Depression Project

Depression Project using MVBC

altmany-export_fig-4c015d5/.gitignore

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+/.ignore
+*.txt
+*.asv
+*~
+*.mex*

altmany-export_fig-4c015d5/ImageSelection.java

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+/*
+ * Based on code snippet from
+ * http://java.sun.com/developer/technicalArticles/releases/data/
+ *
+ * Copyright © 2008, 2010 Oracle and/or its affiliates. All rights reserved. Use is subject to license terms.
+ */
+
+import java.awt.image.BufferedImage;
+import java.awt.datatransfer.*;
+
+public class ImageSelection implements Transferable {
+
+    private static final DataFlavor flavors[] =
+    {DataFlavor.imageFlavor};
+
+    private BufferedImage image;
+
+    public ImageSelection(BufferedImage image) {
+        this.image = image;
+    }
+
+    // Transferable
+    public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException {
+        if (flavor.equals(flavors[0]) == false) {
+            throw new UnsupportedFlavorException(flavor);
+        }
+        return image;
+    }
+
+    public DataFlavor[] getTransferDataFlavors() {
+        return flavors;
+    }
+
+    public boolean isDataFlavorSupported(DataFlavor
+    flavor) {
+        return flavor.equals(flavors[0]);
+    }
+}

altmany-export_fig-4c015d5/LICENSE

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+Copyright (c) 2014, Oliver J. Woodford, Yair M. Altman
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the {organization} nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

altmany-export_fig-4c015d5/append_pdfs.m

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+%APPEND_PDFS Appends/concatenates multiple PDF files
+%
+% Example:
+%   append_pdfs(output, input1, input2, ...)
+%   append_pdfs(output, input_list{:})
+%   append_pdfs test.pdf temp1.pdf temp2.pdf
+%
+% This function appends multiple PDF files to an existing PDF file, or
+% concatenates them into a PDF file if the output file doesn't yet exist.
+%
+% This function requires that you have ghostscript installed on your
+% system. Ghostscript can be downloaded from: http://www.ghostscript.com
+%
+% IN:
+%    output - string of output file name (including the extension, .pdf).
+%             If it exists it is appended to; if not, it is created.
+%    input1 - string of an input file name (including the extension, .pdf).
+%             All input files are appended in order.
+%    input_list - cell array list of input file name strings. All input
+%                 files are appended in order.
+
+% Copyright: Oliver Woodford, 2011
+
+% Thanks to Reinhard Knoll for pointing out that appending multiple pdfs in
+% one go is much faster than appending them one at a time.
+
+% Thanks to Michael Teo for reporting the issue of a too long command line.
+% Issue resolved on 5/5/2011, by passing gs a command file.
+
+% Thanks to Martin Wittmann for pointing out the quality issue when
+% appending multiple bitmaps.
+% Issue resolved (to best of my ability) 1/6/2011, using the prepress
+% setting
+
+% 26/02/15: If temp dir is not writable, use the output folder for temp
+%           files when appending (Javier Paredes); sanity check of inputs
+
+function append_pdfs(varargin)
+
+if nargin < 2,  return;  end  % sanity check
+
+% Are we appending or creating a new file
+append = exist(varargin{1}, 'file') == 2;
+output = [tempname '.pdf'];
+try
+    % Ensure that the temp dir is writable (Javier Paredes 26/2/15)
+    fid = fopen(output,'w');
+    fwrite(fid,1);
+    fclose(fid);
+    delete(output);
+    isTempDirOk = true;
+catch
+    % Temp dir is not writable, so use the output folder
+    [dummy,fname,fext] = fileparts(output); %#ok<ASGLU>
+    fpath = fileparts(varargin{1});
+    output = fullfile(fpath,[fname fext]);
+    isTempDirOk = false;
+end
+if ~append
+    output = varargin{1};
+    varargin = varargin(2:end);
+end
+% Create the command file
+if isTempDirOk
+    cmdfile = [tempname '.txt'];
+else
+    cmdfile = fullfile(fpath,[fname '.txt']);
+end
+fh = fopen(cmdfile, 'w');
+fprintf(fh, '-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile="%s" -f', output);
+fprintf(fh, ' "%s"', varargin{:});
+fclose(fh);
+% Call ghostscript
+ghostscript(['@"' cmdfile '"']);
+% Delete the command file
+delete(cmdfile);
+% Rename the file if needed
+if append
+    movefile(output, varargin{1});
+end
+end

altmany-export_fig-4c015d5/copyfig.m

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+function fh = copyfig(fh)
+%COPYFIG Create a copy of a figure, without changing the figure
+%
+% Examples:
+%   fh_new = copyfig(fh_old)
+%
+% This function will create a copy of a figure, but not change the figure,
+% as copyobj sometimes does, e.g. by changing legends.
+%
+% IN:
+%    fh_old - The handle of the figure to be copied. Default: gcf.
+%
+% OUT:
+%    fh_new - The handle of the created figure.
+
+% Copyright (C) Oliver Woodford 2012
+
+% 26/02/15: If temp dir is not writable, use the dest folder for temp
+%           destination files (Javier Paredes)
+% 15/04/15: Suppress warnings during copyobj (Dun Kirk comment on FEX page 2013-10-02)
+
+    % Set the default
+    if nargin == 0
+        fh = gcf;
+    end
+    % Is there a legend?
+    if isempty(findall(fh, 'Type', 'axes', 'Tag', 'legend'))
+        % Safe to copy using copyobj
+        oldWarn = warning('off'); %#ok<WNOFF>  %Suppress warnings during copyobj (Dun Kirk comment on FEX page 2013-10-02)
+        fh = copyobj(fh, 0);
+        warning(oldWarn);
+    else
+        % copyobj will change the figure, so save and then load it instead
+        tmp_nam = [tempname '.fig'];
+        try
+            % Ensure that the temp dir is writable (Javier Paredes 26/2/15)
+            fid = fopen(tmp_nam,'w');
+            fwrite(fid,1);
+            fclose(fid);
+            delete(tmp_nam);  % cleanup
+        catch
+            % Temp dir is not writable, so use the current folder
+            [dummy,fname,fext] = fileparts(tmp_nam); %#ok<ASGLU>
+            fpath = pwd;
+            tmp_nam = fullfile(fpath,[fname fext]);
+        end
+        hgsave(fh, tmp_nam);
+        fh = hgload(tmp_nam);
+        delete(tmp_nam);
+    end
+end

altmany-export_fig-4c015d5/crop_borders.m

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+function [A, vA, vB, bb_rel] = crop_borders(A, bcol, padding)
+%CROP_BORDERS Crop the borders of an image or stack of images
+%
+%   [B, vA, vB, bb_rel] = crop_borders(A, bcol, [padding])
+%
+%IN:
+%   A - HxWxCxN stack of images.
+%   bcol - Cx1 background colour vector.
+%   padding - scalar indicating how much padding to have in relation to
+%             the cropped-image-size (0<=padding<=1). Default: 0
+%
+%OUT:
+%   B - JxKxCxN cropped stack of images.
+%   vA     - coordinates in A that contain the cropped image
+%   vB     - coordinates in B where the cropped version of A is placed
+%   bb_rel - relative bounding box (used for eps-cropping)
+
+% 06/03/15: Improved image cropping thanks to Oscar Hartogensis
+% 08/06/15: Fixed issue #76: case of transparent figure bgcolor
+
+    if nargin < 3
+        padding = 0;
+    end
+    [h, w, c, n] = size(A);
+    if isempty(bcol)  % case of transparent bgcolor
+        bcol = A(ceil(end/2),1,:,1);
+    end
+    if isscalar(bcol)
+        bcol = bcol(ones(c, 1));
+    end
+
+    % Crop margin from left
+    bail = false;
+    for l = 1:w
+        for a = 1:c
+            if ~all(col(A(:,l,a,:)) == bcol(a))
+                bail = true;
+                break;
+            end
+        end
+        if bail
+            break;
+        end
+    end
+
+    % Crop margin from right
+    bcol = A(ceil(end/2),w,:,1);
+    bail = false;
+    for r = w:-1:l
+        for a = 1:c
+            if ~all(col(A(:,r,a,:)) == bcol(a))
+                bail = true;
+                break;
+            end
+        end
+        if bail
+            break;
+        end
+    end
+
+    % Crop margin from top
+    bcol = A(1,ceil(end/2),:,1);
+    bail = false;
+    for t = 1:h
+        for a = 1:c
+            if ~all(col(A(t,:,a,:)) == bcol(a))
+                bail = true;
+                break;
+            end
+        end
+        if bail
+            break;
+        end
+    end
+
+    % Crop margin from bottom
+    bcol = A(h,ceil(end/2),:,1);
+    bail = false;
+    for b = h:-1:t
+        for a = 1:c
+            if ~all(col(A(b,:,a,:)) == bcol(a))
+                bail = true;
+                break;
+            end
+        end
+        if bail
+            break;
+        end
+    end
+
+    % Crop the background, leaving one boundary pixel to avoid bleeding on resize
+    %v = [max(t-padding, 1) min(b+padding, h) max(l-padding, 1) min(r+padding, w)];
+    %A = A(v(1):v(2),v(3):v(4),:,:);
+    if padding == 0  % no padding
+        padding = 1;
+    elseif abs(padding) < 1  % pad value is a relative fraction of image size
+        padding = sign(padding)*round(mean([b-t r-l])*abs(padding)); % ADJUST PADDING
+    else  % pad value is in units of 1/72" points
+        padding = round(padding);  % fix cases of non-integer pad value
+    end
+
+    if padding > 0  % extra padding
+        % Create an empty image, containing the background color, that has the
+        % cropped image size plus the padded border
+        B = repmat(bcol,(b-t)+1+padding*2,(r-l)+1+padding*2);
+        % vA - coordinates in A that contain the cropped image
+        vA = [t b l r];
+        % vB - coordinates in B where the cropped version of A will be placed
+        vB = [padding+1, (b-t)+1+padding, padding+1, (r-l)+1+padding];
+        % Place the original image in the empty image
+        B(vB(1):vB(2), vB(3):vB(4), :) = A(vA(1):vA(2), vA(3):vA(4), :);
+        A = B;
+    else  % extra cropping
+        vA = [t-padding b+padding l-padding r+padding];
+        A = A(vA(1):vA(2), vA(3):vA(4), :);
+        vB = [NaN NaN NaN NaN];
+    end
+
+    % For EPS cropping, determine the relative BoundingBox - bb_rel
+    bb_rel = [l-1 h-b-1 r+1 h-t+1]./[w h w h];
+end
+
+function A = col(A)
+    A = A(:);
+end