[ome-devel] Adding min/max information to PyramidTiffReader

[Sebastien Besson (Staff)]

Hi Paul,

Thanks for getting back to us. We certainly recorded this memoizer limitation in a card but did not have
time to get back to it in time for Bio-Formats 5.2.0.

Unfortunately the required changes to set the minmax within a format reader are breaking. As we are
trying to keep the changes in the Bio-Formats 5.3+ line backwards-compatible, this means we will not be
able to put these changes in place before the next round of breaking changes in Bio-Formats 6.x for which
we currently have no defined roadmap/timeline.

Best,
Sebastien

On 16 Dec 2016, at 12:44, Paul van Schayck <paul at vanschayck.nl<mailto:paul at vanschayck.nl>> wrote:

Hi Melissa,

At the beginning of this year we exchanged a few emails regarding
setting the minmax from within a format reader. This was not working.
You described the problem as the memoizer nog passing along the min
max values. See also below.

I was wondering if you've made any progress on this issue. The linked
Trello card does not exist anymore. This PR looks related, but I'm not
sure it solves it.

https://github.com/openmicroscopy/bioformats/pull/2672

Thanks for any update you can provide on this.

Paul

On Wed, Jan 13, 2016 at 10:19 PM, Melissa Linkert
<melissa at glencoesoftware.com> wrote:
If PyramidTiffReader is definitely being used and the StatsInfo still
doesn't show up in OMERO, then I'd suggest opening a Bio-Formats pull
request with the changes you've made so far, so that we can better see
what the problem might be.

I've pushed my changes to a branch here:

https://github.com/M4I-nanoscopy/bioformats/commit/c8575e6ef17b29b63db88d52fa6b094b23b013eb

When running this I can see this in the log:

2016-01-08 16:44:01,535 INFO  [
loci.formats.ImageReader] (l.Server-3) PyramidTiffReader initializing
2016-01-08 16:44:01,536 INFO  [
loci.formats.in.MinimalTiffReader] (l.Server-3) Reading IFDs
2016-01-08 16:44:01,536 INFO  [
loci.formats.in.MinimalTiffReader] (l.Server-3) Populating metadata
2016-01-08 16:44:01,539 INFO  [
loci.formats.in.BaseTiffReader] (l.Server-3) Populating OME metadata
2016-01-08 16:44:01,539 INFO  [
loci.formats.in.PyramidTiffReader] (l.Server-3) Before minmax

The "Setting minmax" which should be logged does not show up.

Thank you for pushing the commit - I can reproduce the same behavior now.
The details of the problem and what we need to fix are here:

https://trello.com/c/QdCI9tHU/79-memoizer-does-not-pass-along-min-max-values

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


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20161220/15ce389a/attachment.html>