[ome-users] [fiji-devel] bioformats importer scripting crash

[Roger Leigh]

Dear all,

I have opened two tickets for these issues:
https://trac.openmicroscopy.org.uk/ome/ticket/12238
https://trac.openmicroscopy.org.uk/ome/ticket/12238
and I will look at this in more detail this week.


Regards,
Roger

On 23/04/2014 19:31, Curtis Rueden wrote:
> Hi Jeremy,
>
>  > I'm having trouble scripting the bioformats importer pluggin.
>
> There are two different bugs there:
>
> 1) Using "Group files with similar names" via a macro is currently
> broken. This is what causes the NullPointerException you are seeing. At
> a cursory glance: I am guessing there used to be another option "use
> regex" or some such, which was then removed from the code, but not
> completely.
>
> 2) Using "Swap dimensions" via a macro is also broken. It results in
> duplicate macro keys in the case where there are the same number of Z, C
> and/or T positions in the dataset.
>
> I have CCed the ome-users list to inform the Bio-Formats developers of
> these problems.
>
> Regards,
> Curtis
>
> P.S. Ideally we would add some unit tests to prevent these sorts of
> regressions in the future. With the .fake file format it might be doable
> pretty easily...
>
>
>
> On Wed, Apr 23, 2014 at 1:56 PM, Jeremy Bredfeldt
> <jeremybredfeldt at gmail.com <mailto:jeremybredfeldt at gmail.com>> wrote:
>
>     Hi,
>
>     I'm having trouble scripting the bioformats importer pluggin.
>
>     Here's what I did:
>
>     saved blobs.tif to the desktop.
>     started the recorder.
>     used bioformats importer to open blobs.tif.
>     hit create in the recorder.
>     run the macro.
>
>     Here's the resulting exception:
>     (Fiji Is Just) ImageJ 1.48v; Java 1.7.0_51 [64-bit]; Windows 7 6.1;
>     183MB of 46043MB (<1%)
>     java.lang.NullPointerException
>     at ij.Macro.trimKey(Macro.java:154)
>     at ij.gui.GenericDialog.getNextBoolean(GenericDialog.java:938)
>     at
>     loci.plugins.in.FilePatternDialog.harvestResults(FilePatternDialog.java:193)
>     at loci.plugins.in.ImporterDialog.showDialog(ImporterDialog.java:83)
>     at
>     loci.plugins.in.ImporterPrompter.promptFilePattern(ImporterPrompter.java:135)
>     at
>     loci.plugins.in.ImporterPrompter.statusUpdated(ImporterPrompter.java:84)
>     at loci.plugins.in.ImportProcess.notifyListeners(ImportProcess.java:475)
>     at loci.plugins.in.ImportProcess.step(ImportProcess.java:763)
>     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
>     at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>     at loci.plugins.in.Importer.run(Importer.java:79)
>     at loci.plugins.LociImporter.run(LociImporter.java:81)
>     at ij.IJ.runUserPlugIn(IJ.java:199)
>     at ij.IJ.runPlugIn(IJ.java:163)
>     at ij.Executer.runCommand(Executer.java:131)
>     at ij.Executer.run(Executer.java:61)
>     at ij.IJ.run(IJ.java:269)
>     at ij.macro.Functions.doRun(Functions.java:590)
>     at ij.macro.Functions.doFunction(Functions.java:89)
>     at ij.macro.Interpreter.doStatement(Interpreter.java:226)
>     at ij.macro.Interpreter.doStatements(Interpreter.java:214)
>     at ij.macro.Interpreter.run(Interpreter.java:111)
>     at ij.macro.Interpreter.run(Interpreter.java:81)
>     at CLI.Refresh_Macros.runScript(Refresh_Macros.java:56)
>     at common.RefreshScripts.runScript(RefreshScripts.java:328)
>     at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1225)
>     at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1785)
>
>     Here's the macro that was generated with my specific selections:
>     run("Bio-Formats Importer",
>     "open=C:\\Users\\bredfeldt\\Desktop\\blobs.tif color_mode=Default
>     group_files split_timepoints split_channels view=Hyperstack
>     stack_order=XYCZT swap_dimensions file=[]
>     pattern=C:\\\\Users\\\\bredfeldt\\\\Desktop\\\\blobs.tif 1_planes=Z
>     1_planes=C 1_planes=T");
>
>     Let me know if anyone has any suggestions.
>
>     Thanks for your help,
>     Jeremy
>
>     --
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