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

[Jeremy Bredfeldt]

Thanks Curtis. I just used the imagej import-> image sequence function in
my macro instead, which seems to do what I needed. Thanks for looking into
this.

Best regards,
Jeremy


On Wed, Apr 23, 2014 at 2:31 PM, Curtis Rueden <ctrueden at wisc.edu> 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> 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
>>
>> --
>> --
>> Please avoid top-posting, and please make sure to reply-to-all!
>>
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>
>
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