[ome-devel] BD Reader Datetimes of Images / Bio-formats

[Melissa Linkert]

Hi Shawn,

> > MetadataTools.setDefaultCreationDate(store, tiffs[well][0], i);
> 
> Isn't this only storing the first date? The goal is to have the timestamp for each image in the tiff stack, not just the first one. The problem is that sometimes an experiment is stopped and restarted, and the actual datetime stamp of each image is needed.

That will set the acquisition date for each well to be the last modified date
of the first file in the well.

Using the setPlaneDeltaT method in loci.formats.meta.MetadataStore, we
could set the timestamp for each plane in milliseconds since the first
plane was acquired.  Keep in mind though that this may not always be
accurate, especially if the timestamps on the files were changed.  I
wasn't able to find the timestamps anywhere in the metadata files, but maybe
you know of somewhere to find that information.

Regards,
-Melissa

On Thu, Feb 24, 2011 at 10:47:27AM -0600, Garbett, Shawn P wrote:
> > MetadataTools.setDefaultCreationDate(store, tiffs[well][0], i);
> 
> Isn't this only storing the first date? The goal is to have the timestamp for each image in the tiff stack, not just the first one. The problem is that sometimes an experiment is stopped and restarted, and the actual datetime stamp of each image is needed.
> 
> 
> On 2/24/11 7:45 AM, "Melissa Linkert" <melissa at glencoesoftware.com> wrote:
> 
> Hi Shawn,
> 
> Thank you very much for noticing this.  I've just committed a slightly
> modified version of your fix, so the latest trunk build of Bio-Formats
> should solve the problem.
> 
> You can see the relevant commit here:
> 
> http://git.openmicroscopy.org/?p=bioformats.git;a=blobdiff;f=components/bio-formats/src/loci/formats/in/BDReader.java;h=5c9dd968de4ca59e05b2f945246ec4b6c47202cc;hp=550e610e4672a178f6790479aea7bab07c77ef86;hb=96b63e2151d0333e2498d67ac350d5b77a75bdce;hpb=4b62c4f32e0bafc83e3ea5eb4ca98e82e946274d
> 
> > Also I noticed a request for more BD Pathway files. If you have any requests, I could send a set of DVDs.
> 
> What we're most in need of right now is data that has more than 2x2 fields, or
> that can be publicly distributed.  If you are willing and able to set either
> type of data, we would be most appreciative.
> 
> Regards,
> -Melissa
> 
> On Wed, Feb 23, 2011 at 03:06:13PM -0600, Garbett, Shawn P wrote:
> > I noticed some code that slipped through the cracks on this reader.
> >
> >       MetadataTools.setDefaultCreationDate(store, id, i);
> >
> >       int well = i / (fieldRows * fieldCols);
> >       int field = i % (fieldRows * fieldCols);
> >
> > Should instead be something like (so that each image preserves it capture time):
> >
> >       int well = i / (fieldRows * fieldCols);
> >       int field = i % (fieldRows * fieldCols);
> >
> >       MetadataTools.setDefaultCreationDate(store, tiffs[well][field], i);
> >
> > But I'm having trouble debug / compiling an importer with this right now.
> >
> > Also I noticed a request for more BD Pathway files. If you have any requests, I could send a set of DVDs.
> >
> > Shawn Garbett
> 
> > _______________________________________________
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> > ome-devel at lists.openmicroscopy.org.uk
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> 
>