[ome-devel] ST FilenamePattern & TheT

[Curtis Rueden]

Hi,

Another option (if you don't have a large number of these datasets) is 
to use the VisBio importer, since VisBio can handle numberings of this 
type. It would identify this dataset as:

   
0001--Hp1gamma_si--W00001--P00001--T00<000-150:30>m--SL00000--Q00--F03-- 
I0025.tif

And the uploaded time points will range from 1 to 6, since there are 6 
time steps. However, VisBio isn't smart enough to realize the time 
numbering is actually meaningful metadata here, so those values won't 
wind up in the database. But at least it gets the data in.

-Curtis

Ilya Goldberg wrote:

>
> On Sep 7, 2004, at 9:35 AM, Joshua Moore wrote:
>
>> Interesting problem--
>>
>>    the EMBL folks have in their file names the exact time of imaging  
>> rather than t1, t2, t3,.... e.g.
>>
>> 0001--Hp1gamma_si--W00001--P00001--T00000m--SL00000--Q00--F03-- 
>> I0025.tif
>> 0001--Hp1gamma_si--W00001--P00001--T00030m--SL00000--Q00--F03-- 
>> I0025.tif
>> 0001--Hp1gamma_si--W00001--P00001--T00060m--SL00000--Q00--F03-- 
>> I0025.tif
>> 0001--Hp1gamma_si--W00001--P00001--T00090m--SL00000--Q00--F03-- 
>> I0025.tif
>> 0001--Hp1gamma_si--W00001--P00001--T00120m--SL00000--Q00--F03-- 
>> I0025.tif
>> 0001--Hp1gamma_si--W00001--P00001--T00150m--SL00000--Q00--F03-- 
>> I0025.tif
>>
>> I can certainly get a regex around this, but what is going to happen  
>> to TheT's?
>
>
> Unfortunately, they won't be interpreted correctly.  This is a case  
> where you're encoding meta-data in the file name, and it won't wind 
> up  where its supposed to in the DB.  The FilenamePattern ST really 
> only  works when the filename contains indexes in the 5-d space - I 
> can't  think of a good way for it to decode meta-data.  If there is 
> some other  way of preserving the meta-data, or annotating it later, 
> then you could  put in a mechanism (using a flag?) to get the 
> dimension indexes through  a lexical sort of whatever is in your 
> regex.  But this kind of throwing  away of important stuff is not very 
> good.
>
> The Import module is declared with a type "any" output, so it can  
> already put out any kind of ST.  If you had a way to generate the  
> indexes (using a flag to get them from a sort), you could also 
> (maybe)  specify that the regex should populate a certain ST.  This is 
> much,  much more than we had in mind for FilenamePattern.
>
> With an hour or so's work, you can probably cut and paste your way to 
> a  customized tiff importer that does exactly what you want.
>
> -Ilya
>