LOCI version is<br><br>LOCI Plugins for ImageJ, revision d3781f8 built 24 april 2012<br>Release 4.4-DEV<br><br><div class="gmail_quote">On Tue, Jun 12, 2012 at 10:42 AM, B Sys <span dir="ltr"><<a href="mailto:bsys.com.ar@gmail.com" target="_blank">bsys.com.ar@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;display:inline!important;font-weight:normal;float:none;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">Hello, I have came across a possible bug when opening a large NRRD file.</span><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
I found it when trying to open it with Fiji, so I had contacted people form the Fiji development team. They told me that it appears to be a BioFormats issue.<br><br><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;display:inline!important;font-weight:normal;float:none;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">I am using Linux 64-bit (Arch Linux), but I have also seen this issue in Ubuntu 64-bit.</span><br>
</div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
<br></div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
You can find a bzipped version of the volume attached, which will uncompress to approximately 3.6GB. I am still trying to find which BioFormats version Fiji is using, but I still couldn't manage to do it.</div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
Surely it is one of the latest, since it says that it is up-to-date.</div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
<br></div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
The error message is the following:</div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
<br></div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
<div>java.lang.IllegalArgumentException: Negative position</div><div><span style="white-space:pre-wrap"> </span>at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)</div><div><span style="white-space:pre-wrap"> </span>at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:120)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:105)</div><div><span style="white-space:pre-wrap"> </span>at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:520)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.common.NIOFileHandle.seek(NIOFileHandle.java:241)</div><div><span style="white-space:pre-wrap"> </span>at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:116)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.formats.in.NRRDReader.openBytes(NRRDReader.java:150)</div><div><span style="white-space:pre-wrap"> </span>at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:184)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:176)</div><div><span style="white-space:pre-wrap"> </span>at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:184)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)</div><div><span style="white-space:pre-wrap"> </span>at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)</div><div><span style="white-space:pre-wrap"> </span>at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:252)</div><div><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)</div><div><span style="white-space:pre-wrap"> </span>at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:188)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImagePlusRea 1der.readProcessors(ImagePlusReader.java:414)</div><div><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:378)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:275)</div><div><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:236)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:214)</div><div><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:112)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.plugins.in.Importer.readPixels(Importer.java:148)</div><div><span style="white-space:pre-wrap"> </span>at loci.plugins.in.Importer.run(Importer.java:87)</div>
<div><span style="white-space:pre-wrap"> </span>at loci.plugins.LociImporter.run(LociImporter.java:79)</div><div><span style="white-space:pre-wrap"> </span>at ij.IJ.runUserPlugIn(IJ.java:185)</div><div><span style="white-space:pre-wrap"> </span>at ij.IJ.runPlugIn(IJ.java:152)</div>
<div><span style="white-space:pre-wrap"> </span>at ij.IJ.runPlugIn(IJ.java:141)</div><div><span style="white-space:pre-wrap"> </span>at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:375)</div><div>
<span style="white-space:pre-wrap"> </span>at HandleExtraFileTypes.run(HandleExtraFileTypes.java:53)</div><div><span style="white-space:pre-wrap"> </span>at ij.IJ.runUserPlugIn(IJ.java:185)</div><div><span style="white-space:pre-wrap"> </span>at ij.IJ.runPlugIn(IJ.java:152)</div>
<div><span style="white-space:pre-wrap"> </span>at ij.IJ.runPlugIn(IJ.java:141)</div><div><span style="white-space:pre-wrap"> </span>at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)</div><div>
<span style="white-space:pre-wrap"> </span>at ij.io.Opener.openImage(Opener.java:288)</div><div><span style="white-space:pre-wrap"> </span>at ij.io.Opener.openImage(Opener.java:309)</div><div><span style="white-space:pre-wrap"> </span>at ij.io.Opener.open(Opener.java:138)</div>
<div><span style="white-space:pre-wrap"> </span>at ij.io.Opener.openAndAddToRecent(Opener.java:224)</div><div><span style="white-space:pre-wrap"> </span>at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)</div>
<div><span style="white-space:pre-wrap"> </span>at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)</div><div><span style="white-space:pre-wrap"> </span>at java.lang.Thread.run(Thread.java:662)</div></div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
<br></div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
Let me know if I can help in any other way,</div><div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:small;white-space:normal;font-family:arial;word-spacing:0px">
Carlos</div><br>
</blockquote></div><br>