[ome-devel] SPW ome-tiffs & how to proceed?

[Munro, Ian]

Thanks Will

Current guesstimates for our typical plate size are 140Mb. 
This might increase in the future but  it’s hard to say. 

I can’t really anticipate what the downloader might want to do.
The intention is to modify FIIMfit to handle whatever sort of ome-tiff that we end up producing. 
They can then look at/analyse  the downloaded  data that way.
If they then want to analyse with different software then bio-formats is out there for them.


Thanks for all the help

Ian



On 18 Aug 2014, at 15:27, William Moore <will at lifesci.dundee.ac.uk> wrote:

> Hi Ian,
> 
> The only downside to "one big SPW file" is that the size of it could get beyond what is practical to download in web.
> 
> We have to build a zip file on the fly that contains all the files in the file-set. This has to happen faster than the http request timeout.
> Then the zip has to be a reasonable size to download, which will depend on bandwidth etc.
> I don't know the upper limit on what will actually work, but I imagine it's possible to have a plate exceed several GB?
> 
> Also, I'm wondering if all software that reads one.tiff will handle SPW data?
> Maybe if your users are using BioFormats to read the data, it may handle SPW just as easily as single ome.tiffs?
> But is that also true of other packages that read one.tiff?
> 
> Anyway, it doesn't affect my web code - just wanted to flag a couple of considerations.
> 
> Should have a PR open soon….
> 
> 
>  Will.
> 
> 
> 
> On 18 Aug 2014, at 15:16, "Munro, Ian" <i.munro at imperial.ac.uk> wrote:
> 
>> Hi again Will
>> 
>> After further discussions  we’re leaning towards putting the whole plate set into one big file. (option 2) in my original post).
>> If you think that’s likely to cause any problems with implementing downloading then please let me know?
>> 
>> Ian
>> 
>> 
>> On 18 Aug 2014, at 13:18, Munro, Ian <i.munro at imperial.ac.uk> wrote:
>> 
>>> Thanks again Will 
>>> 
>>> That information helps a lot. Am I then correct  that if I were to get the binaryOnly option working , as suggested by Curtis, that 
>>> the whole plate would download as it’s a file set?
>>> 
>>> Ian
>>> 
>>> 
>>> 
>>> On 18 Aug 2014, at 13:09, William Moore <will at lifesci.dundee.ac.uk> wrote:
>>> 
>>>> Hi Ian,
>>>> 
>>>> For "fixing downloads", it turns out that there's not much difference whether you have "1 big file for the whole plate"
>>>> or if you've created the plate in OMERO via script/API.
>>>> 
>>>> In both cases, for all the selected images, we just lookup the fileset(s) and download all the linked files.
>>>> 
>>>> I guess the main question is what you want to be in the download:
>>>> 
>>>> If you have "1 big file for the whole plate" then you'll only be able to download the whole plate at a time,
>>>> since there will be a single file-set for all the images.
>>>> 
>>>> If you import the images into OMERO separately, there will be a fileset for each image and you will
>>>> just download the files you need for the selected images (with no SPW info).
>>>> 
>>>> Will.
>>>> 
>>>> 
>>>> 
>>>> On 18 Aug 2014, at 12:57, "Munro, Ian" <i.munro at imperial.ac.uk> wrote:
>>>> 
>>>>> Thanks for the reply  Will
>>>>> 
>>>>> The final decision is down to the PIs I’m trying to gather information about our options.
>>>>> Would it be easier to fix the download for this option than say having 1 big file for the whole plate?
>>>>> 
>>>>> 
>>>>> Ian
>>>>> 
>>>>> 
>>>>> On 18 Aug 2014, at 12:16, William Moore <will at lifesci.dundee.ac.uk> wrote:
>>>>> 
>>>>>> Hi Ian,
>>>>>> 
>>>>>> On 15 Aug 2014, at 15:24, "Munro, Ian" <i.munro at imperial.ac.uk> wrote:
>>>>>>> 
>>>>>>> 6)  Store data as ome-tiffs with no SPW xml but add this info in OMERO after import (either via dataset-to-plate script or the API)
>>>>>>>  Estimated bloat. Unclear -ask OME team
>>>>>>>  Pros. Might allow one file per FOV & work with future plate tools.
>>>>>>>  Cons: Might not work - ask OME team
>>>>>>>            Big software effort and end of project is approaching rapidly.
>>>>>>> 
>>>>>> 
>>>>>> If you are happy to try this approach, I should be able to fix web so that you can download
>>>>>> the original files for selected wells, just as if you'd selected multiple images in a Dataset.
>>>>>> 
>>>>>> Of course, the images you download will have no SPW data associated with them,
>>>>>> but if that's OK for you, then let's give this a try…
>>>>>> 
>>>>>> 
>>>>>> Will.
>>>>>> 
>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> ome-devel mailing list
>>>>>>> ome-devel at lists.openmicroscopy.org.uk
>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>>>>> 
>>>>> 
>>>> 
>>> 
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>> 
>