The Stace video is located in //nanomia/RAID/database/stace.  If the transcode on beowulffish is back up and running follow this step to process the Stace video.  (Note: currently processing in this manner does not work as modifications to the transcode program on beowulffish has caused problems for transcoding .VOB files.   I have not been able to test this new script due to this bug.  Thus, caveat emptor).

Ssh into beowulffish then copy the stace files to be processed over to the scratch space on beowulffish.  For example:

cp /nanomia/RAID/database/stace/VTS_01_1 /mnt/scratch/doliver

Copy the scripts liburnclipvob and runclipbeovob into the same destination directory:

cp /nanomia/RAID/database/stace/*vob /mnt/scratch/doliver

Process the file using this command (again this script has not been tested and possibly a change to the script may be needed):

runclipbeovob -p stace VTS_01_1

As the current transcode function to convert vob files to ppm images on beowulffish does not work, the transcode command on mako can be used.  There is not enough room currently on mako to process the ppm files so for this reason and for the speed gain on beowulffish copying the newly created ppm files from mako to beowulffish should be the next step.  Process these using the parallel version of the code then convert the output ppm files into an mpeg for easy viewing and delete the input and output frames. (10-31-05. D.cline . transcoding vob files should now work  on beowulffish. It has however not been tested. It is recommended to first try the runclipbeo and transcoding steps on beowulffish first before going through the extra steps to copy the ppm images to mako)

Here are the commands to use:

To create ppm images from vob movies, the user first uses a secure shell into mako.  Create a directory using mkdir.   For example:

mkdir /mako/mnt/disk2/doliver/VTS_01_1

Copy the VOB movie into this directory.  For example:

cp nanomia/RAID/database/stace/VTS_01_1 /mako/mnt/disk2/doliver/VTS_01_1

Change into the directory: 

cd /mako/mnt/disk2/doliver/VTS_01_1

To convert the movie into ppm images issue the following command from the directory 
that contains the vob movie on mako:

transcode -i [VOBmoviename] -o [ppmfilename] -x vob,null -y ppm,null -k -z -g 704x480

ie. transcode -i VTS_01_1.VOB -o f0 -x vob,null -y ppm,null -k -z -g 704x480

The files can be copied onto beowulffish by sshing into beowulffish.  Change into the directory of your choice. For example:

cd /mnt/scratch/doliver/stace/VTS_01_1

Copy the entire mako directory over to beowulffish.

cp /mako/mnt/disk2/doliver/VTS_01_1 .

It is now time to process the ppm files.  Either copy the mbarivis_command file for the respective movie segment from nanomia/RAID/database/stace into the ppm directory and edit it to reflect the parameters and frame numbers you wish to process or create a new text document.

Here is the command to be issued for the first half hour clip: 

runpmbarivision --mbari-cache-size=15 --mbari-min-event-area=40 --mbari-max-event-area=1000 --mbari-tracking-mode=BoundingBox --input-frames=-000000-054983@0 --output-frames=000000-054983@0 --mbari-save-events-xml=../VTS_01_1.events.xml --mbari-save-event-summary=../VTS_01_1.summary f0  VTS_01_1_

This command sets some of the mbarivision parameters to ones that were originally used to process the Stace video.  These can be changed or new ones added depending on the user's needs.  The input frames are dependent on the results from transcode and so, should be changed based on the number of frames created.  The output frames should match the input frames.  The names of documents created from the processing and their path can be changed to reflect the user's preference.  The names of the output frames can be specified by the user.  

Here is a rundown of the commands:
  
runpmbarivision - name of AVED's parallel processing program.

--mbari-cache-size=15 - sets cache size.  Benthic is usually set to 15 while midwater to 10.  This can be played with to find optimal results.

--mbari-min-event-area=40 - sets minimum size of event.  The manganese nodules are very small so this was set to a small number.  Midwater video is set to 50.

--mbari-max-event-area=1000 - sets maximum event size.  Same setting used in midwater.

--mbari-tracking-mode=BoundingBox - sets type of tracking.  Midwater video is set as Kalman Filter while Benthic video is set as bounding box.

--input-frames=-000000-054983@0 - specifies range of input frames to be processed.  A half hour approximates 55000 frames.  This range was derived from number of frames created when the first movie clip was broken into frames using transcode.  

--output-frames=000000-054983@0 - specifies range of output frames processed.  This range was set equal to the number of input frames.

--mbari-save-events-xml=../VTS_01_1.events.xml - specifies the path and name of the xml document to be saved.  This setting saves resulting document in parent directory.

--mbari-save-event-summary=../VTS_01_1.summary  - - specifies the directory path and name of the summary file to be saved.  Saves document in parent directory.

f0  - the name of the seed for the input frames.  This name was specified in the previously issued transcode command.  See above.

VTS_01_1_ - the name of the output frames that are created.  This name can be changed based on user's perference.

Once the output frames are created, the user can remove the input frames by issuing the rm command or move the files if the user wishes to save them by issuing  the mv command.  
To create the mpeg movie, cd into the output ppm directory and issue the command:

runmpeg_encode [processed ppm directory] 704 480 [results directory and name of output file] [start frame] [end frame]

ie. runmpeg_encode . 704 480 /mnt/scratch/doliver/stace/VTS_01_1/VTS_01_1/VTS_01_1.results.mpeg 000000 054983 

The user can then remove or move the output frames depending on the user's needs.