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

Tue Mar 11 15:56:44 GMT 2014

Hi Patrick,

> 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?

You are correct that adding the 'true' argument is necessary to
correctly populate the Plane objects.  That was only removed because it is
introduced in a prior commit in the same open pull request:

https://github.com/melissalinkert/bioformats/commit/bd88abca7cbe8dbec99e2ad55c70bf08728dbc62

so including it in both commits would have resulted in a Git merge conflict.

Regards,
-Melissa

On Mon, Mar 10, 2014 at 10:35:56PM -0700, Patrick Riley wrote:
> 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