[ome-devel] Supporting per-plane info from Fluoview FV 1000

[Melissa Linkert]

Hi Patrick,

> I have a patch attached below that I'd like someone to take a look at.
> 
> In /loci/formats/in/FV1000Reader.java
> a bunch of per-plane information is available but not put into the metadata
> store (and therefore won't show up in conversions to OME-TIFF for example)
> 
> The attached patch pulls out these fields from the pty files so that you
> get Plane fields like this:

Thank you very much for the patch.  A very slightly modified version of
your patch is here:

https://github.com/melissalinkert/bioformats/commit/7528d58f35188147c72ca4bfa2533a6fbb9f05a5

and is included in this open Github pull request for review:

https://github.com/openmicroscopy/bioformats/pull/859

If anything looks amiss there, please let me know.  The only changes
from your original patch were to remove the formatting change in FormatTools,
fix the units for DeltaT, and add some error handling when parsing the X and
Y position values.

Once that pull request is marked as being merged, the dev_5_0 branch of
Bio-Formats' Git repository will contain this change (and so it will be
included in the 5.0.1 release).

> A few questions;
> * The units for the PositionX, PositionY, PositionZ are not clear to me.
> The input format gives it's units, but schema documentation just says
> "units are in the microscope reference frame"] and I'm not sure what that
> means.

All that means is that units are not explicitly defined for those
values; they are meant to be stored in OME-XML exactly as they were
written in the original file, without any conversion.

> * I'm relying on Axis 7 containing the stage information, but I have no
> idea if that is always expected. Do you have better documentation?

As far as I know, that's correct.

> * This works on the files I have, but if there are regression tests for
> this format somewhere that need to be updated, I haven't found them (and
> it's not clear to me how to run this, so pointers appreciated).

Data regression tests are run automatically against all commits included
in open Github PRs, the results of which are displayed here:

http://ci.openmicroscopy.org/view/Bio-Formats

As a patch submitter, though, that's typically not something you need to
worry too much about - anything that goes wrong there will be caught by
the code reviewer(s).

Regards,
-Melissa

On Fri, Mar 07, 2014 at 08:16:55AM -0800, Patrick Riley wrote:
> I have a patch attached below that I'd like someone to take a look at.
> 
> In /loci/formats/in/FV1000Reader.java
> a bunch of per-plane information is available but not put into the metadata
> store (and therefore won't show up in conversions to OME-TIFF for example)
> 
> The attached patch pulls out these fields from the pty files so that you
> get Plane fields like this:
> 
>           <Plane DeltaT="0.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4184E7" TheC="0" TheT="0" TheZ="0"/>
>          <Plane DeltaT="0.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4184E7" TheC="1" TheT="0" TheZ="0"/>
>          <Plane DeltaT="0.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4184E7" TheC="2" TheT="0" TheZ="0"/>
>          <Plane DeltaT="1512.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4187E7" TheC="0" TheT="0" TheZ="1"/>
>          <Plane DeltaT="1512.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4187E7" TheC="1" TheT="0" TheZ="1"/>
>          <Plane DeltaT="1512.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4187E7" TheC="2" TheT="0" TheZ="1"/>
>          <Plane DeltaT="3025.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.419E7" TheC="0" TheT="0" TheZ="2"/>
>          <Plane DeltaT="3025.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.419E7" TheC="1" TheT="0" TheZ="2"/>
>          <Plane DeltaT="3025.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.419E7" TheC="2" TheT="0" TheZ="2"/>
>          <Plane DeltaT="4537.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4193E7" TheC="0" TheT="0" TheZ="3"/>
>          <Plane DeltaT="4537.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4193E7" TheC="1" TheT="0" TheZ="3"/>
>          <Plane DeltaT="4537.0" PositionX="3.1997411E7"
> PositionY="4.0177623E7" PositionZ="2.4193E7" TheC="2" TheT="0" TheZ="3"/>
> 
> A few questions;
> * The units for the PositionX, PositionY, PositionZ are not clear to me.
> The input format gives it's units, but schema documentation just says
> "units are in the microscope reference frame"] and I'm not sure what that
> means.
> * I'm relying on Axis 7 containing the stage information, but I have no
> idea if that is always expected. Do you have better documentation?
> * This works on the files I have, but if there are regression tests for
> this format somewhere that need to be updated, I haven't found them (and
> it's not clear to me how to run this, so pointers appreciated).
> * I also haven't programmed in Java for a while, so if I've done random
> stuff wrong, please let me know!
> 
> Thanks.
> -- 
> Patrick Riley
> pfr at google.com


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