function [Bset,nB,mtr] = palm_shuffree(varargin)
% A single function to generate a set of permutations and/or
% sign-flips. This function is a faster replacement to
% palm_shuftree.m when all observations are freely exchangeable,
% i.e., when there are no block restrictions and no tree needs
% to be constructed.
% 
% Usage
% [Bset,nB] = palm_shuffree(M,nP0,CMC,EE,ISE,idxout)
% 
% Inputs:
% - M        : Design matrix.
% - nP0      : Requested number of permutations.
% - CMC      : Use Conditional Monte Carlo?
% - EE       : Allow permutations?
% - ISE      : Allow sign-flips?
%              If you supply the EE argument, you must
%              also supply ISE argument. If one is omited,
%              the other needs to be omited too.
%              Default is true for EE, and false for ISE.
% - idxout   : (Optional) If true, the output isn't a cell
%              array with permutation matrices, but an array
%              with permutation indices.
% 
% Outputs:
% - Bset     : Set of permutations and/or sign flips.
% - nB       : Number of permutations and/or sign-flips.
% - mtr      : Some metrics. See palm_metrics.m for details.
% 
% _____________________________________
% Anderson M. Winkler
% FMRIB / University of Oxford
% Jan/2014
% http://brainder.org

% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% PALM -- Permutation Analysis of Linear Models
% Copyright (C) 2015 Anderson M. Winkler
% 
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% any later version.
% 
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
% GNU General Public License for more details.
% 
% You should have received a copy of the GNU General Public License
% along with this program.  If not, see <http://www.gnu.org/licenses/>.
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

% Accept arguments
if nargin < 2 || nargin > 6 || nargin == 4,
    error('Incorrect number of arguments');
end
M   = varargin{1};
nP0 = varargin{2};
if nargin > 2,
    CMC = varargin{3};
else
    CMC = false;
end
if nargin > 4,
    EE  = varargin{4};
    ISE = varargin{5};
else
    EE  = true;
    ISE = false;
end
if nargin > 5,
    idxout = varargin{6};
else
    idxout = false;
end
if ~EE && ~ISE,
    error('EE and/or ISE must be enabled, otherwise there is nothing to shuffle.')
end

% Sequence of unique values to shuffle
N = size(M,1);
[~,~,seq] = unique(M,'rows');
seqS = sortrows(horzcat(seq,(1:N)'));
U    = unique(seq);
nU   = numel(U);

% Logs, to help later
lfac = palm_factorial(N);

% Number of unique permutations & sign flips
maxP  = 1;
maxS  = 1;
lmaxP = 0;
lmaxS = 0;
if EE,
    nrep = zeros(size(U));
    for u = 1:nU,
        nrep(u) = sum(seqS(:,1) == U(u));
    end
    lmaxP = lfac(N+1) - sum(lfac(nrep+1));
    maxP  = round(exp(lmaxP));
    if nU == N,
        if isinf(maxP),
            fprintf('Number of possible permutations is exp(%g) = %d!.\n',lmaxP,N);
        else
            fprintf('Number of possible permutations is %g = %d!.\n',maxP,N);
        end
    else
        if isinf(maxP),
            fprintf('Number of possible permutations is exp(%g).\n',lmaxP);
        else
            fprintf('Number of possible permutations is %g.\n',maxP);
        end
    end
end
if ISE,
    lmaxS = N * log(2);
    maxS  = 2^N;
    if isinf(maxS),
        fprintf('Number of possible sign-flips is exp(%g) = 2^%d.\n',lmaxS,N);
    else
        fprintf('Number of possible sign-flips is %g = 2^%d.\n',maxS,N);
    end
end
maxB  =  maxP * maxS;
lmaxB = lmaxP + lmaxS;

% String for the screen output below
if EE && ~ISE,
    whatshuf = 'permutations only';
    stype    = 'perms';
elseif ISE && ~EE,
    whatshuf = 'sign-flips only';
    stype    = 'flips';
elseif EE && ISE,
    whatshuf = 'permutations and sign-flips';
    stype    = 'both';
end

% This ensures that there is at least 1 permutation (no permutation)
% and 1 sign-flipping (no sign-flipping). These are modified below as
% needed.
Pset = seqS(:,2);
Sset = ones(N,1);

% Generate the Pset and Sset
if nP0 == 0 || nP0 >= maxB,
    % Run exhaustively if the user requests more permutations than possible.
    % Note that here CMC is irrelevant.
    fprintf('Generating %g shufflings (%s).\n',maxB,whatshuf);
    if EE,
        Pset = horzcat(Pset,zeros(N,maxP-1));
        for p = 2:maxP,
            seqS = palm_nextperm(seqS);
            Pset(:,p) = seqS(:,2);
        end
    end
    if ISE,
        if N <= 52,
            Sset = palm_d2b(0:maxS-1,N)';
            Sset(~~Sset) = -1;
            Sset( ~Sset) =  1;
            Sset = flipud(Sset);
        else
            Sset = false(N,maxS);
            for s = 2:maxS,
                Sset(:,s) = palm_incrbin(Sset(:,s-1));
            end
        end
    end
elseif nP0 < maxB,
    % Or use a subset of possible permutations. The nested conditions
    % are to avoid repetitions, and to compensate fewer flips with more
    % perms or vice versa as needed in the tight situations
    fprintf('Generating %g shufflings (%s).\n',nP0,whatshuf);
    if EE,
        if nP0 >= maxP,
            Pset = horzcat(Pset,zeros(N,maxP-1));
            for p = 2:maxP,
                seqS = palm_nextperm(seqS);
                Pset(:,p) = seqS(:,2);
            end
        else
            Pset = horzcat(Pset,zeros(N,nP0-1));
            if CMC,
                for p = 1:nP0,
                    Pset(:,p) = randperm(N)';
                end
            else
                Pseq = zeros(size(Pset));
                Pseq(:,1) = seqS(:,2);
                for p = 2:nP0,
                    whiletest = true;
                    while whiletest,
                        Pset(:,p) = randperm(N)';
                        Pseq(:,p) = seqS(Pset(:,p));
                        whiletest = any(all(bsxfun(@eq,Pseq(:,p),Pseq(:,1:p-1))));
                    end
                end
            end
        end
    end
    if ISE,
        if nP0 >= maxS,
            Sset = palm_d2b(0:maxS-1,N)';
            Sset(~~Sset) = -1;
            Sset( ~Sset) =  1;
        else
            if CMC,
                Sset = double(rand(N,nP0) > .5);
                Sset(:,1) = 0;
                Sset(~~Sset) = -1;
                Sset( ~Sset) =  1;
            else
                Sset = zeros(N,nP0);
                for p = 2:nP0,
                    whiletest = true;
                    while whiletest,
                        Sset(:,p) = rand(N,1) > .5;
                        whiletest = any(all(bsxfun(@eq,Sset(:,p),Sset(:,1:p-1))));
                    end
                end
                Sset(~~Sset) = -1;
                Sset( ~Sset) =  1;
            end
        end
    end
end

% Generate the set of shufflings, mixing permutations and
% sign-flippings as needed.
nP = size(Pset,2);
nS = size(Sset,2);
if nS == 1,
    % If only 1 sign-flip is possible, ignore it.
    Bset = Pset;
elseif nP == 1,
    % If only 1 permutation is possible, ignore it.
    Bset = bsxfun(@times,Pset,Sset);
elseif nP0 == 0 || nP0 >= maxB,
    % If the user requested too many shufflings, do all
    % those that are possible.
    Bset = zeros(N,maxB);
    b = 1;
    for p = 1:size(Pset,2),
        for s = 1:size(Sset,2),
            Bset(:,b) = Pset(:,p) .* Sset(:,s);
            b = b + 1;
        end
    end
else
    % The typical case, with an enormous number of possible
    % shufflings, and the user choses a moderate number
    Bset = zeros(N,nP0);
    % 1st shuffling is no shuffling, regardless
    Bset(:,1) = (1:N)';
    if CMC,
        % If CMC, no need to take care of repetitions.
        for b = 2:nP0,
            Bset(:,b) = Pset(:,randi(nP)) .* Sset(:,randi(nS));
        end
    else
        % Otherwise, avoid them
        [~,bidx] = sort(rand(nP*nS,1));
        bidx = bidx(1:nP0);
        [pidx,sidx] = ind2sub([nP nS],bidx);
        for b = 2:nP0,
            Bset(:,b) = Pset(:,pidx(b)) .* Sset(:,sidx(b));
        end
    end
end
nB = size(Bset,2);

% Sort back to the original order
Bset = sortrows(Bset);

% Compute some metrics
if nargout == 3,
    mtr      = zeros(9,1);
    mtr(1:2) = lmaxB;
    mtr(4)   = 2^nU - 1;
    [mtr(5),mtr(6),mtr(7),mtr(8),mtr(9)] = palm_metrics(Bset,seq,stype);
end

% If the desired outputs are permutation matrices instead of indices
if ~ idxout,
    Bset = palm_swapfmt(Bset);
end