http://imagej.273.s1.nabble.com/Error-when-using-BioFormats-Import-for-Macro-tp5010825p5010847.html
Thank you. Please, that would be helpful. May I also ask if there's a
> 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.
>>
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