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

[Curtis Rueden]

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
> 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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