vars-users Mailing List for Video Annotation and Reference System

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j.d...@ho... 		 	   		  
Dear Colleague,

I installed VARS and I run it following the instructions given but in 
the interface (see the image atached) I can not load a video. Please 
tell me how I can integrate videos to annotate them.

Regards,

A. Belaïd

-- 
============================================================================
Prof. Abdel Belaïd

Address Lab: LORIA UMR 7503
Campus scientifique, B.P. 239
54506 Vandoeuvre-Les-Nancy, France
Tel: (33)3 83 59 20 82 Mobile: (33) 6 13 27 47 76 Fax: (33)3 83 27 83 19

Home page : http://www.loria.fr/~abelaid/
Research Group Web Site : http://read.loria.fr/
=============================================================================

Hello vars , this is daiki nomura from Japan.

I would like to use vars on Windows XP, but when I started
knowledgebase.bat it shows me lots of errors "connection
to port 1527 refused". I stopped firewall and virus
checker but the results were same. 

testconn.bat says "there is no path"

varsCreateDB.bat shows me new window and it seems to me
derby database server process, but derby shut down soon
saying "Invalid authentication".

This must be a FAQ (I saw FAQ) but I stucked... What shoud
I do ?

ps.
Cmd terminal shows Japanese error messages, so above
"messages" probably not the same one of English. I hope
they make sense.

regards

--------------------------------------
Enjoy MLB with MAJOR.JP! Ichiro, Matsuzaka, Matsui, and more!
http://pr.mail.yahoo.co.jp/mlb/

Hi Gordon,

> I'm trying to install the latest version of VARS, and having some  
> problems.
>
> I've never encountered maven before, so it could easily be problems  
> at my end.
>
> I've checked out qtx4j from SVN and when I try mvn project I get  
> the following
> error:
>
> [ERROR] BUILD ERROR
> [INFO]  
> ---------------------------------------------------------------------- 
> --
> [INFO] Failed to resolve artifact.
>
> No versions are present in the repository for the artifact with a  
> range [1.1,)
>   org.mbari:mbarix4j:jar:null
>
> What should I do next?
>

Maven usually fetches dependencies across the internet from maven  
repositories. mbarix4j isn't stored in any publicly available  
repository yet, but it is included in VARS SVN. You have to install  
it manually into your local repository (stored in $HOME/.m2/ 
repository). The way to do this is:
    1) cd to the root of the VARS project
    2) at the command line run: mvn install:install-file - 
Dgroup=org.mbari -DartifactId=mbarix4j -Dversion=1.2 -Dpackaging=jar - 
Dfile=./vars-ui/src/main/lib/mbarix4j-1.2.jar

Also, you're the very first person to ask to build VARS from source  
outside of MBARI. So, I expect you may run into some other issues.  
Here's a few that you should be aware of:
	1) You will want to setup a testing database for running VARS  
against. I don't recommend running tests against your production  
database. The strategy you take is up to you, but what I've found  
that works very well is to setup a job to copy/duplicate your  
production database to a development one every night. This way you  
can run tests against your 'real' database without worrying that your  
testing db is drifting away from what your production one is.
	2) You will need to configure VARS for your database during build.  
To do this you can modify the file vars-deploy/vars-conf/src/main/ 
filters/dev.properties
	3) When building VARS run: mvn clean install -Denvironment=dev - 
Dmaven.test.skip=true
	4) A standalone VARS application will be built to vars-deploy/vars- 
app/target/vars-app-[VERSION]-standalone.zip. If everything is setup  
right you can just unzip the installation and run VARS from the batch  
files or shell scripts.
	5) I just added support for building VARS webstart applications to  
the build script. Unfortunately, web start applications require that  
the JARS be signed with a security certificate and I didn't want to  
check the details of our certificate into a public SVN repositiory.  
So for the build to fully succeed you will either need to: A) Create  
a security certification and setup the details of it in vars-deploy/ 
vars-jnlp/build.xml or B) disable the building of the vars-jnlp  
module. To disable the build you will need to edit vars-deploy/ 
pom.xml and comment out the line: <module>vars-jnlp</module>

If you just want to build VARS and worry about configuring it for a  
database later. Do the following:
	1) Build VARS
	2) Unzip vars-deploy/vars-app/target/vars-app-[VERSION]- 
standalone.zip somewhere (I'll refer to this location as VARS_HOME).
	3) Find VARS_HOME/lib/vars-conf-[VERSION].jar. This contains the  
configuration information.
		A) Unzip it somewhere
		B) copy all the *.properties and *.xml files from it into VARS_HOME/ 
conf.
	4) Get rid of VARS_HOME/lib/vars-conf-[VERSION].jar. (i.e. delete it  
or copy it somewhere else)
	5) Open VARS_HOME/conf/vars.properties and change the line:
		castor.database=conf/vars.castor-cfg.xml to
		castor.database=vars.castor-cfg.xml
	6) You can configure VARS for your database by editing VARS_HOME/ 
conf/vars.castor-cfg.xml

Anyway, if you have any other questions, I'm happy to help
Brian Schlining
Software Engineer
http://www.mbari.org

Hi Roger,

There's a new release of VARS at http://vars.sourceforge.net/  
(vars-4.1-alpha) with initial support for annotating video files.  
Note: there is one new prerequisite for running VARS; you will need  
to install Java Advanced Imaging (See http://java.sun.com/products/ 
java-media/jai/downloads/download-1_1_2.html). If you have any  
questions, please don't hesitate to contact me.

Cheers
Brian

> Many thanks for the feedback and advice.
>
> Regards
>
> Roger Coggan
>
> Hi Roger,
>
>> I would be extremely grateful if you could keep me informed of any  
>> developments you are making that may help solve (or avoid) our  
>> current problems.
>> We halted progress on our VARS evaluation in December 2006, but  
>> now have a need to progress (new Financial year in the UK - new  
>> projects coming on-line).
>
> No problem. I'll be sure to send you information on VARS as I make  
> changes.
>
>>  We run Dell branded PC systems (usually Windows XP), and  
>> currently I want to get VARS working on a stand-alone Video  
>> Workstation (i.e. not networked into the corporate LAN).
>
> Just a note. VARS is really designed as a client that works against  
> a relational database. You can run the database on the same  
> computer as VARS, but you don't have too and in most cases you  
> probably want to have the database on a dedicated database server.
>
>> The workstation had been purchased as a video editing and analysis  
>> suite, and we are currently loading up existing digital video and  
>> digitising old VHS video, ready for (non-linear) editing and  
>> archiving. The next step is to get VARS up and running so that we  
>> can progress the analysis side of the work.
>>
>> This leads me to a query. Will VARS work on digital &/or digitised  
>> video files?
>
> Yes. I'm trying put a new release of VARS that works with video  
> files on the sourceforge web site. I had hoped to roll it out last  
> week, but I ran into a few bugs on PC's that I'm still working  
> through. This release (VARS-4.1) should be considered 'alpha'  
> quality, but I expect to release updates fairly rapidly as I get  
> feedback from our internal users.
>
> Currently, there are some requirements for the format of the video  
> files. They are:
> 1) They need to be in a QuickTime movie container. The codec of the  
> movie doesn't matter so much as long as it can be played in a  
> QuickTime player.
> 2) The movie container needs to have a timecode track for indexing  
> into the movie. Adding a timecode track is pretty simple to do. If  
> you have questions about how to go about it let me know. Your non- 
> linear editor should be able to do that though.
>
>> I was party to a discussion recently that suggested VARS (and the  
>> French 'Adelie' system) would only work with non-digital, tape  
>> formats (e.g. VHS, SVHS).
>> Since digital video has been around for some time, and the push is  
>> now to move to High Definition digital video, I thought this  
>> suggestion may be based on rumour rather than fact.
>> Please could you advise.
>
> Until this year we did not use digital video files, so VARS did not  
> work with them. This is changing this year and we're actually  
> putting together a pretty interesting system. (See http:// 
> www.mbari.org/mars/general/eits.html). The upshot is that we will  
> have a camera running 24/7 sending video back to shore. This video  
> is stored in digital files. Rather than have someone watch all the  
> video, we have put together a software system that 'watches' the  
> video and notes events/objects of interest. These events are stored  
> in a VARS database. A some point a person can review the events on  
> the video and identify the objects to some greater level of detail  
> using VARS.
>
>>  Could you also advise if there is a way of reading-in a GPS  
>> navigation file into VARS, so that the video material can be  
>> georeferenced (rather than merely time-stamped).
>
> What we do at MBARI is we have a separate software application that  
> combines the VARS data with geo-referenced information. The data in  
> VARS is stored in relational database tables and can be updated and  
> modified by using standard SQL. Writing a script or application to  
> update VARS annotations with locations is relatively simple and  
> your tech department should be able to help you.
>
>
>> I should explain that, by profession, I am a biologist. However, I  
>> do have support of a good IT and technical department who are  
>> helping in this evaluation.
>>
>
> I'll be sure to keep that in mind ;-)
>
> Cheers
>
> -- B

Brian Schlining
Software Engineer
http://www.mbari.org

Hi Kerry,

> I have recently downloaded the VARS software to investigate whether =20=

> it would be of use in analysing my deep-sea video data. I have =20
> followed the instructions on how to install the programme in =20
> windows and have installed Java and QuickTime for JAVA. I have =20
> managed to edit the file bin/derbysetup.bat, adding my IP address =20
> and domain name. However, the instructions then say to edit the =20
> line <param name=3D=E2=80=9Durl=E2=80=9D value=3D=E2=80=9Djdbc:=E2=80=A6=
.=E2=80=9D  in the file conf/=20
> vars_database.xml. I cannot find a file by this name. I have =20
> searched other xml files for the terms <param name=3D=E2=80=9Durl=E2=80=9D=
 =20
> value=3D=E2=80=9Djdbc:=E2=80=A6.=E2=80=9D  and found them in a file =
called vars.castor-=20
> cfg.DERBY.xml, which I have edited in the way described in the =20
> instructions.
The fix may be as simple as as copying the file vars.castor-=20
cfg.DERBY.xml to vars.castor-cfg.xml. The DERBY file is just a =20
template I've provided for convenience. The VARS software is actually =20=

looking for vars.castor-cfg.xml.

> However I have just tried to open the annotation software and it =20
> comes up with an error saying it cannot load the knowledge =20
> database. Any idea what I am doing wrong?
>
You're not doing anything wrong, the instructions are probably =20
outdated. (i.e. the software changes faster than the =20
documentation...sorry, I'll try to fix that in the next release). =20
Anyway, It sounds like you're on the right track. The file =20
vars_database.xml was changed to vars.castor-cfg.xml.

Are you going to run it on windows? There may be a bug in the =20
varsSetup.bat file. I've attached the corrected one. I do most of my =20
development on a Mac so sometimes a bug sneaks through in my DOS =20
scripting.

If you have any problems please feel free to contact me and I'll try =20
to get you up and running. I'll try to roll out a new release in the =20
next day or 2 that addresses these issues.

-- B
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Brian Schlining
MBARI
Software Engineer

Carpe Cerevisi

=EF=BF=BC

Hi Gordon,

How's it going?

> We have a project where we will be recording video from a camera  
> mounted on
> trawl net headlines using a Fast Forward Video Outrider DVR
> http://www.ffv.com/Support/OutriderTechRef21.pdf .
>
> This stores video on disk in QuickTime files using the Zoran JPEG  
> codec.
>
> My understanding is that VARS currently doesn't work with video  
> files (only
> tapes) but you are in the process of developing support for video  
> files.
>
> Could you please confirm that this is correct, and if so what is a  
> realistic
> (but not binding) estimate on when this would be working.

That's correct. As we speak, I'm adding support to VARS for Video  
Files. I expect to have the first milestone release of VARS with  
QuickTime Movie support out in a few weeks. The goal of this release  
is to have support for annotating video files; however, the workflow  
will still need some polishing.

Here's a few notes about it that you might want to be aware of:
	- Currently files will be referenced by a URL. The idea is to store  
movie files on a web server, although local 'file' URL's will work  
to. To open up a movie file in VARS you will need to supply a full  
URL to the location of the file. URL's tend to be obnoxiously long so  
I expect this to be a bit of an annoyance. I'll look at improving  
this later on.
	- I've wrestled with how to index movie files. There are 2 options:  
runtime (i.e. elapsed time since the start of the movie) or using a  
time-code track. The time-code track works much, much better. So the  
first release will only work with files that have a time-code track.  
I'll be providing a tool that allows you to easily add a time-code  
track to existing QuickTime movies. If you want to add time-code  
tracks as part of your workflow I can send you a code snippet in Java  
to get you started.

> We plan on starting collecting the data in May, and would like to  
> be able to
> process it not too long afterwards.

No worries,  I expect to have a release out by May.

Cheers
B

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Brian Schlining
MBARI
Software Engineer
br...@mb...
(831)775-1855
http://www.mbari.org/staff/brian

Quid quid latine dictum sit, altum videtur

Hi Genoveva,
> Ok, I think we are making progress... but not quite there yet. =20
> Turns out that the name I was using was indeed wrong so I changed =20
> it in both places (to goteborg-bc8ce1), and now I get the database =20
> to start, but not the VARS Annotation application. When I run =20
> varsAnno.bat, VARS tries to initialize but soon I get two error =20
> messages:
>
> 1. =E2=80=9CQuickTime for Java not installed=E2=80=9D which is a lie, =
because =20
> QuickTime IS installed in my machine!

OK, what this means is that the Java installed on your machine can't =20
find the QuickTime libraries. It's annoying, but there's a relatively =20=

easy fix for this.
1) Look in the directory C:\Program Files\Java and find the JRE with =20
the highest number (It will be something like C:\Program Files\Java=20
\jre1.5.0_10).
2) Open that directory and look in lib\ext for QTJava.zip (The full =20
path will be something like C:\Program Files\Java\jre1.5.0_10\lib\ext).
3) If QTJava.zip isn't there, it may have been installed under a =20
different version of Java. You can run a windows search in the C:=20
\Program Files\Java directory for QTJava.zip. If you find it, copy it =20=

to the lib\ext directory of your newest JRE.
	- If you don't find QTJava.zip, you should download the =
QuickTime =20
installer or the iTunes installer and run it again. It will put =20
QTJava.zip in the correct place.

Be aware that if you upgrade Java later on, you'll have to copy it to =20=

the new Java's lib\ext directory or reinstall QuickTime.

> 2. =E2=80=9CRXTX, the serial libraries used to support serial port I/O =
are =20
> missing or not properly installed. VARS cannot operate =E2=80=A6 =
exiting =20
> VARS=E2=80=9D, which I don=E2=80=99t know what it means
RXTX is used to talk to VCR's through a serial port. This one is my =20
bad, I've attached a new varsSetup.bat that should fix this.

  =EF=BF=BCSorry that you're having to suffer through the installation. =
:-=20
( But you're almost there! Let me know if you get it running. Once =20
it's up I can give you a few more tips and pointers for configuring =20
VARS.

Cheers

B

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Brian Schlining
MBARI
Software Engineer
br...@mb...
(831)775-1855
http://www.mbari.org/staff/brian

This is your last chance. After this, there is no turning back. You =20
take the blue pill - the story ends, you wake up in your bed and =20
believe whatever you want to believe. You take the red pill - you =20
stay in Wonderland and I show you how deep the rabbit-hole goes.
	~ Morpheus (The Matrix)

Hi Mike,
> Thanks for your help this morning.  I am going through a reinstall =20
> of previous versions of the VARS to mirror the setup Yingjie was =20
> using for development purposes.  In the process, I am running into =20
> similar problems loading the knowledgebase.  I did exactly what we =20
> did on the phone w/ v. 3.0.1, but still running into errors w/ =20
> versions 1.0.3 and 1.0.4.  No problems with 0.9.3 though.  Are the =20
> older versions still supported or have the updates nullified there =20
> utility?  I=92ve attached a log of the debug script.
The log says you are trying to connect to 'scira' but it's either =20
unreachable by your computer or the derby database wasn't started. =20
Were you able to start derby using derbyStart.bat?

>
> Thanks,
>
> Mike
>
>
>
> Michael P. McKee (I.T. Specialist / Research Assistant)
>
> National Undersea Research Center
>
> University of Connecticut - Avery Point
Brian Schlining
Software Engineer
http://www.mbari.org

Hi Genoveva

> I really appreciate your help with this. I think it would be a good =20=

> thing for us here at TMBL to get our ROV data organized, after all =20
> these years, and it does seem like VARS is the right tool for that. =20=

> However, my computer skills are just those of a user, not a =20
> programmer or developer or anything like that, so I=92m afraid it=92s =20=

> going to take me some effort (and time!) to get this program to run =20=

> on my machine.
No worries, I'm happy to help get you up and running. The log you =20
sent me was very helpful; it showed that the database wasn't starting

In a nutshell, there's 2 things that need to be configured to get =20
VARS up and running:
1) Configure a database server. In your case you are running the =20
'Derby' that comes with VARS. To get Derby up and running you'll need =20=

to edit in conf/derbySetup.bat. (More about that below)
2) Tell VARS about the database (where it lives and what kind of =20
database it is) This is done in conf/vars.castor-cfg.xml

> I have tried your suggestions and these are the results:
>
>
>
> 1)      vars.castor-cfg.DERBY.xml is a template file that I assist =20
> folks with setting up VARS. You have to change the name of it to =20
> vars.castor-cfg.xml in order for VARS to see it.
>
>
>
> There is another file in this directory with that name already, so =20
> it won=92t let me change it. I have now also edited this one (ie, =20
> conf/vars.castor-cfg.xml) to have the right machine name (which by =20
> the way is =93goteborg-bc8ce1.gu.se=94 in case it helps)
OK.  The contents of conf/vars.castor-cfg.xml should look like this:

<?xml version=3D"1.0" ?>
<!DOCTYPE databases PUBLIC
     "-//EXOLAB/Castor JDO Configuration Schema Version 1.0//EN"
     "http://castor.exolab.org/jdo-conf.dtd">
<!--
     $Id: vars.castor-cfg.xml 406 2006-10-31 23:30:13Z hohonuuli $
     sets up JDBC connection for Castor
-->
<jdo-conf>

   <database name=3D"vars" engine=3D"derby">

     <!--
       We are wrapping our driver class with a connection pool =20
managed by apache
       DBCP. DBCP should be able to wrap any driver class with a =20
connection pool.
     -->
     <data-source class-name=3D"org.apache.commons.dbcp.BasicDataSource">
       <param name=3D"driver-class-name" =20
value=3D"org.apache.derby.jdbc.ClientDriver" />
       <param name=3D"username" value=3D"varsuser" />
       <param name=3D"password" value=3D"vars0sourceforge" />
       <param name=3D"url" value=3D"jdbc:derby://goteborg-bc8ce1.gu.se:=20=

1527/VARS;user=3Dvarsuser;password=3Dvars0sourceforge" />
       <param name=3D"max-active" value=3D"10" />
     </data-source>

     <mapping href=3D"vars.castor.xml" />
     <mapping href=3D"annotation.castor.xml" />
     <mapping href=3D"knowledgebase.castor.xml" />
   </database>

   <transaction-demarcation mode=3D"local" />
</jdo-conf>
<!--
     NOTE: Despite the fact that you specify a database name here and =20=

in the
     code, the database that Castor uses is the default database of =20
the user.
-->

> 2) You can see if you can start your derby database server by =20
> running derbyStart.bat
>
>
>
> Nothing seems to happen when I run this file. The command prompt =20
> window opens up, runs something, and then closes down again right =20
> away (perhaps this is what is supposed to happen??)

Did you edit conf/derbySetup.bat? There's a line in that file like this:

SET DERBY_SERVER_HOST=3Dcomputer.domain.com

You will need to change it to this:

SET DERBY_SERVER_HOST=3Dgoteborg-bc8ce1.gu.se

Once you've changed that, try running derbyStart.bat again. A window =20
should pop and stay open and say something like 'Apache Derby Network =20=

Server - 10.2.1.6 - (452058) started and ready to accept connections =20
on port 1527 at 2007-02-23 16:31:54.252 GMT '. If it doesn't stay =20
open, then it means the name of your machine isn't quite right. You =20
can try running derbyStart.bat again using goteborg-bc8ce1 or =20
localhost instead of goteborg-bc8ce1.gu.se and see if it starts. Once =20=

you get the database to start you should modify conf/vars.castor-=20
cfg.xml to use the same name (ie. ...jdbc:derby://goteborg-=20
bc8ce1:1527... or ...jdbc:derby://localhost:1527...

Let me know if you get it working.
Cheers
B

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Brian Schlining
MBARI
Software Engineer
br...@mb...
(831)775-1855
http://www.mbari.org/staff/brian

Age. Fac ut gaudeam.

Hi Mike,

Just following up a bit more....
> I am definitely willing to learn but, since Yingjie is off the =20
> project and unreachable, I am fumbling around in the dark trying to =20=

> complete the GPS logging integration.  Could you take a quick look =20
> at the report and let me know if we=92re close.
LIke I mentioned, I look into it as a soon as I can but it's likely I =20=

won't get to it until after Christmas (I'm off on vacation soon!!)

> Also, for a novice=85..would it be more prudent to use Apache Ant or =20=

> Eclipse IDE to build and compile the VARS?
Definitely use Ant for building. You'll want to checkout VARS from =20
SVN (subversion - I'm no longer using CVS for VARS). Details for the =20
checkout can be found at http://sourceforge.net/svn/?group_id=3D151101. =20=

If you're running on windows you can use a free SVN client for the =20
checkout, one I like is http://www.smartcvs.com/smartsvn/. Once you =20
have the code checked out you can run ant. Here's a few tips for =20
using ant with VARS:

'ant about' ---> Explains the projects structure
'ant -p' ---> Explains the different ant targets that you can call
'ant all' ---> You should try running this the first time you build =20
vars. It fetches the dependencies and builds a testing database.
'ant test.anno', 'ant test.kb', 'ant test.query' ---> Launch the =20
various apps running against the testing database.

In order to run your tests you will need to modify the =20
'build.properties' file. Change the line: JDBC_URL_TEST  =3D =20
jdbc:derby://oyashio.shore.mbari.org:1527/=20
VARS;user=3Dvarsuser;password=3Dvars0sourceforge. The url should match =20=

the machine you're building, so you'll need to change =20
'oyashio.shore.mbari.org' to match your computer; it'll be something =20
like:
JDBC_URL_TEST  =3D jdbc:derby://computername.domain.edu:1527/=20
VARS;user=3Dvarsuser;password=3Dvars0sourceforge

I've entered your code into our issue tracker so it'll remind me to =20
take a look at it.
Cheers
B

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Brian Schlining
MBARI
Software Engineer
br...@mb...
(831)775-1855
http://www.mbari.org/staff/brian

I went to the woods because I wished to live deliberately, to front =20
only the essential facts of life, and see if I could not learn what =20
it had to teach, and not, when I came to die, discover that I had not =20=

lived.
	~ Henry Thoreau

Hi Mike
> Good news is that I can run the Annotation app w/o any hiccups.  =20
> Bad news is that changing the varsCreatedb.bat file didn=92t do the =20=

> trick for uploading MBARI=92s knowledgebase.  Here are the code =20
> changes I made.  Also, I started the knowledgebase before the =20
> annotation app.  I hope that was the right thing to do.  Did I miss =20=

> anything?
>
>
>
> @echo off
>
> REM $Id: varsCreateDb.bat 325 2006-07-13 21:09:24Z hohonuuli $
>
>
>
> call varsSetup
>
>
>
> java -Xms256m -Xmx512m -cp %VARS_CLASSPATH% =20
> org.mbari.vars.knowledgebase.actions.LoadKnowledgebaseAction "C:=20
> \Program Files\VARS\vars-1.0.4\database\knowledgebase.xml"

Your script looks AOK. You will need to drop the concepts in your =20
VARS database first. Since you don't have any real data in there you =20
should probably just drop all the VARS related tables and recreate =20
them with the DDL. If it still doesn't work send me any error message =20=

you get. Also rather than double clicking on the bat file, it's =20
better to open a command prompt and run the batch file there. That =20
way you can capture any error output.
Cheers
B
Brian Schlining
Software Engineer
http://www.mbari.org

Hi Mike,
> I totally understand that you=E2=80=99re swamped with other projects.
Ain't that the truth ;-)

> I really appreciate your rapid responses to my emails.  It=E2=80=99s a =
=20
> busy time of year for us here at NURC too.  I have but one last =20
> request.  Do you have the vars_database.xml for mapping to MySQL?  =20
> I=E2=80=99m guessing the configuration isn=E2=80=99t much different =
than that =20
> for SQLServer.  I downloaded the JDBC driver for MySQL and =20
> extracted the file mysql-connector-java-5.0.4-bin.jar to VARS_HOME/=20
> lib.  I=E2=80=99m pretty sure that the xml doc is all I need to point =
to =20
> the computer hosting the MySQL database.

I've attached a vars_database.xml for MySQL. You'll need to modify =20
the url parameter in it to point to your database server.

You're right about the JDBC driver. If you're running on a Mac just =20
drop the it in the lib directory and the launch scripts will pick it =20
up. On windows, you'll need to edit varsSetup.bat and add the JDBC =20
driver to the classpath by adding ';"%VARS_LIB%\mysql-connector-=20
java-5.0.4-bin.jar"' (Without the single quotes) to the end of the =20
VARS_CLASSPATH .

I'm in the middle of rolling out a new version of VARS here at MBARI. =20=

It's a bit of a pain since we replicate the VARS database out to our =20
ships. Once that's complete, I'll finish the porting and testing =20
against MySQL. Hopefully, I'll finish early next week. Then it's on =20
to polish up the Knowledgebase application....

You gotta love software 'cause you never really finish working on =20
something ;-)

Anyway hope all is well.

Cheers
B

Brian Schlining
Software Engineer
http://www.mbari.org

=EF=BF=BC

Hi Mike,

I'm still catching up on emails here....
> I was excited to see that you added a DDL for MySQL b/c I was just  
> about to create all the tables by hand. Please let me know if there  
> are any major bugs with this implementation.  This is my first  
> attempt at using MySQL as a back end.
One bug. Haven't tracked it down yet.

>  Also, I noticed that there is now a Java kit for Sony RS-422  
> device control.  Does this mean that the Rosetta Stone is no longer  
> needed to communicate with VCRs?

I'm using RXTX for serial comm between VARS and the VCR. I *think*  
I've included the Univeral Binary for the native code on Macs, so no  
Rosetta is needed. BTW if you're using a Blackmagic Design video  
capture card (what we use), you can use it's serial port on a Mac.  
(Plug and Go!!) So you won't need an additional serial port adapter  
or RS232-422 adpater. Unfortunately, the same can't be said on  
windows; the Blackmagic's serial port can't be used by VARS on windows.

Cheers
B

Brian Schlining
Software Engineer
http://www.mbari.org

Hi Mike,

> So=85back to the MySQL setup=85.
>
> The DDL you just sent appears to have a bunch of alter commands in =20
> line prior to creating the tables, views and procedures.  These get =20=

> flagged when executing the code.  Does this DDL need to be reworked =20=

> before running it in MySQL query browser?

The DDL I sent you was for sqlserver. Here...this may clarify things. =20=

You can fetch the latest DDL's at:

SQL Server DDL: http://vars.svn.sourceforge.net/viewvc/vars/trunk/=20
vars/src/main/database/sqlserver/vars.ddl?view=3Dmarkup

MySQL DDL: http://vars.svn.sourceforge.net/viewvc/vars/trunk/vars/src/=20=

main/database/mysql/vars.ddl?view=3Dmarkup

You should be able to execute the DDL with the DROP statements. If =20
you can't just cut them out of the DDL. By the way, the DDL for MySQL =20=

isn't quite correct yet. I'd hoped to test it more this week but I've =20=

been sidetracked onto other tasks. Hopefully next week I'll get a =20
correct one. You can try the MySQL one and the Annotation and Query =20
apps will fun fine; the Knowledgebase App won't start though.

Cheers
B
Brian Schlining
Software Engineer
http://www.mbari.org

Hi Mike,

> After creating a VARS database on our SQL server and running the =20
> DDL to create all the tables=E2=80=A6.
>
> I am unable to connect to the db through VARS.  I updated the XML =20
> file as suggested, but it=E2=80=99s giving me an =E2=80=9Cunable to =
load =20
> knowledgebase=E2=80=9D error when I run the annotation, knowledgebase, =
or =20
> query batch files.  Are there any other necessary changes to =20
> existing files that I=E2=80=99m missing?  FYI=E2=80=A6I am able to =
talk to the =20
> SQL database and confirm all the tables in MS Access through an =20
> ADP.  However, I did get one warning message in SQL when running =20
> the DDL.  I=E2=80=99ve attached a text file of both the output in the =20=

> command prompt window and the warning message from SQL Server.  Any =20=

> suggestions?
First, what version of VARS are you running? If you haven't already, =20
you should get the latest version, 1.0.4. I've attached a DDL I just =20
dumped out of my testing database for MS SQL Server. I know VARS will =20=

run on it. Thanks for the heads up about the error. For your use that =20=

error won't affect you

The error that was reported:

> org.mbari.vars.dao.DAOException: Failed to open a connection to the =20=

> VARS database: No configuration has been loaded for the database vars.

Looks like there may ba configuration problem with the Java =20
classpath. Again, get the latest version and try again. If you still =20
get the same problem I'll look into it later today.

=EF=BF=BC

Cheers
B

Brian Schlining
Software Engineer
http://www.mbari.org

Hi Mike,

Good to hear from you. I was wondering what you were up to. Sorry to =20
hear about the hard drive crash, hopefully you can get things going =20
again. I'm working on 'yet another VARS release', to be posted soon. =20
No changes to the database between 1.0.3 and 1.04 (to be release in a =20=

week or two), so you can use the same DDL. The SQL server DDL is =20
available at http://vars.svn.sourceforge.net/viewvc/vars/trunk/vars/=20
src/main/database/sqlserver/vars.ddl?view=3Dmarkup
> Long time=85no email.  Hope all is well in Monterey.  In case you =20
> we=92re wondering, we haven=92t dropped off the planet but have hit a =20=

> few bottlenecks in our VARS development and implementation =20
> process.  Long story short=85.Yingjie=92s hard drive crashed prior to =20=

> her completing her action items this past summer=85and none of her =20
> code was backed up.  I was able to recover most of the data, but =20
> she is unfortunately on to other projects and I have to pick up the =20=

> slack.    After I make some sense of her Java code, I may be in =20
> contact with you.  In the meantime, I=92m migrating the VARS back end =20=

> to Microsoft SQL Server on our data server.  At the workshop last =20
> December, I recall you saying that you have a DDL to setup up the =20
> database in SQL.  However, I wasn=92t able to find any info on the =20
> sourceforge site.  Is the code still available?
>
p.s. Say Hi to Yingjie for me

Cheers
B
Brian Schlining
Software Engineer
http://www.mbari.org

Hi Fernando,

> Just one small clarification: when I referred to positional info I =20
> didn=92t mean the cassette time but rather GPS position. If I =20
> understood it right it is possible to fetch it in real time. Is =20
> that what RXTX is for?

RXTX is a software library that allows Java programs to use serial =20
ports on your computer, kind of like firewire, but much slower. It's =20
used by VARS for communicating with the VCR. If the VCR is configured =20=

correctly and connected through RXTX, VARS can also read/write UTC =20
time onto a track on the video tape.

At MBARI, positional information (i.e. GPS + depth) is not added in =20
real time. Instead, it's added by a script that runs once a day. To =20
do this you need to have some method of keying your positional data =20
to your video annotations; we use UTC time as a key. We've used 2 =20
different methods of keying, each has some pros and cons:

1) Log timecode with UTC time as the VCR is recording.
PROS: Independent of VARS and your video storage format.
CONS: Requires writing a custom application to read timecode from the =20=

VCR. (If you have any technically savvy staff around (I know, I =20
know...not likely), I have both Java and C implementations of code =20
that does this that they can use as a starting basis. Both are based =20
on RS-422 (e.g. serial ports) though, so they probably won't help =20
with your firewire issue.)

2) Write UTC time directly onto the tape, VARS can grab this time =20
when you make an annotation. (This is the method we currently use.)
PROS: VARS can take care of this for you right out of the box.
CONS: Requires a VCR that supports RS-422. Have to configure the VCR =20
correctly.

Anyway, if you happen to come up with a clever idea for keying your =20
position info to your annotations, but need some modifications to =20
VARS, let me know and I'll see what I can do

Cheers
B

p.s. Just FYI, by May 2007 VARS will be modified to add support for =20
digital video formats such as QuickTime movies and MPEGs.
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Brian Schlining
MBARI
Software Engineer
br...@mb...
(831)775-1855
http://www.mbari.org/staff/brian

I went to the woods because I wished to live deliberately, to front =20
only the essential facts of life, and see if I could not learn what =20
it had to teach, and not, when I came to die, discover that I had not =20=

lived.
	~ Henry Thoreau

Hi Fernando,

> Do you have any unpublished piece of software that interfaces VARS =20
> with the VCR through a firewire port? Or do you know of any other =20
> team that has customised VARS by developing firewire interfacing code?
Unfortunately, we do not have a firewire port of the VCR control. =20
I've had requests for this feature, but so far no one has implemented =20=

it. I'd be happy to provide technical information to anyone willing =20
to tackle it though. We don't need that feature here (at MBARI), so =20
I'm not able to devote any time to implement firewire support.

>  Is it a problem that I don=92t have a positional info source on?
You're correct. The VCR control in VARS does 2 things:
1) Control playback of the VCR
2) Fetch the timecode from the video source when an annotation is =20
created.

Most people can live without control of the VCR, but fetching =20
timecode is very important if you want to identify the video frame =20
that an annotation is associated with.

>  Is it possible to manually edit that piece of info on the database?

Yes. You can manually edit it directly in the Annotation application. =20=

To do so select the 'Observation' tab on the left side of the =20
annotation application. One of the rows is labeled 'TimeCode'. If you =20=

click on the 'edit' button next to that row a dialog will pop up =20
allowing you to modify the timecode.

Alternatively, if you like to write code, the timecode is stored in =20
the database in the 'VideoFrame' table and you can modify that using =20
standard SQL. If you decide to go this route and need advice please =20
feel free to contact me.

Cheers and Good Luck

Brian Schlining
Software Engineer
http://www.mbari.org

Hi Cyprian,
> do you know if VARS could be used directly with a DVD player/ 
> recorder instead of digital DV tapedeck?

Not 'out of the box'. The catch with DVD players is that you probably  
don't have any way to programmatically interact with the DVD player.  
Without that you couldn't control playback (start, stop, fast- 
forward, etc.), which in itself is annoying but not a show stopper.  
The real problem is indexing the DVD movie, so that you can tell  
where the annotation belongs. On VCR's you can use timecode, not sure  
what a DVD uses although we probably could think something up. Using  
an external DVD player may be impossible; I don't know if they have  
any protocol that's analogous to the VCR's RS-422 comm. So, even if  
we could index the DVD we have no way to read the indexes from the  
DVD player.

Anyway the short answer is 'Not without quite a bit of research/work'

Cheers
B
Brian Schlining
Software Engineer
http://www.mbari.org

BEGIN:VCARD
VERSION:2.1
X-GWTYPE:USER
FN:Cyprian Payne
N:Payne;Cyprian
TEL;WORK:02920 515673
TITLE:Data Specialist
EMAIL;WORK;PREF;NGW:Cyp...@cc...
END:VCARD

Brian, thanks very much for this info .
CYprian

>>> br...@mb... 02/15/06 6:10 pm >>>
Hi Cyprian,

> I am still pushing for the vars system to be installed here but am =20
> now being asked for alternatives to compare it with. Do you know of =20
> any other/commercial software that does this type of thing?

We looked at a commercial annotation tool a while back. It was a neat =20
tool but didn't really address the problems we were trying to tackle =20
(i.e. consistent and searchable annotations). There's other =20
annotation tools about but they appear to have the same short-=20
comings. Here's a list of the ones I know about:

http://www.research.ibm.com/VideoAnnEx/usermanual.html=20
http://www.dfki.de/~kipp/anvil/=20
http://icampus.mit.edu/projects/xmas.shtml=20
http://www.transana.org/=20
http://www.noldus.com/site/doc200401012=20

Brian Schlining
Software Engineer
http://www.mbari.org=20

Hi Cyprian,

> I am still pushing for the vars system to be installed here but am  
> now being asked for alternatives to compare it with. Do you know of  
> any other/commercial software that does this type of thing?

We looked at a commercial annotation tool a while back. It was a neat  
tool but didn't really address the problems we were trying to tackle  
(i.e. consistent and searchable annotations). There's other  
annotation tools about but they appear to have the same short- 
comings. Here's a list of the ones I know about:

http://www.research.ibm.com/VideoAnnEx/usermanual.html
http://www.dfki.de/~kipp/anvil/
http://icampus.mit.edu/projects/xmas.shtml
http://www.transana.org/
http://www.noldus.com/site/doc200401012

Brian Schlining
Software Engineer
http://www.mbari.org

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