[ome-users] writing xml chain files for matlab scripts

[Ilya Goldberg]

Hi Anh
There is a problem we discovered with postgres 7.4 in the way we set 
timestamps which worked for all version of postgres until 7.4
This problem was fixed July 28:
http://bugs.openmicroscopy.org.uk/show_bug.cgi?id=227
http://bugs.openmicroscopy.org.uk/show_bug.cgi?id=552

Because you've been installing from CVS since then, this fix will be in 
your code.  However, if you are installing over an existing database, 
the problem will persist because we have not supplied a database patch 
for this (though we will if enough people ask).

You can fix this manually like so:
psql ome
alter table analysis_chain_executions alter column timestamp set 
default 'now()';
alter table ome_sessions alter column started set default 'now()';
alter table ome_sessions alter column last_access set default 'now()';
alter table module_executions alter column timestamp set default 
'now()';
\q

-Ilya



On Aug 10, 2005, at 2:08 PM, Anh Vu wrote:

> I imported and execute the chain and everything ran smoothly. One of
> the things I noticed from view chain results is that the time stamp
> seems to be repeats of the executed chain ID 1, which happens to be
> the time when I first imported a dataset of images into OME.
>
> Anh
>
> On 8/9/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
>> Anh,
>>
>>> There is an ome_pixelsTest.m file in the test folder and I was
>>> wondering if you have a definition file(.ome) so that we can import
>>> the matlab ome_pixelsTest.m file as a module.
>> No ome_pixelsTest.m is a very old file. It probably should be
>> deprecated.
>>
>>> I guess what I wanted is an example file that handles the
>>> input image from the dataset and output it accordingly.
>> I wrote an example XML file for you today. It is based on the Matlab
>> function histeq so it doesn't include a .m file.
>>
>> The Analysis Module:
>>         HistogramEqualization.ome
>> The Analysis Chain:
>>         HistogramEqualization.ome
>>
>> Import the files in this order. The first three are required:
>>
>> src/xml/OME/Analysis/Core/PixelIndicies.ome
>> src/xml/OME/Analysis/Core/PixelSlices.ome
>> src/xml/OME/Analysis/Core/PixelSliceModules.ome
>> src/xml/OME/Analysis/Filters/HistogramEqualization.ome
>> src/xml/OME/Tests/HistogramEqualization.ome
>>
>> Write if you have questions.
>>
>> Tom
>>
>> On Aug 8, 2005, at 9:32 PM, Anh Vu wrote:
>>
>>> There is an ome_pixelsTest.m file in the test folder and I was
>>> wondering if you have a definition file(.ome) so that we can import
>>> the matlab ome_pixelsTest.m file as a module. I guess what I wanted 
>>> is
>>> an example file that handles the input image from the dataset and
>>> output it accordingly. The matlab input and output test files don't
>>> seem to describe how matlab and it def file would handle the inputed
>>> image from the dataset we run against.
>>>
>>> Thanks!
>>> Anh
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>
>>
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