[ome-devel] In house written .ims file question
Melissa Linkert
melissa at glencoesoftware.com
Mon May 15 20:21:29 BST 2017
Hi Neil,
> 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
As mentioned previously, Bio-Formats does not currently support the
"Noc" attribute, as we do not have any .ims files that use the current
version of the Imaris 5.5 specification. Bio-Formats reads the
channel count from the "NumberOfChannels" attribute; we can certainly
update it to support "Noc", but we would first need a file for testing
purposes.
> 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.
>
> Do you have a .ims file you can share that I can compare to, and hopefully
> add the missing attributes?
Unfortunately, no, we don't have any publicly available .ims files.
If you are able to open your files in Imaris, then this is almost
certainly a problem we need to fix in Bio-Formats. We would need a
test file to ensure a proper fix though, so if you are willing to send
one of your files please do so here:
http://qa.openmicroscopy.org.uk/qa/upload/
Uploaded files are treated as confidential, and are only used by the
OME team for internal testing unless you give us explicit permission
to make them public.
Regards,
-Melissa
On Mon, May 15, 2017 at 1:39 PM, Anthony, Neil <nantho2 at emory.edu> wrote:
> Hi Melissa, I hope the weekend was fun.
>
> 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
>
> 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.
>
> Do you have a .ims file you can share that I can compare to, and hopefully
> add the missing attributes?
>
> Thanks
> Neil
>
>
> java.lang.IllegalArgumentException: Invalid C size: 0
> at loci.formats.FormatTools.getZCTCoords(FormatTools.java:620)
> at loci.formats.FormatTools.getZCTCoords(FormatTools.java:560)
> at loci.formats.FormatReader.getZCTCoords(FormatReader.java:1097)
> at
> loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:434)
> at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:311)
> at loci.formats.FormatReader.setId(FormatReader.java:1397)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
> 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:217)
> at ij.IJ.runPlugIn(IJ.java:181)
> at ij.Executer.runCommand(Executer.java:137)
> at ij.Executer.run(Executer.java:66)
> at java.lang.Thread.run(Thread.java:745)
>
> ________________________________
> From: Anthony, Neil
> Sent: Thursday, February 2, 2017 10:44:34 AM
> To: Melissa Linkert
>
> Subject: Re: [ome-devel] In house written .ims file question
>
>
> Hi Melissa,
>
> 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
>
> 435 in ImarisHDFReader.java:
>
> int[] zct = getZCTCoords(no);
> from the exception:
>
> at
> loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:435)
>
> Maybe it is something your end, I don't know.
>
> 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.
>
> Thanks for your time.
>
> Neil
>
>
> ________________________________
> From: Anthony, Neil
> Sent: Tuesday, January 31, 2017 9:13:17 PM
> To: Melissa Linkert
> Subject: RE: [ome-devel] In house written .ims file question
>
> Hi Melissa, thanks for the details.
>
> I think the error might be my end. I'll double check that all the
> attributes match up and post the result here asap.
>
> Thanks for your time.
>
> Neil
>
>
> -----Original Message-----
> From: Melissa Linkert [mailto:melissa at glencoesoftware.com]
> Sent: Monday, January 30, 2017 11:55 AM
> To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk>
> Cc: Anthony, Neil <nantho2 at emory.edu>
> Subject: Re: [ome-devel] In house written .ims file question
>
> Hi Neil,
>
>> I have written some matlab code to write .ims files, but on opening
>> with Bioformats I get the below pasted error list. The files open
>> fine with Imaris (the underlying file format is listed as v5.5, but it
>> appears that different things in the HDF5 structure come and go with
>> different versions of Imaris. I'm currently using 8.4)
>>
>> Do you guys have a breakdown of the group and attribute structure that
>> Bioformats uses?
>
> Our reference page for Imaris HDF is:
>
> http://www.openmicroscopy.org/site/support/bio-formats5.3/formats/bitplane-imaris.html
>
> and the relevant section of Bio-Formats' Imaris HDF reader:
>
> https://github.com/openmicroscopy/bioformats/blob/v5.3.2/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java#L480
>
> 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
> http://open.bitplane.com/Default.aspx?tabid=268). 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.
>
> 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.
> Files can be uploaded to:
>
> http://qa.openmicroscopy.org.uk/qa/upload/
>
> Regards,
> -Melissa
>
>
> On Mon, Jan 30, 2017 at 8:46 AM, Anthony, Neil <nantho2 at emory.edu> wrote:
>> Hi all, I hope the data treats you well.
>>
>> I have written some matlab code to write .ims files, but on opening
>> with Bioformats I get the below pasted error list. The files open
>> fine with Imaris (the underlying file format is listed as v5.5, but it
>> appears that different things in the HDF5 structure come and go with
>> different versions of Imaris. I'm currently using 8.4)
>>
>> Do you guys have a breakdown of the group and attribute structure that
>> Bioformats uses?
>>
>> Thanks
>> Neil
>>
>>
>> java.lang.IllegalArgumentException: Invalid C size: 0
>> at loci.formats.FormatTools.getZCTCoords(FormatTools.java:620)
>> at loci.formats.FormatTools.getZCTCoords(FormatTools.java:560)
>> at loci.formats.FormatReader.getZCTCoords(FormatReader.java:1099)
>> at
>> loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:435)
>> at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:312)
>> at loci.formats.FormatReader.setId(FormatReader.java:1399)
>> at
>> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
>> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
>> 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:217)
>> at ij.IJ.runPlugIn(IJ.java:181)
>> at ij.Executer.runCommand(Executer.java:137)
>> at ij.Executer.run(Executer.java:66)
>> at java.lang.Thread.run(Thread.java:745)
>>
>>
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>
> ________________________________
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
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