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<div>Hi Melissa, I hope the weekend was fun.<br>
<br>
I just wanted to follow up and let you know that I'm still not able to open my custom written .ims file. I'm running Bio-Formats 5.4.0 and I see an error with "Invalid C size: 0" (see below), but when I inspect with HDFView I see that my Noc attribute is 1...
The location is /DataSetInfo/Image/Noc<br>
<br>
In looking through the subtleties between different versions of Imaris files I see that not all attributes are needed for Imaris to open the files, and I wonder if we have a situation where the information is being pulled from a different attribute.<br>
<br>
Do you have a .ims file you can share that I can compare to, and hopefully add the missing attributes?<br>
<br>
Thanks<br>
Neil<br>
<br>
<br>
java.lang.IllegalArgumentException: Invalid C size: 0<br>
at loci.formats.FormatTools.getZCTCoords(FormatTools.java:620)<br>
at loci.formats.FormatTools.getZCTCoords(FormatTools.java:560)<br>
at loci.formats.FormatReader.getZCTCoords(FormatReader.java:1097)<br>
at loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:434)<br>
at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:311)<br>
at loci.formats.FormatReader.setId(FormatReader.java:1397)<br>
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)<br>
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)<br>
at loci.plugins.in.Importer.showDialogs(Importer.java:140)<br>
at loci.plugins.in.Importer.run(Importer.java:76)<br>
at loci.plugins.LociImporter.run(LociImporter.java:78)<br>
at ij.IJ.runUserPlugIn(IJ.java:217)<br>
at ij.IJ.runPlugIn(IJ.java:181)<br>
at ij.Executer.runCommand(Executer.java:137)<br>
at ij.Executer.run(Executer.java:66)<br>
at java.lang.Thread.run(Thread.java:745)<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Anthony, Neil<br>
<b>Sent:</b> Thursday, February 2, 2017 10:44:34 AM<br>
<b>To:</b> Melissa Linkert<br>
<b>Subject:</b> Re: [ome-devel] In house written .ims file question</font>
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<p>Hi Melissa,</p>
<p>I found time to look at the attributes in my files, and it does have a Noc (number of channels) set in the Image group as you mention. I looked at the error and it looks like it errors on line</p>
<p>435 in <span>ImarisHDFReader.java</span>:</p>
<p></p>
<div><span class="x_pl-k">int</span>[] zct <span class="x_pl-k">=</span> getZCTCoords(no);</div>
from the exception:<br>
<p></p>
<p></p>
<div> at loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:435)<br>
<br>
Maybe it is something your end, I don't know.<br>
<br>
Looking back at my attributes vs the Bitplane document I see that I have unit=micron and they show unit=um, so maybe that is affecting things too. I'll keep you updated if that unit text changes anything once I try it out.<br>
<br>
Thanks for your time.<br>
<br>
Neil<br>
<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Anthony, Neil<br>
<b>Sent:</b> Tuesday, January 31, 2017 9:13:17 PM<br>
<b>To:</b> Melissa Linkert<br>
<b>Subject:</b> RE: [ome-devel] In house written .ims file question</font>
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<div class="PlainText">Hi Melissa, thanks for the details.<br>
<br>
I think the error might be my end. I'll double check that all the attributes match up and post the result here asap.<br>
<br>
Thanks for your time.<br>
<br>
Neil<br>
<br>
<br>
-----Original Message-----<br>
From: Melissa Linkert [<a href="mailto:melissa@glencoesoftware.com">mailto:melissa@glencoesoftware.com</a>]
<br>
Sent: Monday, January 30, 2017 11:55 AM<br>
To: OME External Developer List <ome-devel@lists.openmicroscopy.org.uk><br>
Cc: Anthony, Neil <nantho2@emory.edu><br>
Subject: Re: [ome-devel] In house written .ims file question<br>
<br>
Hi Neil,<br>
<br>
> I have written some matlab code to write .ims files, but on opening <br>
> with Bioformats I get the below pasted error list. The files open <br>
> fine with Imaris (the underlying file format is listed as v5.5, but it <br>
> appears that different things in the HDF5 structure come and go with <br>
> different versions of Imaris. I'm currently using 8.4)<br>
><br>
> Do you guys have a breakdown of the group and attribute structure that Bioformats uses?<br>
<br>
Our reference page for Imaris HDF is:<br>
<br>
<a href="http://www.openmicroscopy.org/site/support/bio-formats5.3/formats/bitplane-imaris.html">http://www.openmicroscopy.org/site/support/bio-formats5.3/formats/bitplane-imaris.html</a><br>
<br>
and the relevant section of Bio-Formats' Imaris HDF reader:<br>
<br>
<a href="https://github.com/openmicroscopy/bioformats/blob/v5.3.2/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java#L480">https://github.com/openmicroscopy/bioformats/blob/v5.3.2/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java#L480</a><br>
<br>
The error message you are seeing is a result of the channel count not being found in the file. Bio-Formats expects the channel count to be set in a "NumberOfChannels" attribute; according to the current specification from Bitplane, it looks like this has been
replaced by the "Noc" attribute in the "Image" group (section 3.2 of <a href="http://open.bitplane.com/Default.aspx?tabid=268">
http://open.bitplane.com/Default.aspx?tabid=268</a>). If your code sets "Noc" and the resulting file has the correct dimensions in Imaris, then this is likely something we need to fix in Bio-Formats.<br>
<br>
If you are willing to upload one or more of the .ims files that exhibit this problem, then we should have enough information to test a fix, or better advise you as to what needs to change in the file.<br>
Files can be uploaded to:<br>
<br>
<a href="http://qa.openmicroscopy.org.uk/qa/upload/">http://qa.openmicroscopy.org.uk/qa/upload/</a><br>
<br>
Regards,<br>
-Melissa<br>
<br>
<br>
On Mon, Jan 30, 2017 at 8:46 AM, Anthony, Neil <nantho2@emory.edu> wrote:<br>
> Hi all, I hope the data treats you well.<br>
><br>
> I have written some matlab code to write .ims files, but on opening <br>
> with Bioformats I get the below pasted error list. The files open <br>
> fine with Imaris (the underlying file format is listed as v5.5, but it <br>
> appears that different things in the HDF5 structure come and go with <br>
> different versions of Imaris. I'm currently using 8.4)<br>
><br>
> Do you guys have a breakdown of the group and attribute structure that Bioformats uses?<br>
><br>
> Thanks<br>
> Neil<br>
><br>
><br>
> java.lang.IllegalArgumentException: Invalid C size: 0<br>
> at loci.formats.FormatTools.getZCTCoords(FormatTools.java:620)<br>
> at loci.formats.FormatTools.getZCTCoords(FormatTools.java:560)<br>
> at loci.formats.FormatReader.getZCTCoords(FormatReader.java:1099)<br>
> at loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:435)<br>
> at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:312)<br>
> at loci.formats.FormatReader.setId(FormatReader.java:1399)<br>
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)<br>
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)<br>
> at loci.plugins.in.Importer.showDialogs(Importer.java:140)<br>
> at loci.plugins.in.Importer.run(Importer.java:76)<br>
> at loci.plugins.LociImporter.run(LociImporter.java:78)<br>
> at ij.IJ.runUserPlugIn(IJ.java:217)<br>
> at ij.IJ.runPlugIn(IJ.java:181)<br>
> at ij.Executer.runCommand(Executer.java:137)<br>
> at ij.Executer.run(Executer.java:66)<br>
> at java.lang.Thread.run(Thread.java:745)<br>
><br>
><br>
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