[ome-users] Opera scanner Flex files: bfopen very slow

[Fethallah Benmansour]

Hi Sebastien,

Indeed setGroupFiles(false), solved the problem, and I have modified my m
files accordingly to make it accessible as a parameter at the openbf level.
So, thanks for offering.
Do you know if there's an option such as verbose(0) ?Now, that I know that
the images are loaded properly, I don't want to see all the details each
time an image is loaded.

Cheers,

--
Fethallah


--
Fethallah Benmansour


On Tue, Jan 14, 2014 at 3:49 PM, Sebastien Besson <s.besson at dundee.ac.uk>wrote:

>  Hi Fetallah,
>
>  in general, the API documentation for Bio-Formats should be browsable
> via the Javadocs
> which are located at:
> http://ci.openmicroscopy.org/job/BIOFORMATS-stable/javadoc/ for
> Bio-Formats 4.4.x
> or
> http://ci.openmicroscopy.org/job/BIOFORMATS-5.0/javadoc/ for Bio-Formats
> 5.0.x
>
>  As Christophe already answered, setting setGroupFile(false) before
> calling setId(id) should disable
> the file grouping. Do you think exposing this groupFile option directly in
> the top level bfopen would
> be valuable for you?
>
>  Cheers,
> Sebastien
>
>  On 14 Jan 2014, at 14:20, Fethallah Benmansour <
> fethallah.benmansour at gmail.com> wrote:
>
>  Thanks Christophe, you made my day :-)
>
>  I suspected something as simple as that. Where can I find the complete
> documentation for bf objects ?
>
>  Thanks into advance,
>
>  --
> Fethallah
>
>
> On Tue, Jan 14, 2014 at 3:12 PM, Christophe TREFOIS <
> christophe.trefois at uni.lu> wrote:
>
>>  Did you try setting setGroupFile(false) on the bf object?
>>
>>
>>
>> Best,
>>
>>
>>
>> --
>>
>> Christophe
>>
>>
>>
>> *From:* ome-users-bounces at lists.openmicroscopy.org.uk [mailto:
>> ome-users-bounces at lists.openmicroscopy.org.uk] *On Behalf Of *Fethallah
>> Benmansour
>> *Sent:* mardi 14 janvier 2014 09:52
>> *To:* ome-users at lists.openmicroscopy.org.uk
>> *Subject:* [ome-users] Opera scanner Flex files: bfopen very slow
>>
>>
>>
>> Dear All,
>>
>>
>>
>> I have tried to load one flex file using the matlab function bfopen.
>>
>> If the flex file is isolated in one directory, then the function reads it
>> immediately.
>>
>> However, if the file belongs to the plate directory with many flex files
>> near it, then the loading take about 1.5 hours (not to say forever).
>>
>> In fact, it does the following steps:
>>
>>
>>
>> #
>>
>> Storing well indices
>>
>> #
>>
>> Looking for other .flex files
>>
>> #
>>
>> Looking for files that are in the same dataset as
>> Y:\SomeLocation\Meas_01(2014-01-09_17-02-50)\003003004.flex
>>
>> #
>>
>> Measurement files not found.
>>
>> #
>>
>> Making sure that all .flex files are valid
>>
>> #
>>
>> Grouping together files in the same dataset
>>
>>
>>
>> ...etc
>>
>>
>>
>> The plate is huge indeed (about 20 Gigs of data).
>>
>>
>>
>> Is there a way to force it to read only one specific file, without
>> extracting the metadata from the whole plate ?
>>
>>
>>
>> Thanks into advance,
>>
>>
>>
>> --
>>
>> Fethallah
>>
>
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>
>
>
>   Dr Sébastien Besson
> Open Microscopy Environment / Harvard Medical School
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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