[ome-users] Initializing a movie without loading to mem

[Curtis Rueden]

Hi Guy,


> You are right of course - my OutOfMemoryError was because my javaVM memory
> default (when called from IDL) was too small. I've upped it to -Xmx2G in an
> idlde.ini file and all seems fine now.


Great, glad to hear it. Please let us know if you have any further
questions or problems.

By the way, to call from IDL, are you using the
ij_read_bio_formats.proscript linked from:
   http://loci.wisc.edu/bio-formats/idl

Or did you develop your own way? If you have any improvements or
suggestions for that Bio-Formats IDL page, we would be happy to hear them!

Regards,
Curtis


On Wed, Jul 11, 2012 at 6:01 AM, Guy Blanchard <gb288 at cam.ac.uk> wrote:

> Curtis, thanks for prompt reply.
> You are right of course - my OutOfMemoryError was because my javaVM memory
> default (when called from IDL) was too small. I've upped it to -Xmx2G in an
> idlde.ini file and all seems fine now.
> Apologies.
> Guy
>
>  ____________________________________________
> Dr Guy Blanchard
> Department of Physiology, Development & Neuroscience
> University of Cambridge
> Cambridge CB2 3DY
> UK
> gb288 at cam.ac.uk
> ____________________________________________
>
> On 10 Jul 2012, at 17:34, Curtis Rueden wrote:
>
> Hi Guy,
>
>
>> However, 'FileStitcher->SetId, filename' will never work for some
>> applications where I have too many images to open at any one time (whole
>> series is 70Gb+).
>> Is it possible to initialise the image series with FileStitcher without
>> loading any images, or only a necessary subset?
>
>
> FileStitcher.setId(String) is only supposed to read a single file from the
> detected grouping. It does do a directory listing to synthesize the group's
> file pattern (unless you explicitly pass one in), but only actually parses
> one file. For performance reasons, it assumes all other files in the group
> have the same dimensions.
>
> If you are experiencing different behavior, it is a bug. What are your
> symptoms? How many files, how long does it take for setId to return (if it
> does return)? Or do you get an OutOfMemoryError?
>
> Regards,
> Curtis
>
>
> On Tue, Jul 10, 2012 at 8:32 AM, Guy Blanchard <gb288 at cam.ac.uk> wrote:
>
>> Hi,
>> >From IDL, I'm using your FileStitcher which is working well to identify
>> the FilePattern of groups of images, and then accessing specific images
>> thereafter is all good.
>>
>> However, 'FileStitcher->SetId, filename' will never work for some
>> applications where I have too many images to open at any one time (whole
>> series is 70Gb+).
>> Is it possible to initialise the image series with FileStitcher without
>> loading any images, or only a necessary subset?
>>
>> I couldn't find any class methods that would do the job, and
>> documentation that you point to on your website didn't seem as far as I
>> could see to address this. Sorry if I missed it.
>>
>> Of your Memory Management options, these seem the kind of thing, but I
>> can't see how I can implement them with or combine with FileStitcher.
>>         • Crop the view area
>>         • Open only a subset of images
>>         • Use Virtual Stack
>>
>> Any help gratefully received.
>> Many thanks,
>> Guy
>>
>>
>>
>> ____________________________________________
>> Dr Guy Blanchard
>> Department of Physiology, Development & Neuroscience
>> University of Cambridge
>> Cambridge CB2 3DY
>> UK
>> gb288 at cam.ac.uk
>> ____________________________________________
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20120711/ea497370/attachment.html>