[ome-devel] Supporting per-plane info from Fluoview FV 1000
Patrick Riley
pfr at google.com
Tue Mar 11 16:38:29 GMT 2014
Makes sense. Thanks!
On Tue, Mar 11, 2014 at 8:56 AM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:
> 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
>
--
Patrick Riley
pfr at google.com
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