BigStitcher input file error

Hello Everyone, I used Bigstitcher plugin in Fiji to open an image in order to generate PSF. After I specified the path, I got the following error. The image I am trying to open is binary stack.

Error from console window
[Wed Jul 03 11:15:16 EDT 2019] [ERROR] Module threw exception
java.lang.NullPointerException
at java.io.File.(File.java:277)
at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.detectViewsInFile(FileListDatasetDefinitionUtil.java:1116)
at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.detectViewsInFiles(FileListDatasetDefinitionUtil.java:1050)
at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.createDataset(FileListDatasetDefinition.java:642)
at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:141)
at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:122)
at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:109)
at net.preibisch.stitcher.plugin.BigStitcher.run(BigStitcher.java:74)
at org.scijava.command.CommandModule.run(CommandModule.java:199)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

error from exception window
(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52n; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 893MB of 49000MB (1%)
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: java.lang.NullPointerException
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:305)
… 5 more
Caused by: java.lang.NullPointerException
at java.io.File.(File.java:277)
at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.detectViewsInFile(FileListDatasetDefinitionUtil.java:1116)
at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.detectViewsInFiles(FileListDatasetDefinitionUtil.java:1050)
at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.createDataset(FileListDatasetDefinition.java:642)
at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:141)
at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:122)
at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:109)
at net.preibisch.stitcher.plugin.BigStitcher.run(BigStitcher.java:74)
at org.scijava.command.CommandModule.run(CommandModule.java:199)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
… 1 more

1 Like

Hi @Chen,

Welcome to the forum!

A couple of follow up questions:

  1. Is your Fiji up-to-date?
  2. What kind of image (what format) are you opening?

John

I just update my Fiji and got the same error message. The image format is binary stack.

Chen