spk = spk*Fs; %converts to units of spikes/sec
l_spk = length(spk);
s_spk = sum(spk);
m_spk = s_spk/l_spk;
spk = spk - m_spk;
% [Pxx_,f_] = psd(spk,nfft,Fs,window,noverlap,dflag);
% %converts to units of (spk/Hz)^2
% Pxxn_ = Pxx_ * tstep_s;
% JD/aug16 : update to use pwelch instead of deprecated psd
[Pxxn,f] = pwelch(spk,window,noverlap,nfft,Fs);
%converts to units of (spk/Hz)^2
Pxx = Pxxn / tstep_s;
%prepares the data to compute the autocorrelation
Pxxx = zeros(nfft,1);
Pxxx(1:nfft/2+1,1) = Pxx(1:nfft/2+1,1);
for k = 2:nfft/2
Pxxx(nfft+2-k,1) = Pxx(k,1);
end;
%computes the autocorrelation function
Cxxx = fft(Pxxx,nfft);
%normalizes to get the usual definition of autocorrelation
Cxxx = Cxxx/nfft;
tvect = -(nfft/2)*tstep:tstep:(nfft/2)*tstep;
Cxx = zeros(nfft+1,1);
for k = 1:nfft/2
Cxx(k,1) = real(Cxxx(nfft/2 + k,1));
end;
Cxx(nfft/2+1,1) = real(Cxxx(1,1));
for k = nfft/2+2:nfft+2
Cxx(k,1) = real(Cxxx(k-nfft/2,1));
end
end
function n = convertToSpiketrain(timestamps, binsize)
if nargin<2
binsize=1;
end
spiketrain=(timestamps/1000); %now in ms
spiketrain=spiketrain-spiketrain(1); %offset gone
roundedSpiketrain = round(spiketrain);
if binsize==1
n=zeros(1,roundedSpiketrain(end));
n( roundedSpiketrain(find(roundedSpiketrain>0)) )=1;
else
n = histc( roundedSpiketrain, [0:binsize:roundedSpiketrain(end)] );
end
end
function [imageData, alpha] = export_fig(varargin) %#ok<*STRCL1>
%EXPORT_FIG Exports figures in a publication-quality format
%
% Examples:
% imageData = export_fig
% [imageData, alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -c[<val>,<val>,<val>,<val>]
% 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 ... -d<gs_option>
% export_fig ... -depsc
% export_fig ... -<renderer>
% export_fig ... -<colorspace>
% export_fig ... -append
% export_fig ... -bookmark
% export_fig ... -clipboard
% export_fig ... -update
% export_fig ... -nofontswap
% export_fig ... -font_space <char>
% export_fig ... -linecaps
% export_fig ... -noinvert
% export_fig ... -preserve_size
% export_fig ... -options <optionsStruct>
% 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, tif)
% - Semi-transparent patch objects supported (png, tif)
% - RGB, CMYK or grayscale output (CMYK only with pdf, eps, tif)
% - Variable image compression, including lossless (pdf, eps, jpg)
% - Optional rounded line-caps (pdf, eps)
% - Optionally append to file (pdf, tif)
% - Vector formats: pdf, eps, svg
% - Bitmap formats: png, tif, 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, TIF & PNG are the only formats that support a transparent
% background; only TIF & PNG formats support transparency of patch objects.
%
% The choice of renderer (opengl/zbuffer/painters) has a large impact on the
% output quality. The default value (opengl for bitmaps, painters for vector
% formats) generally gives good results, but if you aren't satisfied
% then try another renderer. Notes:
% 1) For vector formats (EPS,PDF), only painters generates vector graphics
% 2) For bitmap formats, only opengl correctly renders transparent patches
% 3) For bitmap formats, only painters correctly scales 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://xpdfreader.com
%
% SVG output uses the fig2svg (https://github.com/kupiqu/fig2svg) or plot2svg
% (https://github.com/jschwizer99/plot2svg) utilities, or Matlab's built-in
% SVG export if neither of these utilities are available on Matlab's path.
% Note: cropping/padding are not supported in export_fig's SVG output.
%
% Inputs:
% 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.
% -<format> - string(s) containing the output file extension(s). Options:
% '-pdf', '-eps', '-svg', '-png', '-tif', '-jpg' and '-bmp'.
% Multiple formats can be specified, without restriction.
% For example: export_fig('-jpg', '-pdf', '-png', ...)
% Either '-tif','-tiff' can be specified, and either '-jpg','-jpeg'.
% -nocrop - option indicating that empty margins should not be cropped.
% -c[<val>,<val>,<val>,<val>] - option indicating crop amounts. Must be
% a 4-element vector of numeric values: [top,right,bottom,left]
% where NaN/Inf indicate auto-cropping, 0 means no cropping,
% and any other value mean cropping in pixel amounts.
% -transparent - option indicating that the figure background is to be made
% transparent (PNG,PDF,TIF,EPS formats only). Implies -noinvert.
% -m<val> - option where val indicates the factor to magnify the
% on-screen figure pixel dimensions by when generating bitmap
% outputs (does not affect vector formats). 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). Default value: opengl for bitmap formats or
% figures with patches and/or transparent annotations;
% painters for vector formats without patches/transparencies.
% -<colorspace> - option indicating which colorspace color figures should
% be saved in: RGB (default), CMYK or gray. Usage example: '-gray'.
% Note: CMYK is only supported in PDF, EPS and TIF formats.
% -q<val> - option to vary bitmap image quality (PDF, EPS, JPG formats only).
% A larger val, in the range 0-100, produces higher quality and
% lower compression. val > 100 results in 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 image type.
% -p<val> - option to pad a border of width val to exported files, where
% val is either a relative size with respect to cropped image
% size (i.e. p=0.01 adds a 1% border). For EPS & PDF formats,
% val can also be integer in units of 1/72" points (abs(val)>1).
% val can be positive (padding) or negative (extra cropping).
% If used, the -nocrop flag will be ignored, i.e. the image will
% always be cropped and then padded. Default: 0 (i.e. no padding).
% -append - option indicating that if the file already exists the figure is to
% be appended as a new page, instead of being overwritten (default).
% PDF & TIF output formats only.
% -bookmark - option to indicate that a bookmark with the name of the
% figure is to be created in the output file (PDF format only).
% -clipboard - option to save output as an image on the system clipboard.
% Note: background transparency is not preserved in clipboard
% -d<gs_option> - option to indicate a ghostscript setting. For example,
% -dMaxBitmap=0 or -dNoOutputFonts (Ghostscript 9.15+).
% -depsc - option to use EPS level-3 rather than the default level-2 print
% device. This solves some bugs with Matlab's default -depsc2 device
% such as discolored subplot lines on images (vector formats only).
% -update - option to download and install the latest version of export_fig
% -nofontswap - option to avoid font swapping. Font swapping is automatically
% done in vector formats (only): 11 standard Matlab fonts are
% replaced by the original figure fonts. This option prevents this.
% -font_space <char> - option to set a spacer character for font-names that
% contain spaces, used by EPS/PDF. Default: ''
% -linecaps - option to create rounded line-caps (vector formats only).
% -noinvert - option to avoid setting figure's InvertHardcopy property to
% 'off' during output (this solves some problems of empty outputs).
% -preserve_size - option to preserve the figure's PaperSize property in output
% file (PDF/EPS formats only; default is to not preserve it).
% -options <optionsStruct> - format-specific parameters as defined in Matlab's
% documentation of the imwrite function, contained in a struct under
% the format name. For example to specify the JPG Comment parameter,
% pass a struct such as this: options.JPG.Comment='abc'. Similarly,
% options.PNG.BitDepth=4. Valid only for PNG,TIF,JPG output formats.
% handle - The handle of the figure, axes or uipanels (can be an array of
% handles, but the objects must be in the same figure) which is
% to be saved. Default: gcf (handle of current figure).
%
% Outputs:
% imageData - MxNxC uint8 image array of the exported image.
% alpha - MxN single array of alphamatte values in the range [0,1],
% for the case when the background is transparent.
%
% Some helpful examples and tips can be found at:
% https://github.com/altmany/export_fig
%
% See also PRINT, SAVEAS, ScreenCapture (on the Matlab File Exchange)
%{
% Copyright (C) Oliver Woodford 2008-2014, Yair Altman 2015-
% 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.
% 24/02/15: Fix Matlab R2014b bug (issue #34): plot markers are not displayed when ZLimMode='manual'
% 25/02/15: Fix issue #4 (using HG2 on R2014a and earlier)
% 25/02/15: Fix issue #21 (bold TeX axes labels/titles in R2014b)
% 26/02/15: If temp dir is not writable, use the user-specified folder for temporary EPS/PDF files (Javier Paredes)
% 27/02/15: Modified repository URL from github.com/ojwoodford to /altmany
% Indented main function
% Added top-level try-catch block to display useful workarounds
% 28/02/15: Enable users to specify optional ghostscript options (issue #36)
% 06/03/15: Improved image padding & cropping thanks to Oscar Hartogensis
% 26/03/15: Fixed issue #49 (bug with transparent grayscale images); fixed out-of-memory issue
% 26/03/15: Fixed issue #42: non-normalized annotations on HG1
% 26/03/15: Fixed issue #46: Ghostscript crash if figure units <> pixels
% 27/03/15: Fixed issue #39: bad export of transparent annotations/patches
% 28/03/15: Fixed issue #50: error on some Matlab versions with the fix for issue #42
% 29/03/15: Fixed issue #33: bugs in Matlab's print() function with -cmyk
% 29/03/15: Improved processing of input args (accept space between param name & value, related to issue #51)
% 30/03/15: When exporting *.fig files, then saveas *.fig if figure is open, otherwise export the specified fig file
% 30/03/15: Fixed edge case bug introduced yesterday (commit #ae1755bd2e11dc4e99b95a7681f6e211b3fa9358)
% 09/04/15: Consolidated header comment sections; initialize output vars only if requested (nargout>0)
% 14/04/15: Workaround for issue #45: lines in image subplots are exported in invalid color
% 15/04/15: Fixed edge-case in parsing input parameters; fixed help section to show the -depsc option (issue #45)
% 21/04/15: Bug fix: Ghostscript croaks on % chars in output PDF file (reported by Sven on FEX page, 15-Jul-2014)
% 22/04/15: Bug fix: Pdftops croaks on relative paths (reported by Tintin Milou on FEX page, 19-Jan-2015)
% 04/05/15: Merged fix #63 (Kevin Mattheus Moerman): prevent tick-label changes during export
% 07/05/15: Partial fix for issue #65: PDF export used painters rather than opengl renderer (thanks Nguyenr)
% 08/05/15: Fixed issue #65: bad PDF append since commit #e9f3cdf 21/04/15 (thanks Robert Nguyen)
% 12/05/15: Fixed issue #67: exponent labels cropped in export, since fix #63 (04/05/15)
% 28/05/15: Fixed issue #69: set non-bold label font only if the string contains symbols (\beta etc.), followup to issue #21
% 29/05/15: Added informative error message in case user requested SVG output (issue #72)
% 09/06/15: Fixed issue #58: -transparent removed anti-aliasing when exporting to PNG
% 19/06/15: Added -update option to download and install the latest version of export_fig
% 07/07/15: Added -nofontswap option to avoid font-swapping in EPS/PDF
% 16/07/15: Fixed problem with anti-aliasing on old Matlab releases
% 11/09/15: Fixed issue #103: magnification must never become negative; also fixed reported error msg in parsing input params
% 26/09/15: Alert if trying to export transparent patches/areas to non-PNG outputs (issue #108)
% 04/10/15: Do not suggest workarounds for certain errors that have already been handled previously
% 01/11/15: Fixed issue #112: use same renderer in print2eps as export_fig (thanks to Jesús Pestana Puerta)
% 10/11/15: Custom GS installation webpage for MacOS. Thanks to Andy Hueni via FEX
% 19/11/15: Fixed clipboard export in R2015b (thanks to Dan K via FEX)
% 21/02/16: Added -c option for indicating specific crop amounts (idea by Cedric Noordam on FEX)
% 08/05/16: Added message about possible error reason when groot.Units~=pixels (issue #149)
% 17/05/16: Fixed case of image YData containing more than 2 elements (issue #151)
% 08/08/16: Enabled exporting transparency to TIF, in addition to PNG/PDF (issue #168)
% 11/12/16: Added alert in case of error creating output PDF/EPS file (issue #179)
% 13/12/16: Minor fix to the commit for issue #179 from 2 days ago
% 22/03/17: Fixed issue #187: only set manual ticks when no exponent is present
% 09/04/17: Added -linecaps option (idea by Baron Finer, issue #192)
% 15/09/17: Fixed issue #205: incorrect tick-labels when Ticks number don't match the TickLabels number
% 15/09/17: Fixed issue #210: initialize alpha map to ones instead of zeros when -transparent is not used
% 18/09/17: Added -font_space option to replace font-name spaces in EPS/PDF (workaround for issue #194)
% 18/09/17: Added -noinvert option to solve some export problems with some graphic cards (workaround for issue #197)
% 08/11/17: Fixed issue #220: axes exponent is removed in HG1 when TickMode is 'manual' (internal Matlab bug)
% 08/11/17: Fixed issue #221: alert if the requested folder does not exist
% 19/11/17: Workaround for issue #207: alert when trying to use transparent bgcolor with -opengl
% 29/11/17: Workaround for issue #206: warn if exporting PDF/EPS for a figure that contains an image
% 11/12/17: Fixed issue #230: use OpenGL renderer when exported image contains transparency (also see issue #206)
% 30/01/18: Updated SVG message to point to https://github.com/kupiqu/plot2svg and display user-selected filename if available
% 27/02/18: Fixed issue #236: axes exponent cropped from output if on right-hand axes
% 29/05/18: Fixed issue #245: process "string" inputs just like 'char' inputs
% 13/08/18: Fixed issue #249: correct black axes color to off-black to avoid extra cropping with -transparent
% 27/08/18: Added a possible file-open reason in EPS/PDF write-error message (suggested by "craq" on FEX page)
% 22/09/18: Xpdf website changed to xpdfreader.com
% 23/09/18: Fixed issue #243: only set non-bold font (workaround for issue #69) in R2015b or earlier; warn if changing font
% 23/09/18: Workaround for issue #241: don't use -r864 in EPS/PDF outputs when -native is requested (solves black lines problem)
% 18/11/18: Issue #261: Added informative alert when trying to export a uifigure (which is not currently supported)
% 13/12/18: Issue #261: Fixed last commit for cases of specifying axes/panel handle as input, rather than a figure handle
% 13/01/19: Issue #72: Added basic SVG output support
% 04/02/19: Workaround for issues #207 and #267: -transparent implies -noinvert
% 08/03/19: Issue #269: Added ability to specify format-specific options for PNG,TIF,JPG outputs; fixed help section
% 21/03/19: Fixed the workaround for issues #207 and #267 from 4/2/19 (-transparent now does *NOT* imply -noinvert; -transparent output should now be ok in all formats)
% 12/06/19: Issue #277: Enabled preservation of figure's PaperSize in output PDF/EPS file
%}
if nargout
[imageData, alpha] = deal([]);
end
hadError = false;
displaySuggestedWorkarounds = true;
% Ensure the figure is rendered correctly _now_ so that properties like axes limits are up-to-date
drawnow;
pause(0.05); % this solves timing issues with Java Swing's EDT (http://undocumentedmatlab.com/blog/solving-a-matlab-hang-problem)
% Parse the input arguments
fig = get(0, 'CurrentFigure');
[fig, options] = parse_args(nargout, fig, varargin{:});
% Ensure that we have a figure handle
if isequal(fig,-1)
return; % silent bail-out
elseif isempty(fig)
error('No figure found');
else
oldWarn = warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
try jf = get(handle(ancestor(fig,'figure')),'JavaFrame'); catch, jf=1; end
warning(oldWarn);
if isempty(jf)
error('Figures created using the uifigure command or App Designer are not supported by export_fig. See <a href="https://github.com/altmany/export_fig/issues/261">issue #261</a> for details.');
end
end
% 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 = findall(fig, 'FontUnits', 'normalized');
if ~isempty(fontu)
% Some normalized font units found
if ~cls
fig = copyfig(fig);
set(fig, 'Visible', 'off');
fontu = findall(fig, 'FontUnits', 'normalized');
cls = true;
end
set(fontu, 'FontUnits', 'points');
end
end
try
% 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'));
Xlabel = make_cell(get(Hlims, 'XTickLabelMode'));
Ylabel = make_cell(get(Hlims, 'YTickLabelMode'));
Zlabel = make_cell(get(Hlims, 'ZTickLabelMode'));
end
% Set all axes limit and tick modes to manual, so the limits and ticks can't change
% Fix Matlab R2014b bug (issue #34): plot markers are not displayed when ZLimMode='manual'
set(Hlims, 'XLimMode', 'manual', 'YLimMode', 'manual');
set_tick_mode(Hlims, 'X');
set_tick_mode(Hlims, 'Y');
if ~using_hg2(fig)
set(Hlims,'ZLimMode', 'manual');
set_tick_mode(Hlims, 'Z');
end
catch
% ignore - fix issue #4 (using HG2 on R2014a and earlier)
end
% Fix issue #21 (bold TeX axes labels/titles in R2014b when exporting to EPS/PDF)
try
if using_hg2(fig) && isvector(options)
% Set the FontWeight of axes labels/titles to 'normal'
% Fix issue #69: set non-bold font only if the string contains symbols (\beta etc.)
% Issue #243: only set non-bold font (workaround for issue #69) in R2015b or earlier
try isPreR2016a = verLessThan('matlab','8.7'); catch, isPreR2016a = true; end
if isPreR2016a
texLabels = findall(fig, 'type','text', 'FontWeight','bold');
symbolIdx = ~cellfun('isempty',strfind({texLabels.String},'\'));
if ~isempty(symbolIdx)
set(texLabels(symbolIdx), 'FontWeight','normal');
warning('export_fig:BoldTexLabels', 'Bold labels with Tex symbols converted into non-bold in export_fig (fix for issue #69)');
end
end
end
catch
% ignore
end
% Fix issue #42: non-normalized annotations on HG1 (internal Matlab bug)
annotationHandles = [];
try
if ~using_hg2(fig)
annotationHandles = findall(fig,'Type','hggroup','-and','-property','Units','-and','-not','Units','norm');
try % suggested by Jesús Pestana Puerta (jespestana) 30/9/2015
originalUnits = get(annotationHandles,'Units');
set(annotationHandles,'Units','norm');
catch
end
end
catch
% should never happen, but ignore in any case - issue #50
end
% Fix issue #46: Ghostscript crash if figure units <> pixels
oldFigUnits = get(fig,'Units');
set(fig,'Units','pixels');
% Set to print exactly what is there
if options.invert_hardcopy
try set(fig, 'InvertHardcopy', 'off'); catch, end % fail silently in uifigures
end
% 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
hImages = findall(fig,'type','image');
% Handle transparent patches
hasTransparency = ~isempty(findall(fig,'-property','FaceAlpha','-and','-not','FaceAlpha',1));
hasPatches = ~isempty(findall(fig,'type','patch'));
if hasTransparency
% Alert if trying to export transparent patches/areas to non-supported outputs (issue #108)
% http://www.mathworks.com/matlabcentral/answers/265265-can-export_fig-or-else-draw-vector-graphics-with-transparent-surfaces
% TODO - use transparency when exporting to PDF by not passing via print2eps
msg = 'export_fig currently supports transparent patches/areas only in PNG output. ';
if options.pdf
warning('export_fig:transparency', '%s\nTo export transparent patches/areas to PDF, use the print command:\n print(gcf, ''-dpdf'', ''%s.pdf'');', msg, options.name);
elseif ~options.png && ~options.tif % issue #168
warning('export_fig:transparency', '%s\nTo export the transparency correctly, try using the ScreenCapture utility on the Matlab File Exchange: http://bit.ly/1QFrBip', msg);
end
elseif ~isempty(hImages)
% Fix for issue #230: use OpenGL renderer when exported image contains transparency
for idx = 1 : numel(hImages)
cdata = get(hImages(idx),'CData');
if any(isnan(cdata(:)))
hasTransparency = true;
break
end
end
end
try
% Do the bitmap formats first
if isbitmap(options)
if abs(options.bb_padding) > 1
displaySuggestedWorkarounds = false;
error('For bitmap output (png,jpg,tif,bmp) the padding value (-p) must be between -1<p<1')
end
% 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 = findall(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]);
% Correct black axes color to off-black (issue #249)
hAxes = findall(fig, 'Type','axes');
hXs = fixBlackAxle(hAxes, 'XColor');
hYs = fixBlackAxle(hAxes, 'YColor');
hZs = fixBlackAxle(hAxes, 'ZColor');
% The following code might cause out-of-memory errors
try
% Print large version to array
B = print2array(fig, magnify, renderer);
% Downscale the image
B = downsize(single(B), options.aa_factor);
catch
% This is more conservative in memory, but kills transparency (issue #58)
B = single(print2array(fig, magnify/options.aa_factor, renderer));
end
% 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]);
% Revert the black axes colors
set(hXs, 'XColor', [0,0,0]);
set(hYs, 'YColor', [0,0,0]);
set(hZs, 'ZColor', [0,0,0]);
% The following code might cause out-of-memory errors
try
% Print large version to array
A = print2array(fig, magnify, renderer);
% Downscale the image
A = downsize(single(A), options.aa_factor);
catch
% This is more conservative in memory, but kills transparency (issue #58)
A = single(print2array(fig, magnify/options.aa_factor, renderer));
end
% 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, options.crop_amounts);
%A = A(v(1):v(2),v(3):v(4),:);
[alpha, vA, vB] = crop_borders(alpha, 0, options.bb_padding, options.crop_amounts);
if ~any(isnan(vB)) % positive padding
B = repmat(uint8(zeros(1,1,size(A,3))),size(alpha));
B(vB(1):vB(2), vB(3):vB(4), :) = A(vA(1):vA(2), vA(3):vA(4), :); % ADDED BY OH
A = B;
else % negative padding
A = A(vA(1):vA(2), vA(3):vA(4), :);
end
end
if options.png
% Compute the resolution
res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3;
% Save the png
[format_options, bitDepth] = getFormatOptions(options, 'png'); %Issue #269
if ~isempty(bitDepth) && bitDepth < 16 && size(A,3) == 3
% BitDepth specification requires using a color-map
[A, map] = rgb2ind(A, 256);
imwrite(A, map, [options.name '.png'], 'Alpha',double(alpha), 'ResolutionUnit','meter', 'XResolution',res, 'YResolution',res, format_options{:});
else
imwrite(A, [options.name '.png'], 'Alpha',double(alpha), 'ResolutionUnit','meter', 'XResolution',res, 'YResolution',res, format_options{:});
end
% 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
imageData = 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
imageData = 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, options.bb_padding, options.crop_amounts);
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
imageData = A;
end
if options.alpha
imageData = A;
alpha = ones(size(A, 1), size(A, 2), 'single');
end
end
% Save the images
if options.png
res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3;
[format_options, bitDepth] = getFormatOptions(options, 'png'); %Issue #269
if ~isempty(bitDepth) && bitDepth < 16 && size(A,3) == 3
% BitDepth specification requires using a color-map
[A, map] = rgb2ind(A, 256);
imwrite(A, map, [options.name '.png'], 'ResolutionUnit','meter', 'XResolution',res, 'YResolution',res, format_options{:});
else
imwrite(A, [options.name '.png'], 'ResolutionUnit','meter', 'XResolution',res, 'YResolution',res, format_options{:});
end
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
format_options = getFormatOptions(options, 'jpg'); %Issue #269
if quality > 100
imwrite(A, [options.name '.jpg'], 'Mode','lossless', format_options{:});
else
imwrite(A, [options.name '.jpg'], 'Quality',quality, format_options{:});
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'};
format_options = getFormatOptions(options, 'tif'); %Issue #269
imwrite(A, [options.name '.tif'], 'Resolution',options.magnify*get(0,'ScreenPixelsPerInch'), 'WriteMode',append_mode{options.append+1}, format_options{:});
end
end
% Now do the vector formats
if isvector(options)
% Set the default renderer to painters
if ~options.renderer
if hasTransparency || hasPatches
% This is *MUCH* slower, but more accurate for patches and transparent annotations (issue #39)
renderer = '-opengl';
else
renderer = '-painters';
end
end
options.rendererStr = renderer; % fix for issue #112
% Generate some filenames
tmp_nam = [tempname '.eps'];
try
% Ensure that the temp dir is writable (Javier Paredes 30/1/15)
fid = fopen(tmp_nam,'w');
fwrite(fid,1);
fclose(fid);
delete(tmp_nam);
isTempDirOk = true;
catch
% Temp dir is not writable, so use the user-specified folder
[dummy,fname,fext] = fileparts(tmp_nam); %#ok<ASGLU>
fpath = fileparts(options.name);
tmp_nam = fullfile(fpath,[fname fext]);
isTempDirOk = false;
end
if isTempDirOk
pdf_nam_tmp = [tempname '.pdf'];
else
pdf_nam_tmp = fullfile(fpath,[fname '.pdf']);
end
if options.pdf
pdf_nam = [options.name '.pdf'];
try copyfile(pdf_nam, pdf_nam_tmp, 'f'); catch, end % fix for issue #65
else
pdf_nam = pdf_nam_tmp;
end
% Generate the options for print
printArgs = {renderer};
if ~isempty(options.resolution) % issue #241
printArgs{end+1} = sprintf('-r%d', options.resolution);
end
if options.colourspace == 1 % CMYK
% Issue #33: due to internal bugs in Matlab's print() function, we can't use its -cmyk option
%printArgs{end+1} = '-cmyk';
end
if ~options.crop
% Issue #56: due to internal bugs in Matlab's print() function, we can't use its internal cropping mechanism,
% therefore we always use '-loose' (in print2eps.m) and do our own cropping (in crop_borders)
%printArgs{end+1} = '-loose';
end
if any(strcmpi(varargin,'-depsc'))
% Issue #45: lines in image subplots are exported in invalid color.
% The workaround is to use the -depsc parameter instead of the default -depsc2
printArgs{end+1} = '-depsc';
end
try
% Remove background if requested (issue #207)
originalBgColor = get(fig, 'Color');
[hXs, hYs, hZs] = deal([]);
if options.transparent %&& ~isequal(get(fig, 'Color'), 'none')
if options.renderer == 1 % OpenGL
warning('export_fig:openglTransparentBG', '-opengl sometimes fails to produce transparent backgrounds; in such a case, try to use -painters instead');