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Bio-Formats I/O error

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Bio-Formats I/O error

ved sharma
Hello,

I'm trying to open some deltavision timelapse images using Bio-Formats Importer. The first 4 files in my folder open alright. For the 5th file, Importer tries to open it then midway through the progress bar gives the I/O error (see below). From the 6th file onward, Importer keeps giving I/O error. I don't understand why this is happening since all the timelapses were acquired on the same day with the same settings.

I'm on a Windows 7 64-bit machine and tried both ImageJ and Fiji with the latest versions and Bio-Formats ver 5.1.10

Here is the error message:

Sorry, there was an I/O problem during import.

java.io.IOException: The system cannot find the file specified
at sun.nio.ch.FileDispatcher.pread0(Native Method)
at sun.nio.ch.FileDispatcher.pread(FileDispatcher.java:35)
at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:230)
at sun.nio.ch.IOUtil.read(IOUtil.java:206)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:622)
at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:127)
at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:112)
at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:602)
at loci.common.NIOFileHandle.read(NIOFileHandle.java:273)
at loci.common.NIOFileHandle.read(NIOFileHandle.java:261)
at loci.common.NIOFileHandle.read(NIOFileHandle.java:249)
at loci.common.RandomAccessInputStream.read(RandomAccessInputStream.java:596)
at loci.formats.FormatReader.readPlane(FormatReader.java:529)
at loci.formats.FormatReader.readPlane(FormatReader.java:517)
at loci.formats.in.DeltavisionReader.openBytes(DeltavisionReader.java:204)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:225)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
at loci.plugins.in.Importer.readPixels(Importer.java:149)
at loci.plugins.in.Importer.run(Importer.java:86)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:216)
at ij.IJ.runPlugIn(IJ.java:180)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:296)
at ij.IJ.run(IJ.java:271)
at ij.macro.Functions.doRun(Functions.java:603)
at ij.macro.Functions.doFunction(Functions.java:96)
at ij.macro.Interpreter.doStatement(Interpreter.java:230)
at ij.macro.Interpreter.doStatements(Interpreter.java:218)
at ij.macro.Interpreter.run(Interpreter.java:115)
at ij.macro.Interpreter.run(Interpreter.java:85)
at ij.macro.MacroRunner.run(MacroRunner.java:139)
at java.lang.Thread.run(Thread.java:619)

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Re: Bio-Formats I/O error

ved sharma
Solved!

It had nothing to do with Bio-Formats. The files were on an external HD and were not accessible for some reason. Restarted the computer and it's working now. Sorry for the trouble!

Ved

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