Bioformats update creates exceptions for dm4 files

[AAM71]

Dear Listers,

We are using Fiji quite a lot in our Facility. Until recently it was
able to read dm4 files from Gatan (even if this option is not mentioned
in documentation). However, after the update it became impossible -
instead of opening dm4 file Fiji produces the list of exceptions:

begin-----------------

(Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.8.0_51 [64-bit]; Windows
7 6.1; 35MB of 6103MB (<1%)

java.lang.NumberFormatException: For input string: "0 . 0"

at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)

     at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)

     at java.lang.Double.parseDouble(Double.java:538)

     at java.lang.Double.valueOf(Double.java:502)

     at loci.formats.in.GatanReader.parseTags(GatanReader.java:506)

     at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)

     at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)

     at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)

     at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)

     at loci.formats.in.GatanReader.initFile(GatanReader.java:197)

     at loci.formats.FormatReader.setId(FormatReader.java:1426)

     at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)

     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)

     at loci.plugins.in.Importer.showDialogs(Importer.java:137)

     at loci.plugins.in.Importer.run(Importer.java:75)

     at loci.plugins.LociImporter.run(LociImporter.java:78)

     at ij.IJ.runUserPlugIn(IJ.java:212)

     at ij.IJ.runPlugIn(IJ.java:176)

     at ij.IJ.runPlugIn(IJ.java:165)

     at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)

     at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)

     at ij.IJ.runUserPlugIn(IJ.java:212)

     at ij.IJ.runPlugIn(IJ.java:176)

     at ij.IJ.runPlugIn(IJ.java:165)

     at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:486)

     at ij.io.Opener.openImage(Opener.java:360)

     at ij.io.Opener.openImage(Opener.java:239)

     at ij.io.Opener.open(Opener.java:106)

     at ij.io.Opener.openAndAddToRecent(Opener.java:288)

     at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)

     at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)

     at java.lang.Thread.run(Thread.java:745)

end--------------------



I have tried to trace what is the reason and it seems that it is the
updated version of BioFormats plugin.

All versions before 5.1.0-m4 were fine to be able to read dm4 files (if
you install Bioformats plugin to ImageJ). Any version from 5.1.0-m4
upwards (newest is 5.1.3, I believe) produces the list of exceptions and
do not open dm4 files anymore.

I have uploaded the test image I have been using to
http://qa.openmicroscopy.org.uk/qa/upload/

The name of the file is:
T2DM_3VBSED_roi_01_slice_0001.dm4


Can you, please, correct this bug? Or if it is impossible can you,
please, tell me how to install old Bioformats version to Fiji manually.
With ImageJ it is easy, but Fiji seems to have more complicated system.

I have sent thsi bug report to Bioformats list as well.


Sincerely,
Alex
--
Dr. Aleksandr Mironov MD, PhD
Senior Experimental Officer
D.1527, M.Smith Building
EM Core Facility, Faculty of Life Sciences
University of Manchester
Oxford Road
Manchester
M13 9PT
UK

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Melissa Linkert-2]

Hi Alex,

> Can you, please, correct this bug? Or if it is impossible can you,
> please, tell me how to install old Bioformats version to Fiji
> manually. With ImageJ it is easy, but Fiji seems to have more
> complicated system.
>
> I have sent thsi bug report to Bioformats list as well.

Please see the reply to the same post on the ome-users mailing list:

http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-August/005573.html

As noted there, this problem is expected to be fixed in the upcoming
5.1.4 release of Bio-Formats.

Regards,
-Melissa

On Thu, Aug 13, 2015 at 08:31:06AM +0100, Aleksandr Mironov wrote:

> Dear Listers,
>
> We are using Fiji quite a lot in our Facility. Until recently it was
> able to read dm4 files from Gatan (even if this option is not
> mentioned in documentation). However, after the update it became
> impossible - instead of opening dm4 file Fiji produces the list of
> exceptions:
>
> begin-----------------
>
> (Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.8.0_51 [64-bit];
> Windows 7 6.1; 35MB of 6103MB (<1%)
>
> java.lang.NumberFormatException: For input string: "0 . 0"
>
> at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
>
>     at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
>
>     at java.lang.Double.parseDouble(Double.java:538)
>
>     at java.lang.Double.valueOf(Double.java:502)
>
>     at loci.formats.in.GatanReader.parseTags(GatanReader.java:506)
>
>     at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)
>
>     at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)
>
>     at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)
>
>     at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)
>
>     at loci.formats.in.GatanReader.initFile(GatanReader.java:197)
>
>     at loci.formats.FormatReader.setId(FormatReader.java:1426)
>
>     at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
>
>     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
>
>     at loci.plugins.in.Importer.showDialogs(Importer.java:137)
>
>     at loci.plugins.in.Importer.run(Importer.java:75)
>
>     at loci.plugins.LociImporter.run(LociImporter.java:78)
>
>     at ij.IJ.runUserPlugIn(IJ.java:212)
>
>     at ij.IJ.runPlugIn(IJ.java:176)
>
>     at ij.IJ.runPlugIn(IJ.java:165)
>
>     at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
>
>     at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
>
>     at ij.IJ.runUserPlugIn(IJ.java:212)
>
>     at ij.IJ.runPlugIn(IJ.java:176)
>
>     at ij.IJ.runPlugIn(IJ.java:165)
>
>     at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:486)
>
>     at ij.io.Opener.openImage(Opener.java:360)
>
>     at ij.io.Opener.openImage(Opener.java:239)
>
>     at ij.io.Opener.open(Opener.java:106)
>
>     at ij.io.Opener.openAndAddToRecent(Opener.java:288)
>
>     at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
>
>     at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
>
>     at java.lang.Thread.run(Thread.java:745)
>
> end--------------------
>
>
>
> I have tried to trace what is the reason and it seems that it is the
> updated version of BioFormats plugin.
>
> All versions before 5.1.0-m4 were fine to be able to read dm4 files
> (if you install Bioformats plugin to ImageJ). Any version from
> 5.1.0-m4 upwards (newest is 5.1.3, I believe) produces the list of
> exceptions and do not open dm4 files anymore.
>
> I have uploaded the test image I have been using to
> http://qa.openmicroscopy.org.uk/qa/upload/
>
> The name of the file is:
> T2DM_3VBSED_roi_01_slice_0001.dm4
>
>
> Can you, please, correct this bug? Or if it is impossible can you,
> please, tell me how to install old Bioformats version to Fiji
> manually. With ImageJ it is easy, but Fiji seems to have more
> complicated system.
>
> I have sent thsi bug report to Bioformats list as well.
>
>
> Sincerely,
> Alex
> --
> Dr. Aleksandr Mironov MD, PhD
> Senior Experimental Officer
> D.1527, M.Smith Building
> EM Core Facility, Faculty of Life Sciences
> University of Manchester
> Oxford Road
> Manchester
> M13 9PT
> UK
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html