• Canon C5060WZ camera with
underwater housing (manual)
• Canon EOS Rebel T2i digital SLR with
underwater housing
• Canon VIXIA HF G10 digital HD video
camera
Access &
Remote Connections
First
time setup: start at step 1.
After first time setup: skip to step 7.
1.
Obtain username and password for a
computer from JWW
2.
Get access to the lab computers
a)
From inside the lab, login directly to
the terminal.
b)
From off campus, use the UNCW VPN
to join the on-campus network.
c)
From on campus, you will need to use
the UNCW WPA network. Visit TAC
to have your laptop set up to use WPA,
then see JWW to get a WPA password.
3.
Open SSH client
Mac
OS: open Terminal.app (in the
Applications folder)
Windows: download & install WinSCP,
then open a terminal window
4.
Login to the lab computer
At the prompt ($)
login to the remote host via SSH
(replace hostname
with the name of the computer you are
logging in to): $
ssh username@hostname.uncw.edu
Once you log in the first time using the
password you were given, you should
change your password to something more
secure. Do this using the
following command:
$ passwd
You will be prompted for your new
password (you will have to enter it
twice). If you ever lose your
password, JWW can give you a new one.
5.
Start VNC (Virtual Network Computing)
After logging in, type the following: $ vnc4server -geometry
1280x800 -depth 16 -nevershared
After entering the command, the computer
will tell you what display your VNC
session is using (this will be an
integer n, 0 < n < 100).
Make note of this display number.
If this
is the first time you start the VNC
server, you will be prompted for a
password. Choose a good one and
do not forget it.
Feel
free to play around with the geometry
and depth options in vnc4server, but
those options should work pretty well.
When
you are done with the ssh connection,
just type exit
to leave. You should not need to repeat
step 5 again unless the machine you are
logged into has to restart. 6.
Download & install a VNC client on
your computer. There are lots of
free VNC clients out there. Mac: Chicken
of the VNC Windows:
TightVNC (there
are also many others)
7.
Connect using your VNC client. You will
need the host name
(hostname.uncw.edu), your username,
the VNC password your chose earlier,
and the display number.
8.
You should be able to bookmark the
connection for easy future use.
9.
The first time you log in via VNC, you
may notice odd behavior (such as the
screen automatically minimizing) when
you hit particular keys on your
keyboard. If this occurs, open
System Settings in the Launcher,
choose Hardware/Keyboard and the
Shortcuts tab. Look for a
shortcut for the key that is giving
you trouble, and disable it.
10.
Once you log in to VNC, you should see
a desktop and be able to use things on
the desktop just as if you were
sitting at the computer terminal
itself. When you want to take a
break from working, don't bother
logging out or closing
applications. Just quit (or
close the window) your VNC client
application on your local
machine. The VNC desktop will
remain untouched until you open your
VNC client again. This is very
convenient if you need to leave long
processes running on a machine!
Using Ubuntu
Linux
The
Ubuntu operating system (OS) is a
distribution of the Linux family of
OS. It is reasonably
user-friendly, and if you are accustomed
to Windows or Mac OSX it should not take
you long to get comfortable. Like
Mac OSX (which, like Linux, is based on
Unix), you can operate the system either
using the Graphical User Interface (GUI)
(i.e., menus, windows, pointing and
clicking with the mouse, etc.) just like
in Microsoft Windows, or using the
command line.
In the
Ubuntu 12.04 'Unity' desktop,
Applications can be found on the
'Launcher' on the left-hand side of the
desktop. Common applications will
appear there automatically (e.g., Open
Office apps, Firefox). You can
find additional applications by clicking
on the Ubuntu logo at the top of the
Launcher (the "Dash"). Click on
the icons at the bottom of the Dash
window to show applications, folders,
etc. One of the most useful
applications is the Terminal, which
allows you to access the command
line. I recommend opening
Terminal, and then locking it to the
Launcher by right-clicking on the icon
and choosing the "lock to launcher"
option.
I
recommend poking around and exploring
what you can do and what options you can
change. Unless you know what you
are doing, you will not have
administrator access, so there is not
much you can do to hurt anything.
The only bad thing you can do is not
save your data!
Ubuntu has
many applications that are similar to
Windows/Mac applications. The
OpenOffice suite is similar to MS
Office, for example, and includes a word
processor and a spreadsheet application
that are interchangeable with MS Word
and Excel.
As a user,
you have a 'home' folder on the computer(/home/username).
This folder is where your documents,
desktop, and individual preferences are
stored. All of the home
directories are backed up regularly, so
this is a safe place to store your data.
Important usage notes:
• If you are logged in directly at the
terminal in the lab, always log out when
you are done. Do not lock the screen
or choose 'sleep' or 'hibernate' modes.
• Do not turn on the screensaver.
Image
Analysis
A. Storing
pictures and movies
You
can save image and movie files on
paralabrax using a
USB connection from the camera. It
is important that you save any such
files into a directory within your home
folder, and that you maintain a naming
system so you know what is stored
where. Please also create a readme
text file or spreadsheet that is stored
on your desktop that details which files
are associated with which
projects/experiments, and where they are
stored. This is important to
ensure data are not lost after you
forget what you have done!
Storing
movie files from the Canon VIXIA HF G10 When you
are ready to upload movies from this
camera, you can probably find them in
this folder on the memory card: PRIVATE/AVCHD/BDMV/STREAM
The Canon
HD movie file format is .mts. This
is a proprietary file format, so it is
preferable to convert this to a standard
non-proprietary format for long-term
storage and use. To do this:
1. save a
master copy in .mts format. 2. Apply
your chosen naming convention
(experiment, internal code,
photographer, date, etc.) 3. Open
WinFF (in Applications/Video) 4. Choose
conversion options: convert to AVI,
preset MS Compatible AVI. 5. Under
the FFmpeg tab at the bottom of the
window, add the additional command line
parameter: -qscale
1
(qscale
gives the
level of compression; 1 is the lowest
level and 31 is the highest)
6. Click the 'convert' button at the top
of the window.
Note that
converting a large file with minimal
compression will take a long time.
It is also possible to execute ffmpeg
conversions from the command line; if you
are converting lots of files at once this
might be a more efficient option.
Viewing
videos
Double-clicking on a movie file will open
it in the Movie Player. In addition
to the clickable buttons at the bottom of
the window and the commands in the menubar
at the top, you can use the following
keyboard commands:
play/pause: spacebar
skip ahead/back: left & right arrow
keys
single frame ahead/back: < & >
keys
take screenshot: control-s
B. Analysis
with ImageJ/FIJI
ImageJ is a free image analysis program
produced by NIH. In Ubuntu we use
the program FIJI ("Fiji Is Just ImageJ")
which is just a convenient implementation
of ImageJ with some extra plugins and
things. ImageJ is free (well, your tax
dollars paid for it) and you can download
it for your home computer here.
Access
FIJI by typing fijiat the
command line, or find FIJI in the list
of applications in the Dash.
Access Matlab
by typing matlabat the
command line in the terminal. If this
does not work, ask JWW to add Matlab to
your path.
Introduction
to Matlab tutorial (This was
written for a course at UCSB for an
older version of Matlab but is still
mostly applicable. A newer
tutorial is under construction.)
R
The
most user-friendly way to use R is the
RStudio GUI. You can find RStudio
in the applications in the Dash.
All
text and images (except UNCW logo) copyright 2010 J. W
White
