<div dir="ltr">Thanks Melissa,<div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Feb 24, 2014 at 8:09 PM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Lee,<br>
<br>> I do have one question as I'm implementing. This line:<br>
> <a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/CellomicsReader.java#L195" target="_blank">https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/CellomicsReader.java#L195</a><br>
><br>
> prevents the reader from including all of a plate's files unless there is a<br>
> full plate map. It seems a little cruel... just want to make sure it<br>
> belongs there, I have one directory which is a full plate and another which<br>
> is just short of full.<br>
<br>
The main reason for that being in place was to prevent the reader from<br>
being confused when multiple files copied from different plates were<br>
present in the same directory. It's not strictly necessary, and could<br>
definitely be replaced with something a little smarter (which I can<br>
certainly do in an upcoming pull request).<br>
<br></blockquote><div>It really is your call on that - we generally run with grouping off so it doesn't affect us. I'd go with whatever best suits other users and results in a predictable behavior. </div><div><br>
</div><div>--Lee</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Regards,<br>
-Melissa<br>
<br>
On Thu, Feb 13, 2014 at 10:33:03AM -0500, Lee Kamentsky wrote:<br>
> Hi all,<br>
> We packaged a Cellomics dataset as part of the Broad Bioimage Benchmark<br>
> Collection, BBBC018. It's available for download here:<br>
> <a href="http://www.broadinstitute.org/bbbc/BBBC018/BBBC018_v1_images.zip" target="_blank">http://www.broadinstitute.org/bbbc/BBBC018/BBBC018_v1_images.zip</a><br>
><br>
> We renamed the files when we packaged it up - unfortunately. It's not the<br>
> first time that something like this has happened, not under our control.<br>
> When I unpack the zip and use showinf to read the image, I get the<br>
> following stack trace:<br>
><br>
> c:\Temp\bioformats_5.0.0_rc2>showinf -no-upgrade<br>
> c:\Temp\BBBC018_v1_images\00733-actin.DIB<br>
> Checking file format [Cellomics C01]<br>
> Initializing reader<br>
> CellomicsReader initializing c:\Temp\BBBC018_v1_images\00733-actin.DIB<br>
> Exception in thread "main" java.lang.StringIndexOutOfBoundsException:<br>
> String index out of range: 1<br>
> at java.lang.String.charAt(Unknown Source)<br>
> at<br>
> loci.formats.in.CellomicsReader.getWellName(CellomicsReader.java:371)<br>
> at<br>
> loci.formats.in.CellomicsReader.getChannel(CellomicsReader.java:395)<br>
> at<br>
> loci.formats.in.CellomicsReader.initFile(CellomicsReader.java:149)<br>
> at loci.formats.FormatReader.setId(FormatReader.java:1360)<br>
> at loci.formats.ImageReader.setId(ImageReader.java:781)<br>
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)<br>
> at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:993)<br>
> at loci.formats.tools.ImageInfo.main(ImageInfo.java:1075)<br>
> c:\Temp\bioformats_5.0.0_rc2><br>
><br>
> The problem here is that much of the code in the reader assumes that it<br>
> will get a reasonable file name and doesn't catch the cases where the<br>
> assumptions are violated. In this case, the code assumes that the well<br>
> metadata appears after the last underbar: "images\00733-actin.DIB" (it<br>
> should have a format like "A01f00o1.DIB").<br>
><br>
> I'm going to submit a pull request for a patch to this - I have both the<br>
> directory of zip files and a representative directory of Cellomics files<br>
> with their correct file names and I want to make sure what I do works in<br>
> CellProfiler (<a href="https://github.com/CellProfiler/CellProfiler/issues/1043" target="_blank">https://github.com/CellProfiler/CellProfiler/issues/1043</a>).<br>
><br>
> I do have one question as I'm implementing. This line:<br>
> <a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/CellomicsReader.java#L195" target="_blank">https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/CellomicsReader.java#L195</a><br>
><br>
> prevents the reader from including all of a plate's files unless there is a<br>
> full plate map. It seems a little cruel... just want to make sure it<br>
> belongs there, I have one directory which is a full plate and another which<br>
> is just short of full.<br>
><br>
> --Lee<br>
<br>
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<br>
</blockquote></div><br></div></div>