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function img = readstack(fname, varargin)
%READSTACK Read either a list of 2D images (slices), or a 3D image
%
% Syntax
% IMG = readstack(FNAME)
% IMG = readstack(FNAME, INDICES)
% IMG = readstack(FNAME, TYPE, DIM)
%
% Description
%
% IMG = readstack(FNAME)
% FNAME is the base name of the image.
% In the case of a bundle image, this is simply the name of the file.
% In the case of an image stored as several slices, this is the string
% common to each file with wildcard '#', '?' or '0' at the position of
% the slices indices.
% IMG is a 3-dimensional array of type uint8, size: X*Y*Z;
% or a 4 dimensional array for color images (X*Y*3*Z).
%
% IMG = readstack(FNAME, INDICES)
% forces the number of dimensions of resulting array (slices images)
% FNAME: base filename of images, without end number (string)
% INDICES: indices of images to put for result. Ex: [0:39]
%
% IMG = readstack(FNAME, TYPE, DIM)
% forces the type and number of dimensions of resulting array.
% FNAME: name of the single stack file
% TYPE: matlab type of data ('uint8', 'double'...)
% DIM: size of final stack. Ex : [256 256 50].
% There is no support for binary raw stacks.
%
% Examples:
% IMG = readstack('images???.tif');
% IMG = readstack('aStack.tif');
% IMG = readstack('files00.bmp');
% IMG = readstack('files00.bmp', 5:23);
% IMG = readstack('files00slices##.tif');
% IMG = readstack('rawData.raw', 'uint8', [256 256 50]);
%
% See also:
% savestack, imread
%
% ---------
% author: David Legland, david.legland(at)grignon-dot-inra.fr
% created the 10/09/2003.
%% import a raw file.
% First argument is type of image ('uint8' usually),
% and second argument contains size of image to load.
if length(varargin)>1
type = varargin{1};
dim = varargin{2};
img = zeros(dim, type);
f = fopen(fname, 'r');
img(:) = fread(f, dim(1)*dim(2)*dim(3), ['*' type]);
return;
end
% check if image stored in one bubndle file or as several stacks
bundle = sum(ismember('#?', fname))==0;
if exist(fname, 'file')
bundle = length(imfinfo(fname))>1;
end
if ~bundle
% images stored in several 2D files ------------------------
% -> need to know numbers of slices to read.
%% Compute the base name of the image, by removing '#', '?' or '0'
% characters to replace with numbers
chars = '#?0';
index = [];
for c=1:length(chars)
% identify number of chars in file name
n=5;
while isempty(index) && n>1
n = n-1;
index = strfind(fname, repmat(chars(c), [1 n]));
end
% escape if special characters has been found
if ~isempty(index)
break;
end
end
% In the case of several '00' parts, consider only the last one
index = index(length(index));
% create file basename and endname
len = length(fname);
basename = fname(1:index-1);
endname = fname(index+n:len);
%% compute indices of slices to read
if ~isempty(varargin)
% slice indices are given as parameters
range=varargin{1};
else
% identify slices to read by detecting last index of slices
i=0;
while true
% check existence of file for given index
imgname = sprintf(['%s' sprintf('%%0%dd', n) '%s'], basename, i, endname);
if ~exist(imgname, 'file')
break;
end
i = i+1;
end
% read slices from the first one to the last existing one
range = 0:i-1;
end
%% Read each slice of the image
% read slice for each range index
string = [basename sprintf('%%0%dd', n) endname];
% adapt filename format to windows if needed
if ispc
string = strrep(string, '\', '\\');
end
% read the first image
img = imread(sprintf(string, range(1)));
% read each image one after the other
if length(size(img))==2
% allocate memory
img(1, 1, length(range))=0;
% read each gray scale image successively
for i=2:length(range)
img(:,:,i) = imread(sprintf(string, range(i)));
end
else
% pre-allocate memory
img(1, 1, 1, length(range))=0;
% read each color image successively
for i=2:length(range)
img(:,:,:,i) = imread(sprintf(string, range(i)));
end
end
else
% Image stored in one bundle file --------------------------
% get image dimensions
info = imfinfo(fname);
% If input argument is found, it is used as the number of slices to
% read. Anyway, read all the slices.
range = 1:length(info);
if ~isempty(varargin)
range = varargin{1};
end
% read each slice of the 3D image
img = imread(fname, range(1));
if length(size(img))==2 % read gray scale images -----
% pre-allocate memory
img(1, 1, length(range)) = 0;
% add each slice successively
for i=2:length(range)
img(:,:,i) = imread(fname, range(i));
end
else % read color images -----
% pre-allocate memory
img(1, 1, 1, length(range)) = 0;
% add each slice successively
for i=2:length(range)
img(:,:,:,i) = imread(fname, range(i));
end
end
end |
