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

Tue Mar 11 05:35:56 GMT 2014

Thanks Melissa.

I noticed that you removed this part of the patch

-    MetadataTools.populatePixels(store, this);
+    MetadataTools.populatePixels(store, this, true);

My read of the code was that was needed to populate the TheC, TheT, TheZ
values in the Plane objects so that you can actually relate the metadata to
the correct files. Do I understand this correctly?

On Mon, Mar 10, 2014 at 8:23 PM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:

> 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
>
>
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>

-- 
Patrick Riley
pfr at google.com
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