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

[Patrick Riley]

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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