[ome-users] Antwort: Re: no matching signature found for class'loci.formats.FormatTools'.

[Matthias Pospiech]

Sebastien Besson <s.besson at dundee.ac.uk> schrieb am 22.08.2013 17:51:51:

> Von: Sebastien Besson <s.besson at dundee.ac.uk>
> 
> Hi Mathias, 
> 
> Assuming you are using 4.4.8 version (returned by 
> loci.formats.FormatTools.VERSION), this may be bug.

Actually I was using 4.4.6 although I downloaded it yesterday.
I downloaded 4.4.8 and could not reproduce the error. This was 
however with a different image, so that it is not exactly the same
test.

> How did you get this error: did you use one bfopen on an image or a 
> custom script? What type of file are you using?

The file tye is czi. The script that I am using is a stripped bfopen, for 
retrieving the number of images in the file.
If there is an easier way to get the image count I would like to know.

In the end this number is used to read the stack (could be multiple GB) in 

parts of 200 images.

function [ result ] = bfGetNumberOfImages( id )
% Modified bfopen by Matthias Pospiech (Zeiss Microscopy)
%
% There are advantages to using the static approach over javaaddpath:
%     1. If you use bfopen within a loop, it saves on overhead
%        to avoid calling the javaaddpath command repeatedly.
%     2. Calling 'javaaddpath' may erase certain global parameters.
autoloadBioFormats = 1;
 
% Toggle the stitchFiles flag to control grouping of similarly
% named files into a single dataset based on file numbering.
stitchFiles = 0;
 
% To work with compressed Evotec Flex, fill in your LuraWave license code.
%lurawaveLicense = 'xxxxxx-xxxxxxx';
 
% -- Main function - no need to edit anything past this point --
 
% load the Bio-Formats library into the MATLAB environment
status = bfCheckJavaPath(autoloadBioFormats);
assert(status, ['Missing Bio-Formats library. Either add loci_tools.jar '
...
    'to the static Java path or add it to the Matlab path.']);
 
% Prompt for a file if not input
if nargin == 0 || exist(id, 'file') == 0
  [file, path] = uigetfile(bfGetFileExtensions, 'Choose a file to open');
  id = [path file];
  if isequal(path, 0) || isequal(file, 0), return; end
end
 
% initialize logging
loci.common.DebugTools.enableLogging('OFF'); % INFO
 
% Get the channel filler
r = bfGetReader(id, stitchFiles);
 
% Test plane size
if nargin >=4
    planeSize = loci.formats.FormatTools.getPlaneSize(r, varargin{3}, 
varargin{4});
else
    planeSize = loci.formats.FormatTools.getPlaneSize(r);
end
 
if planeSize/(1024)^3 >= 2,
    error(['Image plane too large. Only 2GB of data can be extracted '...
        'at one time. You can workaround the problem by opening '...
        'the plane in tiles.']);
end
 
numSeries = r.getSeriesCount();
result = cell(numSeries, 1);
for s = numSeries
    fprintf('Reading series #%d', s);
    r.setSeries(s - 1);
    numImages = r.getImageCount();
 
    % save images and metadata into our master series list
    result{s} = numImages;
end
r.close();


Matthias Pospiech



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