[ome-devel] ImageConvertor Problem

[Anthony, Neil]

Hi David,
Thanks for setting up the ticket on that.  I hope it’s easy fix.
Please let me know if you need any further details/files etc.

Neil

From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of David Gault (Staff)
Sent: Thursday, March 10, 2016 11:59 AM
To: OME External Developer List
Subject: Re: [ome-devel] ImageConvertor Problem

Hi Neil,

Thank you for raising this issue and providing both sample data and code.

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 https://trac.openmicroscopy.org/ome/ticket/13170

With Thanks,
David Gault

On 9 Mar 2016, at 03:08, Anthony, Neil <nantho2 at EMORY.EDU<mailto:nantho2 at EMORY.EDU>> wrote:

Hi all,

I was wondering if anybody has ever seen this kind of error on conversion:
https://drive.google.com/file/d/0BzfJAGNfrgieUFlnbHdsWmkwdU0/view?usp=sharing
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: https://drive.google.com/file/d/0BzfJAGNfrgieSG9DZ08tRjFfOVU/view?usp=sharing

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: https://drive.google.com/file/d/0BzfJAGNfrgieWTJyQ0FtdUpnZzQ/view?usp=sharing

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:
            String[] args = new String[5];
            args[0] = "-series";
            args[1] = Integer.toString(series);
            args[2] = "-overwrite";
            args[3] = in_id;
            args[4] = out_id;
            imgCon.testConvert(writer, args);
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.

Any pointers would be much appreciated.

Thanks
Neil





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