Hello,
I have a set of TIFF files taken from the same source, but half of the files are not being loaded into ImageJ or Bioformats. Opening in ImageJ does not do anything even after an hour of wait, and using Bioformats gives the following errors:
[ERROR] Error reading IFD type at: 213421728
Reading IFDs
then:
java.io.EOFException: Attempting to read beyond end of file.
at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:378)
at loci.common.RandomAccessInputStream.readInt(RandomAccessInputStream.java:507)
at loci.common.RandomAccessInputStream.readUnsignedInt(RandomAccessInputStream.java:514)
at loci.formats.tiff.TiffParser.getNextOffset(TiffParser.java:1257)
at loci.formats.tiff.TiffParser.getIFDOffsets(TiffParser.java:303)
at loci.formats.tiff.TiffParser.getIFDs(TiffParser.java:217)
at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:448)
at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:583)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.formats.DelegateReader.setId(DelegateReader.java:291)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:228)
at ij.IJ.runPlugIn(IJ.java:192)
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.nio.BufferUnderflowException: null
at java.nio.Buffer.nextGetIndex(Buffer.java:506)
at java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:361)
at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:376)
... 19 common frames omitted
Checking for JAI
Reading movie dimensions
followed by a prompt saying there was an error during import and then in the ImageJ log:
loci.formats.FormatException: loci.common.ReflectException: Cannot execute method: decodeAsRenderedImage
at loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:196)
at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:156)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.formats.DelegateReader.setId(DelegateReader.java:300)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:228)
at ij.IJ.runPlugIn(IJ.java:192)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: loci.common.ReflectException: Cannot execute method: decodeAsRenderedImage
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:316)
at loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:191)
... 13 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:311)
... 14 more
Caused by: java.io.IOException: Illegal page requested from a TIFF file.
at com.sun.media.jai.codecimpl.TIFFImageDecoder.decodeAsRenderedImage(TIFFImageDecoder.java:104)
... 19 more
Again, this is only for half the files while the other half works fine. If anybody has had similar errors or possible solutions, help would be greatly appreciated. Thank you!
