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

[Sebastien Besson]

Hi Fethallah,

the logging level is set by the following line in bfopen.m:
loci.common.DebugTools.enableLogging('INFO');

To decrease the amount of verbosity while opening your image, you
could either increase the logging level, e.g.
loci.common.DebugTools.enableLogging('ERROR');
or if you want no logging at all, you could comment out this line.

Hope this helps,
Sebastien

On 14 Jan 2014, at 15:22, Fethallah Benmansour <fethallah.benmansour at gmail.com<mailto:fethallah.benmansour at gmail.com>> wrote:

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<mailto: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<mailto: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<mailto: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> [mailto: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<mailto: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


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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