<div dir="ltr"><div><div><div><div>Hi Michael,<br><br></div> I <a href="https://github.com/scifio/scifio-itk-bridge/commit/8ffccf457e0f41245167402d318d7e0c57eb127f">just updated</a> the Java-side handling of null readers/ids. I couldn't reproduce your exact issue, but it did look like there was the potential for an unintended state that would cause the null id error you said.<br>
<br></div> Could you clear your /build directory and rebuild? (this will trigger a download of the latest Java code) Then try again with the unset JAVA_HOME.<br><br><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">
/home/michael/Colocalization/ITK-4.5.1-build/lib/jre/bin<br></blockquote><div><br></div><div>As a side note, I believe you need to set JAVA_HOME to the base of your java directory (e.g. just "/home/michael/Colocalization/ITK-4.5.1-build/lib/jre"). At least on OSX 10.8.5, if I set include the /bin sub-directory, it doesn't actually discover Java (slightly counter-intuitive if you're used to adding stuff to your PATH). So you could try again with the distributed JRE as well.<br>
</div><br></div> For what it's worth, I am able to read/write the single-channel.ome.tif dataset with the itkSCIFIOImageIOTest utility, on OSX with java 1.6.0_45.<br><br></div>Let us know how it goes!<br><br>Thanks,<br>
Mark<br><div><br><br><div id=":6nz" class=""><br></div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 10, 2014 at 11:48 AM, Mark Hiner <span dir="ltr"><<a href="mailto:hinerm@gmail.com" target="_blank">hinerm@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div dir="ltr">Hi Michael,<div class="gmail_quote"><div dir="ltr"><div><div><div><br>
<br><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">I guess I just have to install the appropriate plug-in, as my format<br>
is not listed here:<br>
<a href="https://github.com/scifio/scifio" target="_blank">https://github.com/scifio/scifio</a><br></blockquote><br></div></div>I just wanted to let you know that the SCIFIOImageIO always checks formats using Bio-Formats. So there are no extra plugins you need to install; you were using it correctly (assuming your Java version is compatible).<br>
<br></div><div>Anyway, this looks like there could be legitimate bugs coming from Java land. I filed <a href="https://github.com/scifio/scifio-imageio/issues/14" target="_blank">an issue</a> for it, although I haven't been able to reproduce it yet as I am having a completely different issue regarding pixel types right now.<br>
<br></div><div>Once I can better reproduce/resolve these issues I'll let you know.<br><br></div><div>Thanks,<br>Mark<br></div><div><br></div></div><div><div><div class="gmail_extra"><br><br>
<div class="gmail_quote">On Thu, Apr 10, 2014 at 2:42 AM, Michael Meuli <span dir="ltr"><<a href="mailto:michael.meuli@gmail.com" target="_blank">michael.meuli@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Matt,<br>
<br>
I'm sorry for my presumably stupid questions.<br>
I guess I just have to install the appropriate plug-in, as my format<br>
is not listed here:<br>
<a href="https://github.com/scifio/scifio" target="_blank">https://github.com/scifio/scifio</a><br>
(Didn't figure out yet how but I guess I eventually will)<br>
<br>
Best regards and thanks again,<br>
Michael<br>
<div><div><br>
On 9 April 2014 22:14, Michael Meuli <<a href="mailto:michael.meuli@gmail.com" target="_blank">michael.meuli@gmail.com</a>> wrote:<br>
> Hi Matt,<br>
><br>
> If JAVA_HOME is unset:<br>
><br>
> Problem encoutered while reading image file : single-channel.ome.tif<br>
><br>
> itk::ExceptionObject (0x81520e0)<br>
> Location: "unknown"<br>
> File: /home/michael/Colocalization/ITK-4.5.1-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx<br>
> Line: 180<br>
> Description: itk::ERROR: SCIFIOImageIO(0x8150fb0): SCIFIOImageIO<br>
> exited abnormally. Exception in thread "main"<br>
> java.lang.IllegalStateException: ImageReader.getSeries: Current file<br>
> should not be null; call setId(String) first<br>
> at loci.formats.FormatTools.assertId(FormatTools.java:724)<br>
> at loci.formats.ImageReader.getReader(ImageReader.java:200)<br>
> at loci.formats.ImageReader.getSeries(ImageReader.java:441)<br>
> at loci.formats.ReaderWrapper.getSeries(ReaderWrapper.java:343)<br>
> at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:116)<br>
> at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:108)<br>
> at loci.scifio.itk.SCIFIOITKBridge.waitForInput(SCIFIOITKBridge.java:83)<br>
> at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:161)<br>
> at loci.scifio.itk.SCIFIOITKBridge.main(SCIFIOITKBridge.java:693)<br>
><br>
> Thanks,<br>
> Michael<br>
><br>
> On 8 April 2014 20:19, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>> wrote:<br>
>> Hi Michael,<br>
>><br>
>> If JAVA_HOME is unset?<br>
>><br>
>> Thanks,<br>
>> Matt<br>
>><br>
>> On Tue, Apr 8, 2014 at 1:57 PM, Michael Meuli <<a href="mailto:michael.meuli@gmail.com" target="_blank">michael.meuli@gmail.com</a>> wrote:<br>
>>> Hi Matt,<br>
>>><br>
>>> Thanks a lot.<br>
>>> I set JAVA_HOME to<br>
>>> "/home/michael/Colocalization/ITK-4.5.1-build/lib/jre/bin" and still<br>
>>> get the same error.<br>
>>><br>
>>> Thanks again,<br>
>>> Michael<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> On 7 April 2014 22:10, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>> wrote:<br>
>>>> Hi Michael,<br>
>>>><br>
>>>> Does it work with the JRE distributed with the module? I do not think<br>
>>>> Java 8 has been tested yet.<br>
>>>><br>
>>>> Thanks,<br>
>>>> Matt<br>
>>>><br>
>>>> On Mon, Apr 7, 2014 at 3:34 PM, Michael Meuli <<a href="mailto:michael.meuli@gmail.com" target="_blank">michael.meuli@gmail.com</a>> wrote:<br>
>>>>> Hi,<br>
>>>>><br>
>>>>> I'm trying to read the test image "single-channel.ome.tif" from<br>
>>>>> <a href="http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/data.html" target="_blank">http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/data.html</a><br>
>>>>> JAVA_HOME is set to "/usr/lib/jvm/java-8-oracle/jre/bin/java"<br>
>>>>> Running "SCIFIOTestDriver itkSCIFIOImageIOTest" gives me a very similar error.<br>
>>>>> I'm running Ubuntu 13.10 32bit with ITK-4.5.1<br>
>>>>><br>
>>>>> Below is the text of the error message:<br>
>>>>><br>
>>>>> Problem encoutered while reading image file :<br>
>>>>> /home/michael/Colocalization/Data/single-channel.ome.tif<br>
>>>>><br>
>>>>> itk::ExceptionObject (0x8e283f0)<br>
>>>>> Location: "unknown"<br>
>>>>> File: /home/michael/Colocalization/ITK-4.5.1-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx<br>
>>>>> Line: 408<br>
>>>>> Description: itk::ERROR: SCIFIOImageIO(0x8e27000): SCIFIOImageIO:<br>
>>>>> ITKReadImageInformation error:<br>
>>>>> Not a directory<br>
>>>>><br>
>>>>><br>
>>>>> Many thanks<br>
>>>>> Michael<br>
>>>>><br>
>>>>> _______________________________________________<br>
>>>>> Community mailing list<br>
>>>>> <a href="mailto:Community@itk.org" target="_blank">Community@itk.org</a><br>
>>>>> <a href="http://public.kitware.com/cgi-bin/mailman/listinfo/community" target="_blank">http://public.kitware.com/cgi-bin/mailman/listinfo/community</a><br>
>>>>><br>
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