[ome-devel] Import/Export

[Ilya Goldberg]

On Jul 22, 2004, at 8:32 AM, Claude Bonnard wrote:

> Hello,
>
> This is very nice to be able to have a first look at data in the 
> system!
Always nice to hear someone had some success, and an independent 
testimonial that things actually work!

> Import&Export
>
> As mentionned in previsous messages, The import is so far seriously
> limited to (so far in my tests) STK and OME's tiff test file.
> Probably, the ome format (from Bitplane) should work.
> "regular tiff" (I mean what people produce every day) as well as  LSM,
> or zvi files were not imported
We're trying to increase file type support.  The released version hangs 
up on some fairly common tiff files, but improvements are coming very 
shortly (we're up to release candidate 2, and we're all hoping this 
week's release candidate 3 will be "the one").
If you would like us to support file types that are in your opinion 
common, you should make each one a separate feature request in 
bugzilla:
http://bugs.openmicroscopy.org.uk/
This will not only serve as a placeholder, but also as a mechanism for 
keeping various discussions, implementation notes, etc all centrally 
located.  There is no guarantee that it will actually be supported - 
we've only got so many heads+hands.

A plug for our partners at VisBio (http://www.loci.wisc.edu/visbio/):
The 3.0 alpha version of VisBio has support for several more file 
formats, and can talk directly to OME.  You can download it here:
http://www.loci.wisc.edu/visbio/alpha.html
(Hope I'm not being too forward, Curtis and Kevin)

> A browser problem? Downloads of small files (such as 
> n2_plate_P24_w1.tif )
> is OK: the download is fast. But the download of average file (a 18MB 
> stk)
>  hanged after a moment, leaving an incomplete 1.1 mb file. Maybe my 
> client's
> configuration? I user Safari 1.0 (ver85.7).
>  Any advice
>  from Mac users would be good!
No problems downloading a 96M file on Safari 1.2.2 (v125.8) (Panther).  
1.0 had several problems, and 1.2.2 is much better behaved - especially 
with the SVG viewer, CSS, etc.

> ->re-importing of this files (the exported ome) was a failure, leading
> to a very rich log of reading the file, checking for duplicate ,
> terminating by a "successful import of 0 file". OK, there is a 
> duplicate
> in the database, since those files came from it. Surprising: the 
> dataset
> I have selected was another one. Should I expect this type of response?
Good question.  We believe that it should not be possible to import 
duplicate images, and this is checked at several levels.  Did you 
expect the duplicate to appear in your import dataset even though it 
was a duplicate?  That's perfectly possible.  The result would be that 
the duplicate would now belong to two datasets.  We weren't sure what 
the expected behavior would be, so this is an important data point.

>
> -> Removal of data? Is there a (web) way to delete a dataset, images in
> a dataset by any method? I  have notice the message "Sorry: Function
> un-implemented"
Deletion is a very hairy business for something that makes certain 
guarantees about the recoverability and consistency of your data.  Yes 
it should be possible, but we haven't implemented it yet.

> , but I am surprised that it is not possible to save the
> same image in another dataset.
You should register this as a bug as well.  Maybe someone will be 
violently opposed?

>
> Probably some of my questions are already solved for next release.. 
> Which ?
This will be called OME 2.2.1  Look for it in a week or so at the 
regular place:
http://cvs.openmicroscopy.org.uk/
If you are very brave (please don't use this in a production 
environment), you can try out the current release candidate (rc2), 
though I would recommend waiting a couple of days for rc3.

Thank you very much for your valuable feedback!

-Ilya


>
> With my best regards,
>
> Claude
>
>
> -- 
> Claude Bonnard Ph.D.
> ISREC (Swiss Institute for Experimental Cancer Research)
> Microscopy, Imaging and Morphology Core Facility [MIM]
> Lab F216
> Ch des Boveresses 155
> CH-1066 Epalinges
> Switzerland
> phone: [41-21]-692-5891
>   fax: [41-21]-652-6933
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