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Hi Neil,
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<div class="">Thank you for raising this issue and providing both sample data and code.</div>
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<div class="">I was able to reproduce the same results as you had reported. The modified ImageConverter code provided appears fine and is not the cause of the problem. Instead the same results can be observed when reading the raw vsi file directly with the
Bio-Formats CellSensReader. I have not yet fully root caused the issue but I have created a ticket to track the ongoing work and you shall be cc’d on any updates to <a href="https://trac.openmicroscopy.org/ome/ticket/13170" class="">https://trac.openmicroscopy.org/ome/ticket/13170</a></div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 9 Mar 2016, at 03:08, Anthony, Neil <<a href="mailto:nantho2@EMORY.EDU" class="">nantho2@EMORY.EDU</a>> wrote:</div>
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<span lang="EN-US" class="">Hi all,<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">I was wondering if anybody has ever seen this kind of error on conversion:<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""><a href="https://drive.google.com/file/d/0BzfJAGNfrgieUFlnbHdsWmkwdU0/view?usp=sharing" style="color: purple; text-decoration: underline;" class="">https://drive.google.com/file/d/0BzfJAGNfrgieUFlnbHdsWmkwdU0/view?usp=sharing</a><o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">If you look at the second channel you see the image is offset by a small amount and there’s bad data at the top, and then on the third image more shift and more bad data. The raw vsi file I’m converting is here:<span class="Apple-converted-space"> </span><a href="https://drive.google.com/file/d/0BzfJAGNfrgieSG9DZ08tRjFfOVU/view?usp=sharing" style="color: purple; text-decoration: underline;" class="">https://drive.google.com/file/d/0BzfJAGNfrgieSG9DZ08tRjFfOVU/view?usp=sharing</a><o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> </span></div>
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<span lang="EN-US" class="">I’m using the ImageConverter.java code but I’ve adapted it a little such that I can use it in a loop without it exiting. Available here: <a href="https://drive.google.com/file/d/0BzfJAGNfrgieWTJyQ0FtdUpnZzQ/view?usp=sharing" style="color: purple; text-decoration: underline;" class="">https://drive.google.com/file/d/0BzfJAGNfrgieWTJyQ0FtdUpnZzQ/view?usp=sharing</a><o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">Essentially all I’ve done is renamed the class and made it public such that I can use it from my code, and I’ve added a function to reset the fields once it’s finished such that it starts fresh without issue. I use this code in
a loop to convert a number of files and pass the args as follows:<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> String[] args = new String[5];<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> args[0] = "-series";<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> args[1] = Integer.toString(series);<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> args[2] = "-overwrite";<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> args[3] = in_id;<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> args[4] = out_id;<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> imgCon.testConvert(writer, args);<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">where in and out id’s are the in and out paths, and the series variable is an int for the series I want to grab.<o:p class=""></o:p></span></div>
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<span lang="EN-US" class=""> </span></div>
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<span lang="EN-US" class="">Any pointers would be much appreciated.<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">Thanks<o:p class=""></o:p></span></div>
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<span lang="EN-US" class="">Neil<o:p class=""></o:p></span></div>
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