Reading big avi files

[Burt Halvorsen]

Hi,

Wondering how to read more than the first chunk of data in a big avi
file (15.3 GB)

The file is recorded using the Matrox Imaging Library, so the fourcc is "MIL "
The frames are uncompressed
They are 16 bit greyscale

ImageJ reads the first chunk (which is 3183 frames), but leaves out
the remaining 7 AVIX chunks.

I tried the "normal" way and with the virtual stack enabled.

Am I missing out on something, or is there a way.

Final goal is to read the file, find the interesting frames, dump
these out as tiff's or raw. And continue processing these in a medical
workstation.

Any ideas ?

Thanks !

Cheers,
Burt

[Melissa Linkert-2]

Hi Burt,

If you haven't already, you might try using the Bio-Formats plugin for
ImageJ (http://loci.wisc.edu/bio-formats/imagej) to read your AVI file.
If that doesn't work, we would be happy to fix the problem in
Bio-Formats provided that you can send one of the non-working files.

Regards,
-Melissa

On Mon, Aug 09, 2010 at 02:01:05PM +0200, Burt Halvorsen wrote:

> Hi,
>
> Wondering how to read more than the first chunk of data in a big avi
> file (15.3 GB)
>
> The file is recorded using the Matrox Imaging Library, so the fourcc is "MIL "
> The frames are uncompressed
> They are 16 bit greyscale
>
> ImageJ reads the first chunk (which is 3183 frames), but leaves out
> the remaining 7 AVIX chunks.
>
> I tried the "normal" way and with the virtual stack enabled.
>
> Am I missing out on something, or is there a way.
>
> Final goal is to read the file, find the interesting frames, dump
> these out as tiff's or raw. And continue processing these in a medical
> workstation.
>
> Any ideas ?
>
> Thanks !
>
> Cheers,
> Burt

[Chris Richie]

CONTENTS DELETED

The author has deleted this message.

[Chris Richie]

(sorry for the double post, my first one was rejected by the listserv)

I am having a similar problem with my AVI files which are 2GB and uncompressed.  

Although each movie is 9000 frames, only 4638 frames open up - and I do not get an out of memory error.  I also cannot selectively open the frames occurring after 4638 (ex. opening frames 4000-5000 gives just yields a stack with 639 frames).

If I reduce the memory alloted to 1GB (down from 1.4GB) then I can get an OOM error "3371 of 59990 frames will be opened".

I can send a test file, if you can advise me on the best way to transmit it (a 2GB file).

Thanks
chris

[ctrueden]

Hi Chris,

Thanks for the offer to send a test file. I will send you our server
connection information off-list, and we will look into fixing the issue in
Bio-Formats.

-Curtis

On Mon, Aug 23, 2010 at 4:36 PM, Chris Richie <[hidden email]> wrote:

> (sorry for the double post, my first one was rejected by the listserv)
>
> I am having a similar problem with my AVI files which are 2GB and
> uncompressed.
>
> Although each movie is 9000 frames, only 4638 frames open up - and I do not
> get an out of memory error.  I also cannot selectively open the frames
> occurring after 4638 (ex. opening frames 4000-5000 gives just yields a
> stack
> with 639 frames).
>
> If I reduce the memory alloted to 1GB (down from 1.4GB) then I can get an
> OOM error "3371 of 59990 frames will be opened".
>
> I can send a test file, if you can advise me on the best way to transmit it
> (a 2GB file).
>
> Thanks
> chris
> --
> View this message in context:
> http://imagej.588099.n2.nabble.com/Reading-big-avi-files-tp5388730p5454413.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[ctrueden]

Hi everyone,

I am having a similar problem with my AVI files which are 2GB and
> uncompressed.
>
> Although each movie is 9000 frames, only 4638 frames open up - and I do not
> get an out of memory error.
>

Bio-Formats has a fix for the multi-chunk AVI issue in its latest trunk
build. For those interested, you can download Bio-Formats from:
  http://loci.wisc.edu/bio-formats/imagej

-Curtis

On Thu, Aug 26, 2010 at 1:02 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Chris,
>
> Thanks for the offer to send a test file. I will send you our server
> connection information off-list, and we will look into fixing the issue in
> Bio-Formats.
>
> -Curtis
>
>
> On Mon, Aug 23, 2010 at 4:36 PM, Chris Richie <[hidden email]> wrote:
>
>> (sorry for the double post, my first one was rejected by the listserv)
>>
>> I am having a similar problem with my AVI files which are 2GB and
>> uncompressed.
>>
>> Although each movie is 9000 frames, only 4638 frames open up - and I do
>> not
>> get an out of memory error.  I also cannot selectively open the frames
>> occurring after 4638 (ex. opening frames 4000-5000 gives just yields a
>> stack
>> with 639 frames).
>>
>> If I reduce the memory alloted to 1GB (down from 1.4GB) then I can get an
>> OOM error "3371 of 59990 frames will be opened".
>>
>> I can send a test file, if you can advise me on the best way to transmit
>> it
>> (a 2GB file).
>>
>> Thanks
>> chris
>> --
>> View this message in context:
>> http://imagej.588099.n2.nabble.com/Reading-big-avi-files-tp5388730p5454413.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>
>