function CustomBrainRegionStack()

%%%%%% Function description
% THIS IS A MODIFICATION OF THE ZBrainAnalysisOfMAPMaps function published
% in Randett et al. (2015).

% This function takes a .csv input containing signal intensities
% corresponding to the 293 regions (294 minus eyes) of the ZBrain anatomical 
% atlas and returns .tiff files with those regions colored according to the 
% intensity of the signal. About a tenfold difference can be easily seen 
% with the  human eye; greater differences might need to be transformed.  

% This function first asks the user to point it to an Excel file. The Excel
% file must have two columns of length 293. The first column should contain
% positive signal (which will be represented in green in the final image)
% and the second column should contain negative signal (which will be
% represented in purple in the final image). If there is no negative signal
% to represent, the second column should be all 0s. 

%%%%%% Input files

% This function will use three files. These are the pre-downsampled
% versions of the Z-Brain contained in files
% 'AnatomyLabelDatabaseDownsampled.hdf5', and
% 'MaskDatabaseDownsampled.mat', as well as a
% '*SignificantDeltaMedians.tif' stack to be analyze, which is the stack
% output from the 'MakeTheMAPMap.m' function.

% The funciton starts with a promt to direct towards the MAPMap. Multiple
% files can be selected to analyze one after the other. A prompt will
% appear for the downsampled database files if they are not in Matlab's
% path. If the downsampled database files are not there, point to the
% folder containing the AnatomyDabase.hdf5, and MaskDatabase.mat files, and
% they will be downsampled saved the first time the program is run. If you
% dont have these files, download them here:
% http://engertlab.fas.harvard.edu/Z-Brain/downloads.html
%

%%%%%% Input arguments

%%% CalculateLabels
% 1 (default), overlap with antomy labels will be calulcated
% 0 - this calculation will be skipped and mask signals quantified.

%%% LeftVsRight

% 0 (default) - Do not separate left and right side of the brain, look at
%       whole mask
% 1 - Additionally calculate signals on Left Vs Right separately, and output the signals
%       in each mask


%%%%%% OUTPUT

% First will be a stack (*SignalInEachROIImage.tif), with each regions
% drawn with signal proportional to its intensity and scaled to the max of
% the data set. Green = activation, magneta = supression. ROIs are split at
% the middle of the stack, to reveal any strong left/rigth differences.
% These stacks are then made into a 2D image of the Z and X maximum
% projections (*SignalInEachROIProjection.tif)
%
% Two tables are output, one for each the activated and supressed regions,
% ranked for highest average signal within the ROI. The value for signal is
% a number between 0 and 65535, where 65535 would be saturated signal in
% the entire ROI. Also in these tables will be a ranking of the different
% transgenes/labels in the anatomy database for those who show the most
% signal within the activation signals in that ROI. This number represent
% the average brighness of the signal wihtin the activated region of that
% ROI divided by the average brigheness in the 50 pixels surrounding that
% ROI. Therefore, numbers above 1 indicate enrichment of that label in the
% active regions, whereas numbers less than 1 indicate that the label is
% brighter in the adjacent areas. Finally we will output a .mat file called
% '*SignalInEachROI.mat', which contains the names of the anatomical
% regions (in their normal alphabetical order), and the positive and
% negative signal within each anatomical region.



% This function uses two a standard matlab function, which I gratefully
% acknowldege the author of:
%
% uipickfiles.m by Douglas Schwarz
%
% http://www.mathworks.com/matlabcentral/fileexchange/10867-uipickfiles--uigetfile-on-steroids
% http://www.mathworks.com/matlabcentral/fileexchange/view_license?file_info_id=10867
%
% uipickfiles BSD Licence: Copyright (c) 2007, Douglas M. Schwarz 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
%
% 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 OWNER 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.
%
%

XYRez = 1.65; % the resolution of MAP-Maps
ZRez = 3.45;

height = 679;
width = 300;
Zs = 80;

% point to a table with positive (column 1) and negative (column 2) signal.
% The table should be 293 rows long
% The order should match the order in the mask database (ABC by region)
MySpecifiedRegions = uipickfiles('FilterSpec', '*.csv');
nFiles = length(MySpecifiedRegions);

[SpecifiedRegionsPath,name,ext] = fileparts(MySpecifiedRegions{nFiles});
    SpecifiedRegionsFilename = [name, ext];
    cd(SpecifiedRegionsPath);
    
% reads in the spreadsheet provided
    
regionTable = readtable(SpecifiedRegionsFilename);
regionMatrix = table2array(regionTable);

try % if we are already in the correct directory, load in the mask database files. The 'AnatomyLabelDatabaseDownsampled.hdf5' file also needs to be in this directory
    
    load('MaskDatabaseDownsampled.mat');
    MaskDatabasePath = pwd;
    
catch
    MaskDatabasePath = uigetdir(pwd,'Point to the folder with the ZBrain files'); %'MaskDatabaseDownsampled.mat' and 'AnatomyLabelDatabaseDownsampled.hdf5' need to be in this folder
    cd(MaskDatabasePath);
    addpath(MaskDatabasePath);
    try
        load('MaskDatabaseDownsampled.mat');
    catch
        MakeDownsampledFiles(MaskDatabasePath); % if we dont aready have the downsampled database, make it. 
        load('MaskDatabaseDownsampled.mat');
    end
end


% remove the eyes since Nacre fish dont show real signal there.
for j = length(MaskDatabaseNames):-1:1
    if strcmp('Ganglia - Eyes', MaskDatabaseNames{j})
        MaskDatabaseNames(j) = [];
        MaskDatabaseDownsamp(:,j) = [];
        MaskDatabase50OutsideDownsamp(:,j) = [];
        MaskDatabaseOutlinesDownsamp(:,j) = [];
    end
end

% remove any commas from mask names, as this messes up the csv output file

for j = 1:length(MaskDatabaseNames)
    MaskDatabaseNames{j} = strrep(MaskDatabaseNames{j},',', '-');
end

    % HS: this creates two empty cell arrays of 2x 294, one for postive and one for
    % negatve results
    nMasks = size(MaskDatabaseDownsamp, 2);
    PosResults = cell(nMasks, 2);
    NegResults = cell(nMasks, 2);
    
    % here we will get the summed delta median value divided by the number of 
    %pixels within that ROI - AKA the mean signal within the ROI. First column 
    % is for positive (acitvation) signals. Second column is for negative (supressive) signals.
    
    MaskImagePositive = zeros(height, width, Zs);
    MaskImageNegative = zeros(height, width, Zs);
    
    waitMasks = waitbar(0, 'Progress through masks', 'Units', 'normalized', 'position', [0.4,0.7, 0.3, 0.1]);
    % loop through and calculate signal in each mask. Also make an image which
    % draws the mask.
    
    % HS: this creates two blank stacks of the correct size for the image
    % we will make
    % in one, we will color in the masks for the positive regions
    % in the other, we will color in the masks for the negative regions
    
    PositiveRegion = zeros(height, width, Zs);
    NegativeRegion = zeros(height, width, Zs);
    
    for i = 1:nMasks
        
        mask = reshape(full(MaskDatabaseDownsamp(:,i)), [height, width, Zs]);
        
        %if the input you provided isn't 0, the mask will be colored in
        if regionMatrix(i,1) ~= 0;
            PositiveRegion(mask) = regionMatrix(i,1);
        end
        
        if regionMatrix(i,2) ~= 0;
            NegativeRegion(mask) = regionMatrix(i,2);
        end
        
        MaskImagePositive = max(cat(4, MaskImagePositive, PositiveRegion), [], 4);   %if this messes up, change 4 to 3
        
        MaskImageNegative = max(cat(4, MaskImageNegative, NegativeRegion), [], 4);   %if this messes up, change 4 to 3
        waitbar(i/nMasks, waitMasks)
    end
    close(waitMasks)
    
    %normalizes the signal displayed to the maximum signal achieved in any region, 
    % either positive or negative 
    
    maxScaledMaskValue = max(max(MaskImagePositive(:)), max(MaskImageNegative(:)));
    MaskImageNegative = MaskImageNegative./maxScaledMaskValue;
    MaskImagePositive = MaskImagePositive./maxScaledMaskValue;
    
    ScaledMaskStackName = strcat(strrep(SpecifiedRegionsFilename, 'SignificantDeltaMedians.tif', ''), 'SignalInEachROIImage.tif');
    
    
    for z = 1:Zs
        while true % avoid the annoying write error in windows, keep tryin to write until successful
            try
                if z == 1;
                    imwrite(cat(3, squeeze(MaskImageNegative(:,:,z)), squeeze(MaskImagePositive(:,:,z)), squeeze(MaskImageNegative(:,:,z))), ScaledMaskStackName, 'writemode', 'overwrite')
                else
                    imwrite(cat(3, squeeze(MaskImageNegative(:,:,z)), squeeze(MaskImagePositive(:,:,z)), squeeze(MaskImageNegative(:,:,z))), ScaledMaskStackName, 'writemode', 'append')
                end
                break
            catch
            end
        end
    end
    % take the maximum projection to make a 2D image
    MaskImagePosZProject = max(MaskImagePositive,[], 3);
    MaskImagePosXProject = squeeze(max(MaskImagePositive,[], 2));
    MaskImagePosXProject = imresize(MaskImagePosXProject, [height, Zs.*(ZRez/XYRez)]);
    
    MaskImagePosProject = double(cat(2, MaskImagePosZProject, MaskImagePosXProject));
    
    
    MaskImageNegZProject = max(MaskImageNegative,[], 3);
    MaskImageNegXProject = squeeze(max(MaskImageNegative,[], 2));
    MaskImageNegXProject = imresize(MaskImageNegXProject, [height, Zs.*(ZRez/XYRez)]);
    
    MaskImageNegProject = double(cat(2, MaskImageNegZProject, MaskImageNegXProject));
    
    % normalize to the maximum value
    
    maxProject = max(max(MaskImagePosProject(:)), max(MaskImageNegProject(:)));
    MaskImagePosProject = MaskImagePosProject./maxProject;
    MaskImageNegProject = MaskImageNegProject./maxProject;
    
    ProjectionName = strcat(strrep(SpecifiedRegionsFilename, 'SignificantDeltaMedians.tif', ''), 'SignalInEachROIProjection.tif');
    
    imwrite(cat(3,MaskImageNegProject, MaskImagePosProject, MaskImageNegProject), ProjectionName, 'writemode', 'overwrite');
    
    ROIFileStackName = strcat(strrep(SpecifiedRegionsFilename, 'SignificantDeltaMedians.tif', ''), 'SignalInEachROI.mat');
    
    save(ROIFileStackName, 'MaskDatabaseNames')
    
    % rank the ROIs according to signal
    
    [SortedPositiveSignalInMasks, SortedPositiveSignalInMasksIX] = sort(SignalInMasks(:,1), 'descend');
    [SortedNegativeSignalInMasks, SortedNegativeSignalInMasksIX] = sort(SignalInMasks(:,2), 'descend');
    
    % get the names associated with each ROI
    
    for i = 1:nMasks
        ind = SortedPositiveSignalInMasksIX(i);
        PosResults(i,1) = MaskDatabaseNames(ind);
    end
    
    for i = 1:nMasks
        ind = SortedNegativeSignalInMasksIX(i);
        NegResults(i,1) = MaskDatabaseNames(ind);
    end
    
    % in the second column we place the average signal per pixel in that region
    for i = 1:nMasks
        PosResults(i,2) = {num2str(SortedPositiveSignalInMasks(i))};
        NegResults(i,2) = {num2str(SortedNegativeSignalInMasks(i))};
    end
    %  
end

function MakeDownsampledFiles(MaskDatabasePath)

% if we dont already have the downsampled files at MAP-Map resolution, make them from the full resolution files


% Since MAP-Maps are at a downsample resolution from the Z-Brain atlas, we make a downsampled version of the Z-Brain to analyze the MAP-Maps. This saves having to resize everything every time you want to analyze a MAP-Map.
% Here we make the Downsampled Mask database. We also make the masks for
% the 50 pixels surrounding the images which is used as a normalization for the calculation of
% the label signal enrichemnt in the MAP-Map activated areas.

DownsampHeight = 679; % the resolution of MAP-Maps
DownsampWidth = 300;
DownsampZs = 80;

% start with the mask database
cd(MaskDatabasePath)
load('MaskDatabase.mat')
nMasks = size(MaskDatabase, 2);
MaskDatabaseDownsamp = false(DownsampHeight*DownsampWidth*DownsampZs, nMasks);
MaskDatabaseOutlinesDownsamp = false(DownsampHeight*DownsampWidth*DownsampZs, nMasks);
MaskDatabase50OutsideDownsamp = false(DownsampHeight*DownsampWidth*DownsampZs, nMasks);


MaskDownXY = false(DownsampHeight, DownsampWidth, Zs); % preallocate temporary downsampling stacks
MaskDownZ = false(DownsampHeight, DownsampWidth, DownsampZs);

wait = waitbar(0, 'making the downsampled masks.. this will take time but ony has to be done once!');
figure,
for n = 1:nMasks
    MaskTemp = reshape(full(MaskDatabase(:,n)), [height, width, Zs]);
    
    for z = 1:Zs % shrink X/Y
        MaskDownXY(:,:,z) = imresize(squeeze(MaskTemp(:,:,z)), [DownsampHeight, DownsampWidth], 'method', 'nearest');
    end
    
    for w = 1:DownsampWidth % shrink Z
        MaskDownZ(:,w,:) = imresize(squeeze(MaskDownXY(:,w,:)), [DownsampHeight, DownsampZs], 'method', 'nearest');
    end
    
    MaskDatabaseDownsamp(:,n) = reshape(MaskDownZ, [DownsampHeight*DownsampWidth*DownsampZs, 1]);
    
    OutlineTemp = bwdist(MaskDownZ) == 1;
    
    MaskDatabaseOutlinesDownsamp(:,n) = reshape(OutlineTemp, [DownsampHeight*DownsampWidth*DownsampZs, 1]);
    
    
    imshowpair(sum(MaskDownZ, 3)./max(sum(sum(sum(MaskDownZ, 3)))), sum(OutlineTemp, 3)./max(sum(sum(sum(OutlineTemp, 3)))))
    
    mask50Outside = MaskDownZ;  % this will be the mask that has the 50 pixel ring around the actual mask, which is used to normalize the transgene signals to look for enrichement within the ROIs
    
    for z=1:DownsampZs
        mask50Outside(:,:,z) = bwdist(MaskDownZ(:,:,z)) <= 50; % we will use the space outside the mask within 50 pixels to normalize the transgene signals
    end
    mask50Outside = mask50Outside - MaskDownZ;
    
    MaskDatabase50OutsideDownsamp(:,n) = reshape(mask50Outside, [DownsampHeight*DownsampWidth*DownsampZs, 1]);
    
    waitbar(n/nMasks)
end
close(wait)

close all

MaskDatabaseDownsamp = sparse(MaskDatabaseDownsamp);
MaskDatabaseOutlinesDownsamp = sparse(MaskDatabaseOutlinesDownsamp);
MaskDatabase50OutsideDownsamp = sparse(MaskDatabase50OutsideDownsamp);

cd(MaskDatabasePath);
save('MaskDatabaseDownsampled.mat', 'MaskDatabaseNames', 'MaskDatabaseDownsamp', 'MaskDatabaseOutlinesDownsamp', 'MaskDatabase50OutsideDownsamp', 'DateCreated');


try % check to see if we already have the downsampled labels
    StackDatabaseInfo = h5info('AnatomyLabelDatabaseDownsampled.hdf5');
catch % if not, we make them
    
    StackDatabaseInfo = h5info('AnatomyLabelDatabase.hdf5');
    StackDownXY = uint16(zeros(DownsampHeight, DownsampWidth, Zs)); % preallocate temporary downsampling stacks
    StackDownZ = uint16(zeros(DownsampHeight, DownsampWidth, DownsampZs));
    
    
    wait = waitbar(0, 'making the downsampled labels.. this will take time but ony has to be done once!');
    
    nStacks = length(StackDatabaseInfo.Datasets);
    for n = 1:nStacks
        datasetName = strcat('/', StackDatabaseInfo.Datasets(n).Name);
        StackTemp = h5read('AnatomyLabelDatabase.hdf5', datasetName);
        for z = 1:Zs % shrink X/Y
            StackDownXY(:,:,z) = imresize(squeeze(StackTemp(:,:,z)), [DownsampHeight, DownsampWidth], 'method', 'bicubic');
        end
        
        for w = 1:DownsampWidth % shrink Z
            StackDownZ(:,w,:) = imresize(squeeze(StackDownXY(:,w,:)), [DownsampHeight, DownsampZs], 'method', 'bicubic');
        end
        
        h5create('AnatomyLabelDatabaseDownsampled.hdf5', datasetName, [DownsampHeight, DownsampWidth, DownsampZs], 'Datatype', 'uint16', 'ChunkSize', [DownsampHeight, DownsampWidth, 1], 'deflate', 9);
        h5write('AnatomyLabelDatabaseDownsampled.hdf5', datasetName, StackDownZ);
        
        waitbar(n/nStacks)
    end
    close(wait);
    clear all;
    
end
end

% uipickfiles was written

function out = uipickfiles(varargin)
%uipickfiles: GUI program to select files and/or folders.
%
% Syntax:
%   files = uipickfiles('PropertyName',PropertyValue,...)
%
% The current folder can be changed by operating in the file navigator:
% double-clicking on a folder in the list or pressing Enter to move further
% down the tree, using the popup menu, clicking the up arrow button or
% pressing Backspace to move up the tree, typing a path in the box to move
% to any folder or right-clicking (control-click on Mac) on the path box to
% revisit a previously-visited folder.  These folders are listed in order
% of when they were last visited (most recent at the top) and the list is
% saved between calls to uipickfiles.  The list can be cleared or its
% maximum length changed with the items at the bottom of the menu.
% (Windows only: To go to a UNC-named resource you will have to type the
% UNC name in the path box, but all such visited resources will be
% remembered and listed along with the mapped drives.)  The items in the
% file navigator can be sorted by name, modification date or size by
% clicking on the headers, though neither date nor size are displayed.  All
% folders have zero size.
%
% Files can be added to the list by double-clicking or selecting files
% (non-contiguous selections are possible with the control key) and
% pressing the Add button.  Control-F will select all the files listed in
% the navigator while control-A will select everything (Command instead of
% Control on the Mac).  Since double-clicking a folder will open it,
% folders can be added only by selecting them and pressing the Add button.
% Files/folders in the list can be removed or re-ordered.  Recall button
% will insert into the Selected Files list whatever files were returned the
% last time uipickfiles was run.  When finished, a press of the Done button
% will return the full paths to the selected items in a cell array,
% structure array or character array.  If the Cancel button or the escape
% key is pressed then zero is returned.
%
% The figure can be moved and resized in the usual way and this position is
% saved and used for subsequent calls to uipickfiles.  The default position
% can be restored by double-clicking in a vacant region of the figure.
%
% The following optional property/value pairs can be specified as arguments
% to control the indicated behavior:
%
%   Property    Value
%   ----------  ----------------------------------------------------------
%   FilterSpec  String to specify starting folder and/or file filter.
%               Ex:  'C:\bin' will start up in that folder.  '*.txt'
%               will list only files ending in '.txt'.  'c:\bin\*.txt' will
%               do both.  Default is to start up in the current folder and
%               list all files.  Can be changed with the GUI.
%
%   REFilter    String containing a regular expression used to filter the
%               file list.  Ex: '\.m$|\.mat$' will list files ending in
%               '.m' and '.mat'.  Default is empty string.  Can be used
%               with FilterSpec and both filters are applied.  Can be
%               changed with the GUI.
%
%   REDirs      Logical flag indicating whether to apply the regular
%               expression filter to folder names.  Default is false which
%               means that all folders are listed.  Can be changed with the
%               GUI.
%
%   Type        Two-column cell array where the first column contains file
%               filters and the second column contains descriptions.  If
%               this property is specified an additional popup menu will
%               appear below the File Filter and selecting an item will put
%               that item into the File Filter.  By default, the first item
%               will be entered into the File Filter.  For example,
%                   { '*.m',   'M-files'   ;
%                     '*.mat', 'MAT-files' }.
%               Can also be a cell vector of file filter strings in which
%               case the descriptions will be the same as the file filters
%               themselves.
%               Must be a cell array even if there is only one entry.
%
%   Prompt      String containing a prompt appearing in the title bar of
%               the figure.  Default is 'Select files'.
%
%   NumFiles    Scalar or vector specifying number of files that must be
%               selected.  A scalar specifies an exact value; a two-element
%               vector can be used to specify a range, [min max].  The
%               function will not return unless the specified number of
%               files have been chosen.  Default is [] which accepts any
%               number of files.
%
%   Append      Cell array of strings, structure array or char array
%               containing a previously returned output from uipickfiles.
%               Used to start up program with some entries in the Selected
%               Files list.  Any included files that no longer exist will
%               not appear.  Default is empty cell array, {}.
%
%   Output      String specifying the data type of the output: 'cell',
%               'struct' or 'char'.  Specifying 'cell' produces a cell
%               array of strings, the strings containing the full paths of
%               the chosen files.  'Struct' returns a structure array like
%               the result of the dir function except that the 'name' field
%               contains a full path instead of just the file name.  'Char'
%               returns a character array of the full paths.  This is most
%               useful when you have just one file and want it in a string
%               instead of a cell array containing just one string.  The
%               default is 'cell'.
%
% All properties and values are case-insensitive and need only be
% unambiguous.  For example,
%
%   files = uipickfiles('num',1,'out','ch')
%
% is valid usage.

% Version: 1.15, 2 March 2012
% Author:  Douglas M. Schwarz
% Email:   dmschwarz=ieee*org, dmschwarz=urgrad*rochester*edu
% Real_email = regexprep(Email,{'=','*'},{'@','.'})


% Define properties and set default values.
prop.filterspec = '*';
prop.refilter = '';
prop.redirs = false;
prop.type = {};
prop.prompt = 'Select files';
prop.numfiles = [];
prop.append = [];
prop.output = 'cell';

% Process inputs and set prop fields.
prop = parsepropval(prop,varargin{:});

% Validate FilterSpec property.
if isempty(prop.filterspec)
    prop.filterspec = '*';
end
if ~ischar(prop.filterspec)
    error('FilterSpec property must contain a string.')
end

% Validate REFilter property.
if ~ischar(prop.refilter)
    error('REFilter property must contain a string.')
end

% Validate REDirs property.
if ~isscalar(prop.redirs)
    error('REDirs property must contain a scalar.')
end

% Validate Type property.
if isempty(prop.type)
elseif iscellstr(prop.type) && isscalar(prop.type)
    prop.type = repmat(prop.type(:),1,2);
elseif iscellstr(prop.type) && size(prop.type,2) == 2
else
    error(['Type property must be empty or a cellstr vector or ',...
        'a 2-column cellstr matrix.'])
end

% Validate Prompt property.
if ~ischar(prop.prompt)
    error('Prompt property must contain a string.')
end

% Validate NumFiles property.
if numel(prop.numfiles) > 2 || any(prop.numfiles < 0)
    error('NumFiles must be empty, a scalar or two-element vector.')
end
prop.numfiles = unique(prop.numfiles);
if isequal(prop.numfiles,1)
    numstr = 'Select exactly 1 file.';
elseif length(prop.numfiles) == 1
    numstr = sprintf('Select exactly %d items.',prop.numfiles);
else
    numstr = sprintf('Select %d to %d items.',prop.numfiles);
end

% Validate Append property and initialize pick data.
if isstruct(prop.append) && isfield(prop.append,'name')
    prop.append = {prop.append.name};
elseif ischar(prop.append)
    prop.append = cellstr(prop.append);
end
if isempty(prop.append)
    file_picks = {};
    full_file_picks = {};
    dir_picks = dir(' ');  % Create empty directory structure.
elseif iscellstr(prop.append) && isvector(prop.append)
    num_items = length(prop.append);
    file_picks = cell(1,num_items);
    full_file_picks = cell(1,num_items);
    dir_fn = fieldnames(dir(' '));
    dir_picks = repmat(cell2struct(cell(length(dir_fn),1),dir_fn(:)),...
        num_items,1);
    for item = 1:num_items
        if exist(prop.append{item},'dir') && ...
                ~any(strcmp(full_file_picks,prop.append{item}))
            full_file_picks{item} = prop.append{item};
            [unused,fn,ext] = fileparts(prop.append{item});
            file_picks{item} = [fn,ext];
            temp = dir(fullfile(prop.append{item},'..'));
            if ispc || ismac
                thisdir = strcmpi({temp.name},[fn,ext]);
            else
                thisdir = strcmp({temp.name},[fn,ext]);
            end
            dir_picks(item) = temp(thisdir);
            dir_picks(item).name = prop.append{item};
        elseif exist(prop.append{item},'file') && ...
                ~any(strcmp(full_file_picks,prop.append{item}))
            full_file_picks{item} = prop.append{item};
            [unused,fn,ext] = fileparts(prop.append{item});
            file_picks{item} = [fn,ext];
            dir_picks(item) = dir(prop.append{item});
            dir_picks(item).name = prop.append{item};
        else
            continue
        end
    end
    % Remove items which no longer exist.
    missing = cellfun(@isempty,full_file_picks);
    full_file_picks(missing) = [];
    file_picks(missing) = [];
    dir_picks(missing) = [];
else
    error('Append must be a cell, struct or char array.')
end

% Validate Output property.
legal_outputs = {'cell','struct','char'};
out_idx = find(strncmpi(prop.output,legal_outputs,length(prop.output)));
if length(out_idx) == 1
    prop.output = legal_outputs{out_idx};
else
    error(['Value of ''Output'' property, ''%s'', is illegal or '...
        'ambiguous.'],prop.output)
end


% Set style preference for display of folders.
%   1 => folder icon before and filesep after
%   2 => bullet before and filesep after
%   3 => filesep after only
folder_style_pref = 1;
fsdata = set_folder_style(folder_style_pref);

% Initialize file lists.
if exist(prop.filterspec,'dir')
    current_dir = prop.filterspec;
    filter = '*';
else
    [current_dir,f,e] = fileparts(prop.filterspec);
    filter = [f,e];
end
if isempty(current_dir)
    current_dir = pwd;
end
if isempty(filter)
    filter = '*';
end
re_filter = prop.refilter;
full_filter = fullfile(current_dir,filter);
network_volumes = {};
[path_cell,new_network_vol] = path2cell(current_dir);
if exist(new_network_vol,'dir')
    network_volumes = unique([network_volumes,{new_network_vol}]);
end
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
    @(x)file_sort(x,[1 0 0]));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);

% Initialize some data.
show_full_path = false;
nodupes = true;

% Get history preferences and set history.
history = getpref('uipickfiles','history',...
    struct('name',current_dir,'time',now));
default_history_size = 15;
history_size = getpref('uipickfiles','history_size',default_history_size);
history = update_history(history,current_dir,now,history_size);

% Get figure position preference and create figure.
gray = get(0,'DefaultUIControlBackgroundColor');
if ispref('uipickfiles','figure_position');
    fig_pos = getpref('uipickfiles','figure_position');
    fig = figure('Position',fig_pos,...
        'Color',gray,...
        'MenuBar','none',...
        'WindowStyle','modal',...
        'Resize','on',...
        'NumberTitle','off',...
        'Name',prop.prompt,...
        'IntegerHandle','off',...
        'CloseRequestFcn',@cancel,...
        'ButtonDownFcn',@reset_figure_size,...
        'KeyPressFcn',@keypressmisc,...
        'Visible','off');
else
    fig_pos = [0 0 740 494];
    fig = figure('Position',fig_pos,...
        'Color',gray,...
        'MenuBar','none',...
        'WindowStyle','modal',...
        'Resize','on',...
        'NumberTitle','off',...
        'Name',prop.prompt,...
        'IntegerHandle','off',...
        'CloseRequestFcn',@cancel,...
        'CreateFcn',{@movegui,'center'},...
        'ButtonDownFcn',@reset_figure_size,...
        'KeyPressFcn',@keypressmisc,...
        'Visible','off');
end

% Set system-dependent items.
if ismac
    set(fig,'DefaultUIControlFontName','Lucida Grande')
    set(fig,'DefaultUIControlFontSize',9)
    sort_ctrl_size = 8;
    mod_key = 'command';
    action = 'Control-click';
elseif ispc
    set(fig,'DefaultUIControlFontName','Tahoma')
    set(fig,'DefaultUIControlFontSize',8)
    sort_ctrl_size = 7;
    mod_key = 'control';
    action = 'Right-click';
else
    sort_ctrl_size = get(fig,'DefaultUIControlFontSize') - 1;
    mod_key = 'control';
    action = 'Right-click';
end

% Create uicontrols.
frame1 = uicontrol('Style','frame',...
    'Position',[255 260 110 70]);
frame2 = uicontrol('Style','frame',...
    'Position',[275 135 110 100]);

navlist = uicontrol('Style','listbox',...
    'Position',[10 10 250 320],...
    'String',filenames,...
    'Value',[],...
    'BackgroundColor','w',...
    'Callback',@clicknav,...
    'KeyPressFcn',@keypressnav,...
    'Max',2);

tri_up = repmat([1 1 1 1 0 1 1 1 1;1 1 1 0 0 0 1 1 1;1 1 0 0 0 0 0 1 1;...
    1 0 0 0 0 0 0 0 1],[1 1 3]);
tri_up(tri_up == 1) = NaN;
tri_down = tri_up(end:-1:1,:,:);
tri_null = NaN(4,9,3);
tri_icon = {tri_down,tri_null,tri_up};
sort_state = [1 0 0];
last_sort_state = [1 1 1];
sort_cb = zeros(1,3);
sort_cb(1) = uicontrol('Style','checkbox',...
    'Position',[15 331 70 15],...
    'String','Name',...
    'FontSize',sort_ctrl_size,...
    'Value',sort_state(1),...
    'CData',tri_icon{sort_state(1)+2},...
    'KeyPressFcn',@keypressmisc,...
    'Callback',{@sort_type,1});
sort_cb(2) = uicontrol('Style','checkbox',...
    'Position',[85 331 70 15],...
    'String','Date',...
    'FontSize',sort_ctrl_size,...
    'Value',sort_state(2),...
    'CData',tri_icon{sort_state(2)+2},...
    'KeyPressFcn',@keypressmisc,...
    'Callback',{@sort_type,2});
sort_cb(3) = uicontrol('Style','checkbox',...
    'Position',[155 331 70 15],...
    'String','Size',...
    'FontSize',sort_ctrl_size,...
    'Value',sort_state(3),...
    'CData',tri_icon{sort_state(3)+2},...
    'KeyPressFcn',@keypressmisc,...
    'Callback',{@sort_type,3});

pickslist = uicontrol('Style','listbox',...
    'Position',[380 10 350 320],...
    'String',file_picks,...
    'BackgroundColor','w',...
    'Callback',@clickpicks,...
    'KeyPressFcn',@keypresslist,...
    'Max',2,...
    'Value',[]);

openbut = uicontrol('Style','pushbutton',...
    'Position',[270 300 80 20],...
    'String','Open',...
    'Enable','off',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@open);

arrow = [ ...
    '        1   ';
    '        10  ';
    '         10 ';
    '000000000000';
    '         10 ';
    '        10  ';
    '        1   '];
cmap = NaN(128,3);
cmap(double('10'),:) = [0.5 0.5 0.5;0 0 0];
arrow_im = NaN(7,76,3);
arrow_im(:,45:56,:) = ind2rgb(double(arrow),cmap);
addbut = uicontrol('Style','pushbutton',...
    'Position',[270 270 80 20],...
    'String','Add    ',...
    'Enable','off',...
    'CData',arrow_im,...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@add);

removebut = uicontrol('Style','pushbutton',...
    'Position',[290 205 80 20],...
    'String','Remove',...
    'Enable','off',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@remove);
moveupbut = uicontrol('Style','pushbutton',...
    'Position',[290 175 80 20],...
    'String','Move Up',...
    'Enable','off',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@moveup);
movedownbut = uicontrol('Style','pushbutton',...
    'Position',[290 145 80 20],...
    'String','Move Down',...
    'Enable','off',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@movedown);

dir_popup = uicontrol('Style','popupmenu',...
    'Position',[10 350 225 20],...
    'BackgroundColor','w',...
    'String',path_cell,...
    'Value',length(path_cell),...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@dirpopup);

uparrow = [ ...
    '  0     ';
    ' 000    ';
    '00000   ';
    '  0     ';
    '  0     ';
    '  0     ';
    '  000000'];
cmap = NaN(128,3);
cmap(double('0'),:) = [0 0 0];
uparrow_im = ind2rgb(double(uparrow),cmap);
up_dir_but = uicontrol('Style','pushbutton',...
    'Position',[240 350 20 20],...
    'CData',uparrow_im,...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@dir_up_one,...
    'ToolTip','Go to parent folder');
if length(path_cell) > 1
    set(up_dir_but','Enable','on')
else
    set(up_dir_but','Enable','off')
end

hist_cm = uicontextmenu;
pathbox = uicontrol('Style','edit',...
    'Position',[10 375 250 26],...
    'BackgroundColor','w',...
    'String',current_dir,...
    'HorizontalAlignment','left',...
    'TooltipString',[action,' to display folder history'],...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@change_path,...
    'UIContextMenu',hist_cm);
label1 = uicontrol('Style','text',...
    'Position',[10 401 250 16],...
    'String','Current Folder',...
    'HorizontalAlignment','center',...
    'TooltipString',[action,' to display folder history'],...
    'UIContextMenu',hist_cm);
hist_menus = [];
make_history_cm()

label2 = uicontrol('Style','text',...
    'Position',[10 440+36 80 17],...
    'String','File Filter',...
    'HorizontalAlignment','left');
label3 = uicontrol('Style','text',...
    'Position',[100 440+36 160 17],...
    'String','Reg. Exp. Filter',...
    'HorizontalAlignment','left');
showallfiles = uicontrol('Style','checkbox',...
    'Position',[270 420+32 110 20],...
    'String','Show All Files',...
    'Value',0,...
    'HorizontalAlignment','left',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@togglefilter);
refilterdirs = uicontrol('Style','checkbox',...
    'Position',[270 420+10 100 20],...
    'String','RE Filter Dirs',...
    'Value',prop.redirs,...
    'HorizontalAlignment','left',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@toggle_refiltdirs);
filter_ed = uicontrol('Style','edit',...
    'Position',[10 420+30 80 26],...
    'BackgroundColor','w',...
    'String',filter,...
    'HorizontalAlignment','left',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@setfilspec);
refilter_ed = uicontrol('Style','edit',...
    'Position',[100 420+30 160 26],...
    'BackgroundColor','w',...
    'String',re_filter,...
    'HorizontalAlignment','left',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@setrefilter);

type_value = 1;
type_popup = uicontrol('Style','popupmenu',...
    'Position',[10 422 250 20],...
    'String','',...
    'BackgroundColor','w',...
    'Value',type_value,...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@filter_type_callback,...
    'Visible','off');
if ~isempty(prop.type)
    set(filter_ed,'String',prop.type{type_value,1})
    setfilspec()
    set(type_popup,'String',prop.type(:,2),'Visible','on')
end

viewfullpath = uicontrol('Style','checkbox',...
    'Position',[380 335 230 20],...
    'String','Show full paths',...
    'Value',show_full_path,...
    'HorizontalAlignment','left',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@showfullpath);
remove_dupes = uicontrol('Style','checkbox',...
    'Position',[380 360 280 20],...
    'String','Remove duplicates (as per full path)',...
    'Value',nodupes,...
    'HorizontalAlignment','left',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@removedupes);
recall_button = uicontrol('Style','pushbutton',...
    'Position',[665 335 65 20],...
    'String','Recall',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@recall,...
    'ToolTip','Add previously selected items');
label4 = uicontrol('Style','text',...
    'Position',[380 405 350 20],...
    'String','Selected Items',...
    'HorizontalAlignment','center');
done_button = uicontrol('Style','pushbutton',...
    'Position',[280 80 80 30],...
    'String','Done',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@done);
cancel_button = uicontrol('Style','pushbutton',...
    'Position',[280 30 80 30],...
    'String','Cancel',...
    'KeyPressFcn',@keypressmisc,...
    'Callback',@cancel);

% If necessary, add warning about number of items to be selected.
num_files_warn = uicontrol('Style','text',...
    'Position',[380 385 350 16],...
    'String',numstr,...
    'ForegroundColor',[0.8 0 0],...
    'HorizontalAlignment','center',...
    'Visible','off');
if ~isempty(prop.numfiles)
    set(num_files_warn,'Visible','on')
end

resize()
% Make figure visible and hide handle.
set(fig,'HandleVisibility','off',...
    'Visible','on',...
    'ResizeFcn',@resize)

% Wait until figure is closed.
uiwait(fig)

% Compute desired output.
switch prop.output
    case 'cell'
        out = full_file_picks;
    case 'struct'
        out = dir_picks(:);
    case 'char'
        out = char(full_file_picks);
    case 'cancel'
        out = 0;
end

% Update history preference.
setpref('uipickfiles','history',history)
if ~isempty(full_file_picks) && ~strcmp(prop.output,'cancel')
    setpref('uipickfiles','full_file_picks',full_file_picks)
end

% Update figure position preference.
setpref('uipickfiles','figure_position',fig_pos)


% ----------------- Callback nested functions ----------------

    function add(varargin)
        values = get(navlist,'Value');
        for i = 1:length(values)
            dir_pick = fdir(values(i));
            pick = dir_pick.name;
            pick_full = fullfile(current_dir,pick);
            dir_pick.name = pick_full;
            if ~nodupes || ~any(strcmp(full_file_picks,pick_full))
                file_picks{end + 1} = pick; %#ok<AGROW>
                full_file_picks{end + 1} = pick_full; %#ok<AGROW>
                dir_picks(end + 1) = dir_pick; %#ok<AGROW>
            end
        end
        if show_full_path
            set(pickslist,'String',full_file_picks,'Value',[]);
        else
            set(pickslist,'String',file_picks,'Value',[]);
        end
        set([removebut,moveupbut,movedownbut],'Enable','off');
    end

    function remove(varargin)
        values = get(pickslist,'Value');
        file_picks(values) = [];
        full_file_picks(values) = [];
        dir_picks(values) = [];
        top = get(pickslist,'ListboxTop');
        num_above_top = sum(values < top);
        top = top - num_above_top;
        num_picks = length(file_picks);
        new_value = min(min(values) - num_above_top,num_picks);
        if num_picks == 0
            new_value = [];
            set([removebut,moveupbut,movedownbut],'Enable','off')
        end
        if show_full_path
            set(pickslist,'String',full_file_picks,'Value',new_value,...
                'ListboxTop',top)
        else
            set(pickslist,'String',file_picks,'Value',new_value,...
                'ListboxTop',top)
        end
    end

    function open(varargin)
        values = get(navlist,'Value');
        if fdir(values).isdir
            set(fig,'pointer','watch')
            drawnow
            % Convert 'My Documents' to 'Documents' when necessary.
            if ispc && strcmp(fdir(values).name,'My Documents')
                if isempty(dir(fullfile(current_dir,fdir(values).name)))
                    values = find(strcmp({fdir.name},'Documents'));
                end
            end
            current_dir = fullfile(current_dir,fdir(values).name);
            history = update_history(history,current_dir,now,history_size);
            make_history_cm()
            full_filter = fullfile(current_dir,filter);
            path_cell = path2cell(current_dir);
            fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
                @(x)file_sort(x,sort_state));
            filenames = {fdir.name}';
            filenames = annotate_file_names(filenames,fdir,fsdata);
            set(dir_popup,'String',path_cell,'Value',length(path_cell))
            if length(path_cell) > 1
                set(up_dir_but','Enable','on')
            else
                set(up_dir_but','Enable','off')
            end
            set(pathbox,'String',current_dir)
            set(navlist,'ListboxTop',1,'Value',[],'String',filenames)
            set(addbut,'Enable','off')
            set(openbut,'Enable','off')
            set(fig,'pointer','arrow')
        end
    end

    function clicknav(varargin)
        value = get(navlist,'Value');
        nval = length(value);
        dbl_click_fcn = @add;
        switch nval
            case 0
                set([addbut,openbut],'Enable','off')
            case 1
                set(addbut,'Enable','on');
                if fdir(value).isdir
                    set(openbut,'Enable','on')
                    dbl_click_fcn = @open;
                else
                    set(openbut,'Enable','off')
                end
            otherwise
                set(addbut,'Enable','on')
                set(openbut,'Enable','off')
        end
        if strcmp(get(fig,'SelectionType'),'open')
            dbl_click_fcn();
        end
    end

    function keypressmisc(h,evt) %#ok<INUSL>
        if strcmp(evt.Key,'escape') && isequal(evt.Modifier,cell(1,0))
            % Escape key means Cancel.
            cancel()
        end
    end

    function keypressnav(h,evt) %#ok<INUSL>
        if length(path_cell) > 1 && strcmp(evt.Key,'backspace') && ...
                isequal(evt.Modifier,cell(1,0))
            % Backspace means go to parent folder.
            dir_up_one()
        elseif strcmp(evt.Key,'f') && isequal(evt.Modifier,{mod_key})
            % Control-F (Command-F on Mac) means select all files.
            value = find(~[fdir.isdir]);
            set(navlist,'Value',value)
        elseif strcmp(evt.Key,'rightarrow') && ...
                isequal(evt.Modifier,cell(1,0))
            % Right arrow key means select the file.
            add()
        elseif strcmp(evt.Key,'escape') && isequal(evt.Modifier,cell(1,0))
            % Escape key means Cancel.
            cancel()
        end
    end

    function keypresslist(h,evt) %#ok<INUSL>
        if strcmp(evt.Key,'backspace') && isequal(evt.Modifier,cell(1,0))
            % Backspace means remove item from list.
            remove()
        elseif strcmp(evt.Key,'escape') && isequal(evt.Modifier,cell(1,0))
            % Escape key means Cancel.
            cancel()
        end
    end

    function clickpicks(varargin)
        value = get(pickslist,'Value');
        if isempty(value)
            set([removebut,moveupbut,movedownbut],'Enable','off')
        else
            set(removebut,'Enable','on')
            if min(value) == 1
                set(moveupbut,'Enable','off')
            else
                set(moveupbut,'Enable','on')
            end
            if max(value) == length(file_picks)
                set(movedownbut,'Enable','off')
            else
                set(movedownbut,'Enable','on')
            end
        end
        if strcmp(get(fig,'SelectionType'),'open')
            remove();
        end
    end

    function recall(varargin)
        if ispref('uipickfiles','full_file_picks')
            ffp = getpref('uipickfiles','full_file_picks');
        else
            ffp = {};
        end
        for i = 1:length(ffp)
            if exist(ffp{i},'dir') && ...
                    (~nodupes || ~any(strcmp(full_file_picks,ffp{i})))
                full_file_picks{end + 1} = ffp{i}; %#ok<AGROW>
                [unused,fn,ext] = fileparts(ffp{i});
                file_picks{end + 1} = [fn,ext]; %#ok<AGROW>
                temp = dir(fullfile(ffp{i},'..'));
                if ispc || ismac
                    thisdir = strcmpi({temp.name},[fn,ext]);
                else
                    thisdir = strcmp({temp.name},[fn,ext]);
                end
                dir_picks(end + 1) = temp(thisdir); %#ok<AGROW>
                dir_picks(end).name = ffp{i};
            elseif exist(ffp{i},'file') && ...
                    (~nodupes || ~any(strcmp(full_file_picks,ffp{i})))
                full_file_picks{end + 1} = ffp{i}; %#ok<AGROW>
                [unused,fn,ext] = fileparts(ffp{i});
                file_picks{end + 1} = [fn,ext]; %#ok<AGROW>
                dir_picks(end + 1) = dir(ffp{i}); %#ok<AGROW>
                dir_picks(end).name = ffp{i};
            end
        end
        if show_full_path
            set(pickslist,'String',full_file_picks,'Value',[]);
        else
            set(pickslist,'String',file_picks,'Value',[]);
        end
        set([removebut,moveupbut,movedownbut],'Enable','off');
    end

    function sort_type(h,evt,cb) %#ok<INUSL>
        if sort_state(cb)
            sort_state(cb) = -sort_state(cb);
            last_sort_state(cb) = sort_state(cb);
        else
            sort_state = zeros(1,3);
            sort_state(cb) = last_sort_state(cb);
        end
        set(sort_cb,{'CData'},tri_icon(sort_state + 2)')
        
        fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
            @(x)file_sort(x,sort_state));
        filenames = {fdir.name}';
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(dir_popup,'String',path_cell,'Value',length(path_cell))
        if length(path_cell) > 1
            set(up_dir_but','Enable','on')
        else
            set(up_dir_but','Enable','off')
        end
        set(pathbox,'String',current_dir)
        set(navlist,'String',filenames,'Value',[])
        set(addbut,'Enable','off')
        set(openbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function dirpopup(varargin)
        value = get(dir_popup,'Value');
        container = path_cell{min(value + 1,length(path_cell))};
        path_cell = path_cell(1:value);
        set(fig,'pointer','watch')
        drawnow
        if ispc && value == 1
            current_dir = '';
            full_filter = filter;
            drives = getdrives(network_volumes);
            num_drives = length(drives);
            temp = tempname;
            mkdir(temp)
            dir_temp = dir(temp);
            rmdir(temp)
            fdir = repmat(dir_temp(1),num_drives,1);
            [fdir.name] = deal(drives{:});
        else
            current_dir = cell2path(path_cell);
            history = update_history(history,current_dir,now,history_size);
            make_history_cm()
            full_filter = fullfile(current_dir,filter);
            fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
                @(x)file_sort(x,sort_state));
        end
        filenames = {fdir.name}';
        selected = find(strcmp(filenames,container));
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(dir_popup,'String',path_cell,'Value',length(path_cell))
        if length(path_cell) > 1
            set(up_dir_but','Enable','on')
        else
            set(up_dir_but','Enable','off')
        end
        set(pathbox,'String',current_dir)
        set(navlist,'String',filenames,'Value',selected)
        set(addbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function dir_up_one(varargin)
        value = length(path_cell) - 1;
        container = path_cell{value + 1};
        path_cell = path_cell(1:value);
        set(fig,'pointer','watch')
        drawnow
        if ispc && value == 1
            current_dir = '';
            full_filter = filter;
            drives = getdrives(network_volumes);
            num_drives = length(drives);
            temp = tempname;
            mkdir(temp)
            dir_temp = dir(temp);
            rmdir(temp)
            fdir = repmat(dir_temp(1),num_drives,1);
            [fdir.name] = deal(drives{:});
        else
            current_dir = cell2path(path_cell);
            history = update_history(history,current_dir,now,history_size);
            make_history_cm()
            full_filter = fullfile(current_dir,filter);
            fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
                @(x)file_sort(x,sort_state));
        end
        filenames = {fdir.name}';
        selected = find(strcmp(filenames,container));
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(dir_popup,'String',path_cell,'Value',length(path_cell))
        if length(path_cell) > 1
            set(up_dir_but','Enable','on')
        else
            set(up_dir_but','Enable','off')
        end
        set(pathbox,'String',current_dir)
        set(navlist,'String',filenames,'Value',selected)
        set(addbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function change_path(varargin)
        set(fig,'pointer','watch')
        drawnow
        proposed_path = get(pathbox,'String');
        % Process any folders named '..'.
        proposed_path_cell = path2cell(proposed_path);
        ddots = strcmp(proposed_path_cell,'..');
        ddots(find(ddots) - 1) = true;
        proposed_path_cell(ddots) = [];
        proposed_path = cell2path(proposed_path_cell);
        % Check for existance of folder.
        if ~exist(proposed_path,'dir')
            set(fig,'pointer','arrow')
            uiwait(errordlg(['Folder "',proposed_path,...
                '" does not exist.'],'','modal'))
            return
        end
        current_dir = proposed_path;
        history = update_history(history,current_dir,now,history_size);
        make_history_cm()
        full_filter = fullfile(current_dir,filter);
        [path_cell,new_network_vol] = path2cell(current_dir);
        if exist(new_network_vol,'dir')
            network_volumes = unique([network_volumes,{new_network_vol}]);
        end
        fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
            @(x)file_sort(x,sort_state));
        filenames = {fdir.name}';
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(dir_popup,'String',path_cell,'Value',length(path_cell))
        if length(path_cell) > 1
            set(up_dir_but','Enable','on')
        else
            set(up_dir_but','Enable','off')
        end
        set(pathbox,'String',current_dir)
        set(navlist,'String',filenames,'Value',[])
        set(addbut,'Enable','off')
        set(openbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function showfullpath(varargin)
        show_full_path = get(viewfullpath,'Value');
        if show_full_path
            set(pickslist,'String',full_file_picks)
        else
            set(pickslist,'String',file_picks)
        end
    end

    function removedupes(varargin)
        nodupes = get(remove_dupes,'Value');
        if nodupes
            num_picks = length(full_file_picks);
            [unused,rev_order] = unique(full_file_picks(end:-1:1)); %#ok<SETNU>
            order = sort(num_picks + 1 - rev_order);
            full_file_picks = full_file_picks(order);
            file_picks = file_picks(order);
            dir_picks = dir_picks(order);
            if show_full_path
                set(pickslist,'String',full_file_picks,'Value',[])
            else
                set(pickslist,'String',file_picks,'Value',[])
            end
            set([removebut,moveupbut,movedownbut],'Enable','off')
        end
    end

    function moveup(varargin)
        value = get(pickslist,'Value');
        set(removebut,'Enable','on')
        n = length(file_picks);
        omega = 1:n;
        index = zeros(1,n);
        index(value - 1) = omega(value);
        index(setdiff(omega,value - 1)) = omega(setdiff(omega,value));
        file_picks = file_picks(index);
        full_file_picks = full_file_picks(index);
        dir_picks = dir_picks(index);
        value = value - 1;
        if show_full_path
            set(pickslist,'String',full_file_picks,'Value',value)
        else
            set(pickslist,'String',file_picks,'Value',value)
        end
        if min(value) == 1
            set(moveupbut,'Enable','off')
        end
        set(movedownbut,'Enable','on')
    end

    function movedown(varargin)
        value = get(pickslist,'Value');
        set(removebut,'Enable','on')
        n = length(file_picks);
        omega = 1:n;
        index = zeros(1,n);
        index(value + 1) = omega(value);
        index(setdiff(omega,value + 1)) = omega(setdiff(omega,value));
        file_picks = file_picks(index);
        full_file_picks = full_file_picks(index);
        dir_picks = dir_picks(index);
        value = value + 1;
        if show_full_path
            set(pickslist,'String',full_file_picks,'Value',value)
        else
            set(pickslist,'String',file_picks,'Value',value)
        end
        if max(value) == n
            set(movedownbut,'Enable','off')
        end
        set(moveupbut,'Enable','on')
    end

    function togglefilter(varargin)
        set(fig,'pointer','watch')
        drawnow
        value = get(showallfiles,'Value');
        if value
            filter = '*';
            re_filter = '';
            set([filter_ed,refilter_ed],'Enable','off')
        else
            filter = get(filter_ed,'String');
            re_filter = get(refilter_ed,'String');
            set([filter_ed,refilter_ed],'Enable','on')
        end
        full_filter = fullfile(current_dir,filter);
        fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
            @(x)file_sort(x,sort_state));
        filenames = {fdir.name}';
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(navlist,'String',filenames,'Value',[])
        set(addbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function toggle_refiltdirs(varargin)
        set(fig,'pointer','watch')
        drawnow
        value = get(refilterdirs,'Value');
        prop.redirs = value;
        full_filter = fullfile(current_dir,filter);
        fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
            @(x)file_sort(x,sort_state));
        filenames = {fdir.name}';
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(navlist,'String',filenames,'Value',[])
        set(addbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function setfilspec(varargin)
        set(fig,'pointer','watch')
        drawnow
        filter = get(filter_ed,'String');
        if isempty(filter)
            filter = '*';
            set(filter_ed,'String',filter)
        end
        % Process file spec if a subdirectory was included.
        [p,f,e] = fileparts(filter);
        if ~isempty(p)
            newpath = fullfile(current_dir,p,'');
            set(pathbox,'String',newpath)
            filter = [f,e];
            if isempty(filter)
                filter = '*';
            end
            set(filter_ed,'String',filter)
            change_path();
        end
        full_filter = fullfile(current_dir,filter);
        fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
            @(x)file_sort(x,sort_state));
        filenames = {fdir.name}';
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(navlist,'String',filenames,'Value',[])
        set(addbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function setrefilter(varargin)
        set(fig,'pointer','watch')
        drawnow
        re_filter = get(refilter_ed,'String');
        fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
            @(x)file_sort(x,sort_state));
        filenames = {fdir.name}';
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(navlist,'String',filenames,'Value',[])
        set(addbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function filter_type_callback(varargin)
        type_value = get(type_popup,'Value');
        set(filter_ed,'String',prop.type{type_value,1})
        setfilspec()
    end

    function done(varargin)
        % Optional shortcut: click on a file and press 'Done'.
        % 		if isempty(full_file_picks) && strcmp(get(addbut,'Enable'),'on')
        % 			add();
        % 		end
        numfiles = length(full_file_picks);
        if ~isempty(prop.numfiles)
            if numfiles < prop.numfiles(1)
                msg = {'Too few items selected.',numstr};
                uiwait(errordlg(msg,'','modal'))
                return
            elseif numfiles > prop.numfiles(end)
                msg = {'Too many items selected.',numstr};
                uiwait(errordlg(msg,'','modal'))
                return
            end
        end
        fig_pos = get(fig,'Position');
        delete(fig)
    end

    function cancel(varargin)
        prop.output = 'cancel';
        fig_pos = get(fig,'Position');
        delete(fig)
    end

    function history_cb(varargin)
        set(fig,'pointer','watch')
        drawnow
        current_dir = history(varargin{3}).name;
        history = update_history(history,current_dir,now,history_size);
        make_history_cm()
        full_filter = fullfile(current_dir,filter);
        path_cell = path2cell(current_dir);
        fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
            @(x)file_sort(x,sort_state));
        filenames = {fdir.name}';
        filenames = annotate_file_names(filenames,fdir,fsdata);
        set(dir_popup,'String',path_cell,'Value',length(path_cell))
        if length(path_cell) > 1
            set(up_dir_but','Enable','on')
        else
            set(up_dir_but','Enable','off')
        end
        set(pathbox,'String',current_dir)
        set(navlist,'ListboxTop',1,'Value',[],'String',filenames)
        set(addbut,'Enable','off')
        set(openbut,'Enable','off')
        set(fig,'pointer','arrow')
    end

    function clear_history(varargin)
        history = update_history(history(1),'',[],history_size);
        make_history_cm()
    end

    function set_history_size(varargin)
        result_cell = inputdlg('Number of Recent Folders:','',1,...
            {sprintf('%g',history_size)});
        if isempty(result_cell)
            return
        end
        result = sscanf(result_cell{1},'%f');
        if isempty(result) || result < 1
            return
        end
        history_size = result;
        history = update_history(history,'',[],history_size);
        make_history_cm()
        setpref('uipickfiles','history_size',history_size)
    end

    function resize(varargin)
        % Get current figure size.
        P = 'Position';
        pos = get(fig,P);
        w = pos(3); % figure width in pixels
        h = pos(4); % figure height in pixels
        
        % Enforce minimum figure size.
        w = max(w,564);
        h = max(h,443);
        if any(pos(3:4) < [w h])
            pos(3:4) = [w h];
            set(fig,P,pos)
        end
        
        % Change positions of all uicontrols based on the current figure
        % width and height.
        navw_pckw = round([1 1;-350 250]\[w-140;0]);
        navw = navw_pckw(1);
        pckw = navw_pckw(2);
        navp = [10 10 navw h-174];
        pckp = [w-10-pckw 10 pckw h-174];
        set(navlist,P,navp)
        set(pickslist,P,pckp)
        
        set(frame1,P,[navw+5 h-234 110 70])
        set(openbut,P,[navw+20 h-194 80 20])
        set(addbut,P,[navw+20 h-224 80 20])
        
        frame2y = round((h-234 + 110 - 100)/2);
        set(frame2,P,[w-pckw-115 frame2y 110 100])
        set(removebut,P,[w-pckw-100 frame2y+70 80 20])
        set(moveupbut,P,[w-pckw-100 frame2y+40 80 20])
        set(movedownbut,P,[w-pckw-100 frame2y+10 80 20])
        
        set(done_button,P,[navw+30 80 80 30])
        set(cancel_button,P,[navw+30 30 80 30])
        
        set(sort_cb(1),P,[15 h-163 70 15])
        set(sort_cb(2),P,[85 h-163 70 15])
        set(sort_cb(3),P,[155 h-163 70 15])
        
        set(dir_popup,P,[10 h-144 navw-25 20])
        set(up_dir_but,P,[navw-10 h-144 20 20])
        set(pathbox,P,[10 h-119 navw 26])
        set(label1,P,[10 h-93 navw 16])
        
        set(viewfullpath,P,[pckp(1) h-159 230 20])
        set(remove_dupes,P,[pckp(1) h-134 280 20])
        set(recall_button,P,[w-75 h-159 65 20])
        set(label4,P,[w-10-pckw h-89 pckw 20])
        set(num_files_warn,P,[w-10-pckw h-109 pckw 16])
        
        set(label2,P,[10 h-18 80 17])
        set(label3,P,[100 h-18 160 17])
        set(showallfiles,P,[270 h-42 110 20])
        set(refilterdirs,P,[270 h-64 100 20])
        set(filter_ed,P,[10 h-44 80 26])
        set(refilter_ed,P,[100 h-44 160 26])
        set(type_popup,P,[10 h-72 250 20])
    end

    function reset_figure_size(varargin)
        if strcmp(get(fig,'SelectionType'),'open')
            root_units = get(0,'units');
            screen_size = get(0,'ScreenSize');
            set(0,'Units',root_units)
            hw = [740 494];
            pos = [round((screen_size(3:4) - hw - [0 26])/2),hw];
            set(fig,'Position',pos)
            resize()
        end
    end



% ------------------ Other nested functions ------------------

    function make_history_cm
        % Make context menu for history.
        if ~isempty(hist_menus)
            delete(hist_menus)
        end
        num_hist = length(history);
        hist_menus = zeros(1,num_hist+2);
        for i = 1:num_hist
            hist_menus(i) = uimenu(hist_cm,'Label',history(i).name,...
                'Callback',{@history_cb,i});
        end
        hist_menus(num_hist+1) = uimenu(hist_cm,...
            'Label','Clear Menu',...
            'Separator','on',...
            'Callback',@clear_history);
        hist_menus(num_hist+2) = uimenu(hist_cm,'Label',...
            sprintf('Set Number of Recent Folders (%d) ...',history_size),...
            'Callback',@set_history_size);
    end

end


% -------------------- Subfunctions --------------------

function [c,network_vol] = path2cell(p)
% Turns a path string into a cell array of path elements.
if ispc
    p = strrep(p,'/','\');
    c1 = regexp(p,'(^\\\\[^\\]+\\[^\\]+)|(^[A-Za-z]+:)|[^\\]+','match');
    vol = c1{1};
    c = [{'My Computer'};c1(:)];
    if strncmp(vol,'\\',2)
        network_vol = vol;
    else
        network_vol = '';
    end
else
    c = textscan(p,'%s','delimiter','/');
    c = [{filesep};c{1}(2:end)];
    network_vol = '';
end
end

% --------------------

function p = cell2path(c)
% Turns a cell array of path elements into a path string.
if ispc
    p = fullfile(c{2:end},'');
else
    p = fullfile(c{:},'');
end
end

% --------------------

function d = filtered_dir(full_filter,re_filter,filter_both,sort_fcn)
% Like dir, but applies filters and sorting.
p = fileparts(full_filter);
if isempty(p) && full_filter(1) == '/'
    p = '/';
end
if exist(full_filter,'dir')
    dfiles = dir(' ');
else
    dfiles = dir(full_filter);
end
if ~isempty(dfiles)
    dfiles([dfiles.isdir]) = [];
end

ddir = dir(p);
ddir = ddir([ddir.isdir]);
[unused,index0] = sort(lower({ddir.name})); %#ok<ASGLU>
ddir = ddir(index0);
ddir(strcmp({ddir.name},'.') | strcmp({ddir.name},'..')) = [];

% Additional regular expression filter.
if nargin > 1 && ~isempty(re_filter)
    if ispc || ismac
        no_match = cellfun('isempty',regexpi({dfiles.name},re_filter));
    else
        no_match = cellfun('isempty',regexp({dfiles.name},re_filter));
    end
    dfiles(no_match) = [];
end
if filter_both
    if nargin > 1 && ~isempty(re_filter)
        if ispc || ismac
            no_match = cellfun('isempty',regexpi({ddir.name},re_filter));
        else
            no_match = cellfun('isempty',regexp({ddir.name},re_filter));
        end
        ddir(no_match) = [];
    end
end
% Set navigator style:
%	1 => list all folders before all files, case-insensitive sorting
%	2 => mix files and folders, case-insensitive sorting
%	3 => list all folders before all files, case-sensitive sorting
nav_style = 1;
switch nav_style
    case 1
        [unused,index1] = sort_fcn(dfiles); %#ok<ASGLU>
        [unused,index2] = sort_fcn(ddir); %#ok<ASGLU>
        d = [ddir(index2);dfiles(index1)];
    case 2
        d = [dfiles;ddir];
        [unused,index] = sort(lower({d.name})); %#ok<ASGLU>
        d = d(index);
    case 3
        [unused,index1] = sort({dfiles.name}); %#ok<ASGLU>
        [unused,index2] = sort({ddir.name}); %#ok<ASGLU>
        d = [ddir(index2);dfiles(index1)];
end
end

% --------------------

function [files_sorted,index] = file_sort(files,sort_state)
switch find(sort_state)
    case 1
        [files_sorted,index] = sort(lower({files.name}));
        if sort_state(1) < 0
            files_sorted = files_sorted(end:-1:1);
            index = index(end:-1:1);
        end
    case 2
        if sort_state(2) > 0
            [files_sorted,index] = sort([files.datenum]);
        else
            [files_sorted,index] = sort([files.datenum],'descend');
        end
    case 3
        if sort_state(3) > 0
            [files_sorted,index] = sort([files.bytes]);
        else
            [files_sorted,index] = sort([files.bytes],'descend');
        end
end
end

% --------------------

function drives = getdrives(other_drives)
% Returns a cell array of drive names on Windows.
letters = char('A':'Z');
num_letters = length(letters);
drives = cell(1,num_letters);
for i = 1:num_letters
    if exist([letters(i),':\'],'dir');
        drives{i} = [letters(i),':'];
    end
end
drives(cellfun('isempty',drives)) = [];
if nargin > 0 && iscellstr(other_drives)
    drives = [drives,unique(other_drives)];
end
end

% --------------------

function filenames = annotate_file_names(filenames,dir_listing,fsdata)
% Adds a trailing filesep character to folder names and, optionally,
% prepends a folder icon or bullet symbol.
for i = 1:length(filenames)
    if dir_listing(i).isdir
        filenames{i} = sprintf('%s%s%s%s',fsdata.pre,filenames{i},...
            fsdata.filesep,fsdata.post);
    end
end
end

% --------------------

function history = update_history(history,current_dir,time,history_size)
if ~isempty(current_dir)
    % Insert or move current_dir to the top of the history.
    % If current_dir already appears in the history list, delete it.
    match = strcmp({history.name},current_dir);
    history(match) = [];
    % Prepend history with (current_dir,time).
    history = [struct('name',current_dir,'time',time),history];
end
% Trim history to keep at most <history_size> newest entries.
history = history(1:min(history_size,end));
end

% --------------------

function success = generate_folder_icon(icon_path)
% Black = 1, manila color = 2, transparent = 3.
im = [ ...
    3 3 3 1 1 1 1 3 3 3 3 3;
    3 3 1 2 2 2 2 1 3 3 3 3;
    3 1 1 1 1 1 1 1 1 1 1 3;
    1 2 2 2 2 2 2 2 2 2 2 1;
    1 2 2 2 2 2 2 2 2 2 2 1;
    1 2 2 2 2 2 2 2 2 2 2 1;
    1 2 2 2 2 2 2 2 2 2 2 1;
    1 2 2 2 2 2 2 2 2 2 2 1;
    1 2 2 2 2 2 2 2 2 2 2 1;
    1 1 1 1 1 1 1 1 1 1 1 1];
cmap = [0 0 0;255 220 130;255 255 255]/255;
fid = fopen(icon_path,'w');
if fid > 0
    fclose(fid);
    imwrite(im,cmap,icon_path,'Transparency',[1 1 0])
end
success = exist(icon_path,'file');
end

% --------------------

function fsdata = set_folder_style(folder_style_pref)
% Set style to preference.
fsdata.style = folder_style_pref;
% If style = 1, check to make sure icon image file exists.  If it doesn't,
% try to create it.  If that fails set style = 2.
if fsdata.style == 1
    icon_path = fullfile(prefdir,'uipickfiles_folder_icon.png');
    if ~exist(icon_path,'file')
        success = generate_folder_icon(icon_path);
        if ~success
            fsdata.style = 2;
        end
    end
end
% Set pre and post fields.
if fsdata.style == 1
    icon_url = ['file://localhost/',...
        strrep(strrep(icon_path,':','|'),'\','/')];
    fsdata.pre = sprintf('<html><img src="%s">&nbsp;',icon_url);
    fsdata.post = '</html>';
elseif fsdata.style == 2
    fsdata.pre = '<html><b>&#8226;</b>&nbsp;';
    fsdata.post = '</html>';
elseif fsdata.style == 3
    fsdata.pre = '';
    fsdata.post = '';
end
fsdata.filesep = filesep;

end

% --------------------

function prop = parsepropval(prop,varargin)
% Parse property/value pairs and return a structure.
properties = fieldnames(prop);
arg_index = 1;
while arg_index <= length(varargin)
    arg = varargin{arg_index};
    if ischar(arg)
        prop_index = match_property(arg,properties);
        prop.(properties{prop_index}) = varargin{arg_index + 1};
        arg_index = arg_index + 2;
    elseif isstruct(arg)
        arg_fn = fieldnames(arg);
        for i = 1:length(arg_fn)
            prop_index = match_property(arg_fn{i},properties);
            prop.(properties{prop_index}) = arg.(arg_fn{i});
        end
        arg_index = arg_index + 1;
    else
        error(['Properties must be specified by property/value pairs',...
            ' or structures.'])
    end
end
end

% --------------------

function prop_index = match_property(arg,properties)
% Utility function for parsepropval.
prop_index = find(strcmpi(arg,properties));
if isempty(prop_index)
    prop_index = find(strncmpi(arg,properties,length(arg)));
end
if length(prop_index) ~= 1
    error('Property ''%s'' does not exist or is ambiguous.',arg)
end
end