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scifio / scifio-bf-compat

SCIFIO (@scifio/scifio) plug-in allowing use of Bio-Formats readers.
http://scif.io/
BSD 2-Clause "Simplified" License
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OutOfMemoryError: .pst format #11

Closed dietzc closed 9 years ago

dietzc commented 9 years ago

The following exception is thrown when I try to read in .pst files:

java.lang.OutOfMemoryError: Requested array size exceeds VM limit at loci.poi.poifs.storage.HeaderBlockReader.(HeaderBlockReader.java:97) at loci.poi.poifs.filesystem.POIFSFileSystem.(POIFSFileSystem.java:114) at loci.formats.services.POIServiceImpl.initialize(POIServiceImpl.java:86) at loci.formats.services.POIServiceImpl.initialize(POIServiceImpl.java:73) at loci.formats.in.TillVisionReader.initFile(TillVisionReader.java:227) at loci.formats.FormatReader.setId(FormatReader.java:1317) at loci.formats.ImageReader.setId(ImageReader.java:753) at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:405) at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:387) at io.scif.AbstractParser.parse(AbstractParser.java:252) at io.scif.AbstractParser.parse(AbstractParser.java:220) at io.scif.AbstractParser.parse(AbstractParser.java:316) at io.scif.AbstractParser.parse(AbstractParser.java:52) at org.knime.knip.io.ScifioImgSource.getReader(ScifioImgSource.java:401) at org.knime.knip.io.ScifioImgSource.getSeriesCount(ScifioImgSource.java:219) at org.knime.knip.io.nodes.imgreader.ReadFileImgTable$2.next(ReadFileImgTable.java:384) at org.knime.core.node.ExecutionContext.createBufferedDataTable(ExecutionContext.java:245) at org.knime.knip.io.nodes.imgreader.ImgReaderNodeModel.execute(ImgReaderNodeModel.java:402) at org.knime.core.node.NodeModel.execute(NodeModel.java:706) at org.knime.core.node.NodeModel.executeModel(NodeModel.java:555) at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1131) at org.knime.core.node.Node.execute(Node.java:927) at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:559) at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95) at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:179) at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:110) at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:328) at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:204) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:125) at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:248)

I uploaded a sample to FIJI (dbb4A.pst)!

hinerm commented 9 years ago

Looks like a bug in Bio-Formats. This fails with File > Import > Bio-Formats as well. No extra config from SCIFIO is causing this failure - it's just a result of setId on this file.

You'll have to use the bio-formats bug reporting system.

Sorry @dietzc :(