Error when using BioFormats Import for Macro

[JNHBoon]

I'm trying to open a stack of images (400) in .dm4 format using the BioFormats plugin. Tried using the macro recorder and this is what it gave me:


    run("Bio-Formats", "open=[D:\\oxygen_3e-5_1 (missing Minute 3)\\Hour_00\\Minute_00\\Second_00\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0000.dm4] color_mode=Default group_files open_all_series view=Hyperstack stack_order=XYCZT use_virtual_stack axis_1_number_of_images=400 axis_1_axis_first_image=0 axis_1_axis_increment=1 file=[] pattern=[D:\\\\oxygen_3e-5_1 (missing Minute 3)\\\\Hour_00\\\\Minute_00\\\\Second_00\\\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0<000-399>.dm4]");

Unfortunately, when I tried running the macro, it gave me this error. Does anyone know what might be wrong here?


    java.lang.NullPointerException
    at ij.Macro.trimKey(Macro.java:154)
    at ij.gui.GenericDialog.getNextBoolean(GenericDialog.java:936)
    at loci.plugins.in.FilePatternDialog.harvestResults(FilePatternDialog.java:192)
    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:751)
    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:202)
    at ij.IJ.runPlugIn(IJ.java:166)
    at ij.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:61)
    at ij.IJ.run(IJ.java:275)
    at ij.macro.Functions.doRun(Functions.java:591)
    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 ij.macro.Interpreter.run(Interpreter.java:92)
    at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)
    at ij.IJ.runMacro(IJ.java:119)
    at ij.IJ.runMacro(IJ.java:108)
    at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:782)
    at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)
    at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:156)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
    at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

[Melissa Linkert-2]

Hi,

> I'm trying to open a stack of images (400) in .dm4 format using the
> BioFormats plugin. Tried using the macro recorder and this is what it gave
> me:
>
>
>     run("Bio-Formats", "open=[D:\\oxygen_3e-5_1 (missing Minute
> 3)\\Hour_00\\Minute_00\\Second_00\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0000.dm4]
> color_mode=Default group_files open_all_series view=Hyperstack
> stack_order=XYCZT use_virtual_stack axis_1_number_of_images=400
> axis_1_axis_first_image=0 axis_1_axis_increment=1 file=[]
> pattern=[D:\\\\oxygen_3e-5_1 (missing Minute
> 3)\\\\Hour_00\\\\Minute_00\\\\Second_00\\\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0<000-399>.dm4]");
>
> Unfortunately, when I tried running the macro, it gave me this error. Does
> anyone know what might be wrong here?
>
>
>     java.lang.NullPointerException
>     at ij.Macro.trimKey(Macro.java:154)
>     at ij.gui.GenericDialog.getNextBoolean(GenericDialog.java:936)
>     at
> loci.plugins.in.FilePatternDialog.harvestResults(FilePatternDialog.java:192)

This is a known issue with the "Group files with similar names" option,
and is noted on Bio-Formats' issue tracking system:

http://trac.openmicroscopy.org/ome/ticket/12238

If you would like to be automatically notified of updates to that
ticket, please let me know and I will CC you.

Regards,
-Melissa

On Sat, Dec 06, 2014 at 02:40:50PM -0800, JNHBoon wrote:

> I'm trying to open a stack of images (400) in .dm4 format using the
> BioFormats plugin. Tried using the macro recorder and this is what it gave
> me:
>
>
>     run("Bio-Formats", "open=[D:\\oxygen_3e-5_1 (missing Minute
> 3)\\Hour_00\\Minute_00\\Second_00\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0000.dm4]
> color_mode=Default group_files open_all_series view=Hyperstack
> stack_order=XYCZT use_virtual_stack axis_1_number_of_images=400
> axis_1_axis_first_image=0 axis_1_axis_increment=1 file=[]
> pattern=[D:\\\\oxygen_3e-5_1 (missing Minute
> 3)\\\\Hour_00\\\\Minute_00\\\\Second_00\\\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0<000-399>.dm4]");
>
> Unfortunately, when I tried running the macro, it gave me this error. Does
> anyone know what might be wrong here?
>
>
>     java.lang.NullPointerException
>     at ij.Macro.trimKey(Macro.java:154)
>     at ij.gui.GenericDialog.getNextBoolean(GenericDialog.java:936)
>     at
> loci.plugins.in.FilePatternDialog.harvestResults(FilePatternDialog.java:192)
>     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:751)
>     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:202)
>     at ij.IJ.runPlugIn(IJ.java:166)
>     at ij.Executer.runCommand(Executer.java:131)
>     at ij.Executer.run(Executer.java:61)
>     at ij.IJ.run(IJ.java:275)
>     at ij.macro.Functions.doRun(Functions.java:591)
>     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 ij.macro.Interpreter.run(Interpreter.java:92)
>     at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)
>     at ij.IJ.runMacro(IJ.java:119)
>     at ij.IJ.runMacro(IJ.java:108)
>     at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:782)
>     at
> net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)
>     at
> net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:156)
>     at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
>     at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
>     at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
>     at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
>     at
> org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
>     at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>     at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>     at java.lang.Thread.run(Thread.java:745)
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Error-when-using-BioFormats-Import-for-Macro-tp5010825.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[JNHBoon]

Hi Melissa,

Thank you. Please, that would be helpful. May I also ask if there's a
workaround for this issue?


Regards,
Jonathan

On 08-Dec-14 6:49 PM, Melissa Linkert wrote:

> Hi,
>
>> I'm trying to open a stack of images (400) in .dm4 format using the
>> BioFormats plugin. Tried using the macro recorder and this is what it gave
>> me:
>>
>>
>>      run("Bio-Formats", "open=[D:\\oxygen_3e-5_1 (missing Minute
>> 3)\\Hour_00\\Minute_00\\Second_00\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0000.dm4]
>> color_mode=Default group_files open_all_series view=Hyperstack
>> stack_order=XYCZT use_virtual_stack axis_1_number_of_images=400
>> axis_1_axis_first_image=0 axis_1_axis_increment=1 file=[]
>> pattern=[D:\\\\oxygen_3e-5_1 (missing Minute
>> 3)\\\\Hour_00\\\\Minute_00\\\\Second_00\\\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0<000-399>.dm4]");
>>
>> Unfortunately, when I tried running the macro, it gave me this error. Does
>> anyone know what might be wrong here?
>>
>>
>>      java.lang.NullPointerException
>>       at ij.Macro.trimKey(Macro.java:154)
>>       at ij.gui.GenericDialog.getNextBoolean(GenericDialog.java:936)
>>       at
>> loci.plugins.in.FilePatternDialog.harvestResults(FilePatternDialog.java:192)
> This is a known issue with the "Group files with similar names" option,
> and is noted on Bio-Formats' issue tracking system:
>
> http://trac.openmicroscopy.org/ome/ticket/12238
>
> If you would like to be automatically notified of updates to that
> ticket, please let me know and I will CC you.
>
> Regards,
> -Melissa
>
> On Sat, Dec 06, 2014 at 02:40:50PM -0800, JNHBoon wrote:
>> I'm trying to open a stack of images (400) in .dm4 format using the
>> BioFormats plugin. Tried using the macro recorder and this is what it gave
>> me:
>>
>>
>>      run("Bio-Formats", "open=[D:\\oxygen_3e-5_1 (missing Minute
>> 3)\\Hour_00\\Minute_00\\Second_00\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0000.dm4]
>> color_mode=Default group_files open_all_series view=Hyperstack
>> stack_order=XYCZT use_virtual_stack axis_1_number_of_images=400
>> axis_1_axis_first_image=0 axis_1_axis_increment=1 file=[]
>> pattern=[D:\\\\oxygen_3e-5_1 (missing Minute
>> 3)\\\\Hour_00\\\\Minute_00\\\\Second_00\\\\oxygen_3e-5_1_Hour_00_Minute_00_Second_00_Frame_0<000-399>.dm4]");
>>
>> Unfortunately, when I tried running the macro, it gave me this error. Does
>> anyone know what might be wrong here?
>>
>>
>>      java.lang.NullPointerException
>>       at ij.Macro.trimKey(Macro.java:154)
>>       at ij.gui.GenericDialog.getNextBoolean(GenericDialog.java:936)
>>       at
>> loci.plugins.in.FilePatternDialog.harvestResults(FilePatternDialog.java:192)
>>       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:751)
>>       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:202)
>>       at ij.IJ.runPlugIn(IJ.java:166)
>>       at ij.Executer.runCommand(Executer.java:131)
>>       at ij.Executer.run(Executer.java:61)
>>       at ij.IJ.run(IJ.java:275)
>>       at ij.macro.Functions.doRun(Functions.java:591)
>>       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 ij.macro.Interpreter.run(Interpreter.java:92)
>>       at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)
>>       at ij.IJ.runMacro(IJ.java:119)
>>       at ij.IJ.runMacro(IJ.java:108)
>>       at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:782)
>>       at
>> net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)
>>       at
>> net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:156)
>>       at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
>>       at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
>>       at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
>>       at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
>>       at
>> org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
>>       at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>>       at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>       at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>       at java.lang.Thread.run(Thread.java:745)
>>
>>
>>
>>
>> --
>> View this message in context: http://imagej.1557.x6.nabble.com/Error-when-using-BioFormats-Import-for-Macro-tp5010825.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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