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

[Paul van Schayck]

Hi Melissa,

On Fri, Jan 8, 2016 at 4:22 PM, Melissa Linkert
<melissa at glencoesoftware.com> wrote:
> PyramidTiffReader was intended for a very specific case of pyramided
> BigTIFF files, and won't accept all pyramided BigTIFFs by default - see
> the last couple of lines in isThisType(RandomAccessInputStream).  Can
> you confirm that PyramidTiffReader is being used for these files, and
> not the "plain" TiffReader?

Yes, I'm sure the PyramidTiffReader is being used. I'm a colleague of
Raimond Ravelli. He is one of the authors of the zebra fish em map,
for which this reader was originally developed.

> Whether store is an instance of IMinMaxStore will depend on the context;
> during import into OMERO that should be the case, but if you're testing
> with e.g. the showinf command line tool then that won't happen by
> default.  I'd certainly expect that importing into OMERO with the above
> addition would create the StatsInfo correctly, assuming that StatsInfo
> hasn't been disabled during a command line import.

It's good to know that this indeed the case, as I was starting to
suspect this. Is this even the case when you use the -minmax flag of
showinf?

> 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.

You mention that StatsInfo should not be disabled during import.
Hasn't StatsInfo been disabled automatically for any big files since
OMERO 5.1?

Thanks,

Paul