Error when using BioFormats Import for Macro

Posted by JNHBoon on Dec 06, 2014; 10:40pm
URL: http://imagej.273.s1.nabble.com/Error-when-using-BioFormats-Import-for-Macro-tp5010825.html

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)