[ome-users] GatanReader bug

[Martin Jones]

Hi,

I have been unable to open Gatan .dm4 files with bioformats in Fiji with the latest version on Mac OS X 10.9.5 (screenshot of error message attached). Although DM4 doesn’t seem to be officially supported, it worked fine in previous versions (for example the lifeline version) and the code seems to reference DM4_MAGIC_BYTES. I checked the GatanReader.java code for the working and non-working versions and there is a difference in the method that produces the error:

Bio-formats Version 5.1.3 (non-working):
-----------------------------------------------------------------------------------------
else if (labelString.startsWith("xPos")) {
          final Double number = Double.valueOf(value);
          posX = new Length(number, UNITS.REFERENCEFRAME);
        }
        else if (labelString.startsWith("yPos")) {
          final Double number = Double.valueOf(value);
          posY = new Length(number, UNITS.REFERENCEFRAME);
        }
-----------------------------------------------------------------------------------------

Bio-formats Version 5.0.3 (working):
-----------------------------------------------------------------------------------------
        else if (labelString.startsWith("xPos")) {
          posX = Double.parseDouble(value);
        }
        else if (labelString.startsWith("yPos")) {
          posY = Double.parseDouble(value);
        }
-----------------------------------------------------------------------------------------

It looks as though the problem is with parsing the string read from the metadata? I’ve uploaded an example DM4 file named Example_MJ.dm4 to the QA server from my email address martin.jones at crick.ac.uk<mailto:martin.jones at crick.ac.uk>.

Cheers,
Martin



[cid:17A686EF-1E37-40EC-A4B0-A1D26C6C746B at Home]





Dr. Martin Jones

Electron Microscopy STP
The Francis Crick Institute
Lincoln's Inn Fields Laboratory
44 Lincoln’s Inn Fields
London WC2A 3LY

T: +44 (0)20 7269 3346 (Room 1B16)
E: Martin.Jones at crick.ac.uk<mailto:Martin.Jones at crick.ac.uk>
W: www.crick.ac.uk<http://www.crick.ac.uk>


The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.
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