- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-06-10 15:16:24+12:00
- Desc:
- Move dSL to environment
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/7fb/rawfile/4e8b0e008b26cf300baf7a4c9f34903e8cfffaa8/Land_model_matlab/release/convert/findseq.m
function varargout = findseq(A,dim)
% FINDSEQ Find sequences of repeated (adjacent/consecutive) numeric values
%
% FINDSEQ(A) Find sequences of repeated numeric values in A along the
% first non-singleton dimension. A should be numeric.
%
% FINDSEQ(...,DIM) Look for sequences along the dimension specified by the
% positive integer scalar DIM.
%
% OUT = findseq(...)
% OUT is a "m by 4" numeric matrix where m is the number of sequences found.
%
% Each sequence has 4 columns where:
% - 1st col.: the value being repeated
% - 2nd col.: the position of the first value of the sequence
% - 3rd col.: the position of the last value of the sequence
% - 4th col.: the length of the sequence
%
% [VALUES, INPOS, FIPOS, LEN] = findseq(...)
% Get OUT as separate outputs.
%
% If no sequences are found no value is returned.
% To convert positions into subs/coordinates use IND2SUB
%
%
% Examples:
%
% % There are sequences of 20s, 1s and NaNs (column-wise)
% A = [ 20, 19, 3, 2, NaN, NaN
% 20, 23, 1, 1, 1, NaN
% 20, 7, 7, NaN, 1, NaN]
%
% OUT = findseq(A)
% OUT =
% 20 1 3 3
% 1 14 15 2
% NaN 16 18 3
%
% % 3D sequences: NaN, 6 and 0
% A = [ 1, 4
% NaN, 5
% 3, 6];
% A(:,:,2) = [ 0, 0
% NaN, 0
% 0, 6];
% A(:,:,3) = [ 1, 0
% 2, 5
% 3, 6];
%
% OUT = findseq(A,3)
% OUT =
% 6 6 18 3
% 0 10 16 2
% NaN 2 8 2
%
% Additional features:
% - <a href="matlab: web('http://www.mathworks.com/matlabcentral/fileexchange/28113','-browser')">FEX findseq page</a>
% - <a href="matlab: web('http://www.mathworks.com/matlabcentral/fileexchange/6436','-browser')">FEX rude by us page</a>
%
% See also: DIFF, FIND, SUB2IND, IND2SUB
% Author: Oleg Komarov (oleg.komarov@hotmail.it)
% Tested on R14SP3 (7.1) and on R2012a. In-between compatibility is assumed.
% 02 jul 2010 - Created
% 05 jul 2010 - Reorganized code and fixed bug when concatenating results
% 12 jul 2010 - Per Xiaohu's suggestion fixed bug in output dimensions when A is row vector
% 26 aug 2010 - Cast double on logical instead of single
% 28 aug 2010 - Per Zachary Danziger's suggestion reorganized check structure to avoid bug when concatenating results
% 22 mar 2012 - Per Herbert Gsenger's suggestion fixed bug in matching initial and final positions; minor change to distribution of OUT if multiple outputs; added 3D example
% NINPUTS
error(nargchk(1,2,nargin));
% NOUTPUTS
error(nargoutchk(0,4,nargout));
% IN
if ~isnumeric(A)
error('findseq:fmtA', 'A should be numeric')
elseif isempty(A) || isscalar(A)
varargout{1} = [];
return
elseif islogical(A)
A = double(A);
end
% DIM
szA = size(A);
if nargin == 1 || isempty(dim)
% First non singleton dimension
dim = find(szA ~= 1,1,'first');
elseif ~(isnumeric(dim) && dim > 0 && rem(dim,1) == 0) || dim > numel(szA)
error('findseq:fmtDim', 'DIM should be a scalar positive integer <= ndims(A)');
end
% Less than two elements along DIM
if szA(dim) == 1
varargout{1} = [];
return
end
% ISVECTOR
if nnz(szA ~= 1) == 1
A = A(:);
dim = 1;
szA = size(A);
end
% Detect 0, NaN, Inf and -Inf
OtherValues = cell(1,4);
OtherValues{1} = A == 0;
OtherValues{2} = isnan(A) ;
OtherValues{3} = A == Inf;
OtherValues{4} = A == -Inf;
Values = [0,NaN, Inf,-Inf];
% Remove zeros
A(OtherValues{1}) = NaN;
% Make the bread
bread = NaN([szA(1:dim-1),1,szA(dim+1:end)]);
% [1] Get chunks of "normal" values
Out = mainengine(A,bread,dim,szA);
% [2] Get chunks of 0, NaN, Inf and -Inf
for c = 1:4
if nnz(OtherValues{c}) > 1
% Logical to double and NaN padding
OtherValues{c} = double(OtherValues{c});
OtherValues{c}(~OtherValues{c}) = NaN;
% Call mainengine and concatenate results
tmp = mainengine(OtherValues{c}, bread,dim,szA);
if ~isempty(tmp)
Out = [Out; [repmat(Values(c),size(tmp,1),1) tmp(:,2:end)]]; %#ok
end
end
end
% Distribute output
if nargout < 2
varargout = {Out};
else
varargout = num2cell(Out(:,1:nargout),1);
end
end
% MAINENGINE This functions uses run length encoding and retrieve positions
function Out = mainengine(meat,bread,dim,szMeat)
% Make a sandwich
sandwich = cat(dim, bread, meat, bread);
% Find chunks (run length encoding engine)
IDX = diff(diff(sandwich,[],dim) == 0,[],dim);
% Initial and final row/col subscripts
[rIn, cIn] = find(IDX == 1);
[rFi, cFi] = find(IDX == -1);
% Make sure row/col subs correspond (relevant if dim > 1)
In = sortrows([rIn, cIn],1);
Fi = sortrows([rFi, cFi],1);
% Calculate length of blocks
if dim < 3
Le = Fi(:,dim) - In(:,dim) + 1;
else
md = prod(szMeat(2:dim-1));
Le = (Fi(:,2) - In(:,2))/md + 1;
end
% Convert to linear index
InPos = sub2ind(szMeat,In(:,1),In(:,2));
FiPos = sub2ind(szMeat,Fi(:,1),Fi(:,2));
% Assign output
Out = [meat(InPos),... % Values
InPos ,... % Initial positions
FiPos ,... % Final positions
Le ]; % Length of the blocks
end
