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fn_clip.m
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fn_clip.m
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function [x, clip] = fn_clip(x,varargin)
%FN_CLIP Rescale data, restrict the range, color
%---
% function [x clip] = fn_clip(x[,clipflag][,outflag][,nanvalue])
%---
% Rescale and restrict to a specific range ("clip") the data in an array.
% Make a color image if requested.
%
% Input:
% - x array (any dimension)
% - clipflag clipping mode:
% [a b] define manually min and max value
% 'fit','mM' or 'minmax' use minimum and maximum [default]
% 'Xstd' use mean and X times standard deviation
% 'prcA-B' use percentiles (if B is omitted,
% use B = 100-A; if B<30, uses 100-B)
% add '[value]' at the end (e.g. 'fit[0]') to center the
% clipping range on the specified value
%
% - outflag output format
% [a b] define minimum and maximum value [default, with
% a=0 and b=1]
% n integer values between 1 and n (output will be
% of class uint8 if n<=256, uint16 if n<=65536,
% etc.
% 'uint8', 'uint16', .. integer values between 0 and max
% nx3 array returns a (n+1)-dimensional array using this
% colormap
% char array use this colormap (for example 'jet' -> use
% jet(256))
% 'scaleonly' rescale data but do not coerce within the range
% 'getrange' output not the cliped data, but the calculated
% clipping range (can be useful for 'std' and
% 'prc' clipping calculations)
%
% - nanvalue value to give to NaNs
%
% Output:
% - x the clipped image (or the clipping range if outflag is
% 'getrange')
% - clip the clipping range
% Thomas Deneux
% Copyright 2007-2017
if nargin==0, help fn_clip, return, end
% Input
clipflag = []; outflag = []; nanvalue = [];
for k=1:length(varargin)
a = varargin{k};
if ischar(a)
if any(regexp(a,'^fit|mM|minmax')) || any(regexpi(a,'(^prc)|((st|sd|std))'))
clipflag = a;
elseif regexp(a,'^[0-9e\-.]+ +[0-9e\-.]+$') % two numbers
clipflag = str2num(a); %#ok<ST2NM>
else
outflag = a;
end
else
if isvector(a) && length(a)==2 && isempty(clipflag)
clipflag = a;
elseif isempty(outflag)
outflag = a;
else
nanvalue = a;
end
end
end
if isempty(clipflag), clipflag='mM'; end
if isempty(outflag), outflag=[0 1]; end
% Compute clipping range
if isnumeric(clipflag)
if ~isvector(clipflag) || length(clipflag)~=2, error('clipping vector must have 2 elements'), end
clip = row(clipflag);
else
icenterval = regexp(clipflag,'\[.*\]$');
if isempty(icenterval)
centerval=[];
else
centerval = str2double(clipflag(icenterval+1:end-1));
clipflag(icenterval:end)=[];
end
xstd = regexpi(clipflag,'^([\d.]*)(st|sd|std)$','tokens');
if ~isempty(xstd)
xstd = xstd{1}{1};
else
xstd = regexpi(clipflag,'^(st|sd|std)([\d.]*)$','tokens');
if ~isempty(xstd), xstd = xstd{1}{2}; end
end
xprc = regexpi(clipflag,'^prc([\d.]*)[-_]*([\d.]*)$','tokens');
if fn_ismemberstr(clipflag,{'fit' 'mM' 'minmax'})
if isempty(centerval)
clip = [min(x(:)) max(x(:))];
else
clip = centerval + [-1 1]*max(abs(x(:)-centerval));
end
elseif ~isempty(xstd)
x = fn_float(x);
if isempty(xstd), xstd=1; else xstd=str2double(xstd); end
if isempty(centerval), m = mean(x(~isnan(x) & ~isinf(x))); else m = centerval; end
st = std(x(~isnan(x) & ~isinf(x)));
clip = m + [-1 1]*xstd*st;
elseif ~isempty(xprc)
low = str2double(xprc{1}{1});
high = str2double(xprc{1}{2});
if isempty(centerval)
if isnan(high), high=100-low; elseif high<30, high=100-high; end
clip = [prctil(x(:),low) prctil(x(:),high)];
else
if ~isnan(high)
warning 'cannot set independently the percentile of low and high out-of-range when center value is fixed'
if high<30, high=100-high; end
low = (low+high)/2;
end
clip = centerval + [-1 1]*prctil(abs(x(:)-centerval),100-low);
end
else
error('erroneous clipping option')
end
end
if diff(clip)==0, clip = clip+[-1 1]; end
% Check output mode
doclip = true;
if strcmp(outflag,'getrange')
x = clip;
return
elseif strcmp(outflag,'scaleonly')
doclip = false;
elseif ischar(outflag) && any(strfind(outflag,'uint'))
docolor = false;
n = intmax(outflag);
elseif ischar(outflag)
docolor = true;
fname = outflag;
if strfind(fname,'.LUT')
cm = fn_readasciimatrix(fname);
else
cm = feval(fname,256);
end
n = size(cm,1);
elseif ~isvector(outflag)
if size(outflag,2)~=3, error('colormap must have 3 columns'), end
docolor = true;
cm = outflag;
n = size(cm,1);
elseif isscalar(outflag)
docolor = false;
n = outflag;
if mod(n,1) || n<=0, error('scalar for output format must be a positive integer'), end
else
docolor = false;
if length(outflag)~=2, error('vector for output format must have 2 elements'), end
n = 0;
a = outflag(1);
b = outflag(2);
end
% Convert data to float if the data is integer (we avoided doing it before
% because it was not needed in the case of the 'getrange' output flag)
[x, clip] = deal(fn_float(x),fn_float(clip));
% Clip data
x = (x-clip(1))/diff(clip);
if ~doclip, return, end
if ~isempty(nanvalue)
xnan = isnan(x);
end
if isa(x,'double')
upperbound = 1-eps(1); % it is convenient that 1 cannot be reached
else
upperbound = 1-eps(single(1));
end
x = min(upperbound,max(0,x));
% Scaling
if n
if isinteger(n)
x = cast(floor(double(n)*x),'like',n); % values between 0 and n-1
else
x = floor(n*x)+1; % values between 1 and n
end
elseif a==0 && b==1
% nothing to do
else
x = a + x*(b-a); % b cannot be reached
end
% Color and value for NaNs
if docolor
s = size(x); %if s(2)==1, s(2)=[]; end
if ~isempty(nanvalue)
x(xnan) = n+1;
cm(n+1,:) = nanvalue;
end
x = reshape(cm(x,:),[s 3]);
if length(s)>2, x = permute(x,[1 2 length(s)+1 3:length(s)]); end
else
if ~isempty(nanvalue)
x(xnan) = nanvalue;
end
end