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Diffusion Motion correction paper (cluster_pipeline) Browse

R6289/code/mijread_stack.m
3e35ee179701cluster_pipeline

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mijread_stack.m
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function out = mijread_stack(filename)
% mijread, version 1.0
%
% im = mijread;
% im = mijread(filename);
% im = mijread(url);
%
% Read the images or stack of images using the ImageJ library.
% Files must be in TIFF (uncompressed), PNG, GIF, JPEG, DICOM, BMP, PGM or FITS
% format TIFF images can be 1-bit, 8-bits, 16-bits (unsigned), 32-bit
% (real) or RGB color.
% The image could read from the disk (filename) or from a URL (url). If no
% parameter are given to this function, the program open a dialog box to
% choose a image file.
% Example:
% im = mijread;
% im = mijread('http://www.google.com/intl/en_ALL/images/logo.gif');
%
% Part of the package MIJ
% http://bigwww.epfl.ch/sage/soft/mij/
%
% Installation:
% 1. Put the ij.jar (ImageJ) in the folder java of Matlab
% 2. Put the MIJ.class (MIJ) in the folder java of Matlab
%
opener = ij.io.Opener();
if isjava(opener) == 0
sprintf('%s', 'MIJ Message: the ImageJ is not properly installed in the java folder of Matlab.')
image = 0;
return
end
if (nargin == 0)
path = pwd;
dlg = ij.io.OpenDialog('Select an image', '');
path = dlg.getDirectory();
if (isjava(path)==0)
image = 0;
return
end
name = dlg.getFileName();
if (isjava(name)==0)
image = 0;
return
end
name = dlg.getDirectory().concat(dlg.getFileName());
opener.openImage(name).show();
else
name = java.lang.String(filename);
if (name.startsWith('http:') == 1)
opener.openURL(name).show();
else
file = java.io.File(name);
existence = file.exists();
if existence==0;
sprintf('%s', 'MIJ Message: this file do not exist')
image = 0;
return
end
image=opener.openImage(name);
end
end
img=image.getImageStack;
out=zeros(img.getHeight,img.getWidth,img.getSize);
for i=1:img.getSize()
a=img.getProcessor(i);
out(:,:,i)=a.getFloatArray()';
end
%image = MIJ.getCurrentImage();
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