Scientific Graphics for
Visualization and Monitoring
graphs of data from a variety of sources. Users can
explore the data and output publication quality PostScript
and PDF files. ElVis can display and animate several
graph windows simultaneously. The software is
written in Java for portability. Long running
simulations can be monitored by running ElVis and
selecting data from its internal browser. ElVis is
developed by Eliot
Feibush at PPPL.
and ElVis Module
Download and run this
launcher program to install ElVis, check for new versions,
and run ElVis with increased memory. This Java
program also checks for the right version of Java on your
computer. Initially, it installs the latest version
of ElVis in the "Elvis" directory in your home
directory. The launcher then runs ElVis with the
amount of memory you specify. Subsequently, when you
run the launcher, it checks to see if a new version of
ElVis is available. The latest version is dated
5/31/2012. The version date is shown in the title
bar. Update information is available from the
toolbar menu under Help-->What's new or from the update
Users within the PPPL firewall can run the
services directly without entering a
password. Users outside the firewall will
need a FusionGrid certificate to verify their
identity. You can request
a FusionGrid certificate if you are going to
run from outside the firewall.
Running RPLOT from within
at data from a TRANSP run.
You can display a sample
graph and interact with it. Go to File-->Browse
URL. This brings up a file selection box.
Click on xneut.cdf to load a typical graph. Try
Zoom - click
in the graph and drag the selection rectangle to zoom
in on the data. You can also move the cursor
into the graph and type the '=' key to zoom in or the
'-' key to zoom out. Type the letter 'a' to
Scroll - move the cursor into the
graph and type the arrow keys to scroll vertically or
Numeric Values - hold down the cursor
below the X axis and drag to display a vertical
crosshair with the numeric value of each variable.
To look at some 2-D
data, go to File-->Browse URL and select
indexed.cdf. This will display a window with 3
indexed graphs. There are VCR buttons along the top
of the window and a slider below these buttons. Drag
the slider to change the index of the 3 graphs. The
VCR buttons are:
Resize - hold down mouse button 3
(MB3) to get the pop-up menu. Select Max &
Fill to enlarge the graph window. Select Restore
to return the window to its original size.
Jump to the lowest index.
Sequentially display the datasets by decrementing the
< Decrement the index
Stop the animation.
> Increment the
index by 1.
>> Sequentially display
the datasets by incrementing the index.
>| Jump to the highest index.
netCDF Files in ElVis
ElVis can read netCDF
files and display the data stored in variables. If
the netCDF file is stored as a URL on a website then go to
File-->Browse URL. This
up a Load URL browser window for navigating to the netCDF
Click on a link or type a new
address in the textfield and press the Enter key. A file
located in a directory that is served by an HTTP server is
accessible as a URL. The file must be publicly readable,
e.g. in Unix the file permission must contain r--r--r.
If the netCDF file is stored as a file
on disk then run ElVis as an application and go to
File-->Load File. Set "Files of Type" to ".cdf, .nc
files" if it is not already set in the Load File window.
click on the name of the netCDF file, ElVis displays a
GraphWindow containing the list of variables and an empty
graph. The long name of each variable is shown
unless only the short name is in the file. The
dimensions of each variable indicate the arrangement and
number of its data elements. For example, a
one-dimensional variable with 201 elements would be:
Distance . A two-dimensional variable would
be: omegas [25 x 16]. The panel for
configuring a plot is shown below.
To select a one-dimensional variable
for plotting, click on the name of the variable.
Then select a 1-D variable as the X Axis by clicking on a
radio button. Then click on the Plot button below
the list of variables. Multiple variables can be
selected by using Ctrl-Click on the name of each variable;
then click on Plot. If the variable to be plotted
has more elements than the variable for the axis then
additional axis locations are created by
interpolation. If the plotted variable has fewer
elements then the axis variable is point sampled for each
of the plotted elements.
Selecting one or more two-dimensional
variables for plotting will activate the second column of
radio buttons for the Index. When plotting 2-D
variables, select a 1-D variable for the X Axis and a 1-D
variable for the Index. A 2-D variable listed as [25
x 16] is plotted as 16 indexed datasets with 25 values in
each dataset. The index value is shown above the
animated graph or in the legend when the data is presented
as f(x,i). The pop-up menu (click on mouse button 3
or type F9 when the cursor is over the graph) has an item
for Presentation that lets you choose either Animated,
f(x,i), Surface plot, or Contour plot. Clicking the
checkbox for Transpose would plot this variable as 25
indexed datasets containing 16 values in each
dataset. Multiple 2-D variables can be selected by
using Ctrl-Click and then Plot.
a variable with 3 or more dimensions brings up a dimension
pull-down selector for the X Axis and the Index and
textfields for setting index values as shown below.
Choose a different dimension from both of the pull-down
selectors. These 2 dimensions will form a 2-D
variable to be plotted. The corresponding 2
textfields will be grayed-out and inactive. The
remaining, active textfields are used to select the 2-D
"slice" from the variable. Set the index number for
each of these dimensions to specify a two-dimensional
subset of the entire variable. Type in the index
number or use the spinner UI to increment/decrement the
index number. Then click Plot. Extracting the data
from a large file over the Internet can take several
Several graphs can be drawn for a
netCDF file. Go to Window-->Add Row or
Window-->Add Column to add more cells to the
GraphWindow. Click in a cell to set the location of
the next plot.
The configuration of a
GraphWindow for a netCDF file can be saved and restored
with a template file. This is useful for
redisplaying a set of graphs without having to manually
reconfigure the window and choose variables.
Templates also enable comparing data from several
different files with variables of the same name and number
of dimensions. It also lets other users look at
graphs created by a collaborator. The template
contains the number of rows and columns and the variables
that form each graph. Run ElVis as an application to
save and load templates as files on disk. An Elvis
directory is created for templates in the user's home
directory. To create a template, enter its name in
the visible field of the pull down selector for Templates
as shown below. Then click Save. Use the
pull-down selector to load a template from the directory
of available templates. Click Delete to delete the
a netCDF file is downloaded using Browse-->URL, ElVis
checks the URL directory for a corresponding template
file. If the template is there then ElVis
automatically downloads the template and applies it to the
GraphWindow. This will display the graphs with the
variables as specified in the template. For example,
if you browse for sim1.cdf then ElVis will also look for
sim1.cdft as the template. If a corresponding
template is not found, then ElVis checks the netCDF file
for a global attribute named "elvis_template" and loads
Long running simulations
or analysis programs can be monitored through netCDF
files. A program may add data to a file as it
runs. A simulation typically writes data after each
time step. After loading a netCDF file, ElVis can
periodically poll the file, check for additional data, and
update the graphs. The polling rate is set with the
digital clock user interface that shows
hours:minutes:seconds. Highlight part of the time
interval and use the spinner to increment or decrement the
polling frequency. Click on Start to begin
monitoring. The button will then change to Stop to
If the file has a global
attribute named "running" that is set to true, then ElVis will
automatically start monitoring the file when it is
loaded. When the simulation changes running to false then ElVis will
automatically stop monitoring. The polling frequency
is stored in the template file. Here is a sample program for creating a
netCDF file that ElVis can monitor.
Customize Data URL
page for the browser is specified by an applet parameter:
You can set the start page by downloading the
link to Run the ElVis Applet (runElVis1.6.html) and changing the
value of the parameter. For example, change
w3.pppl.gov/elvis/data to www.myinstitute.gov/mydata. Then create
a web page containing a link to the modified file for starting
ElVis with a customized data directory.
Gnuplot data in ElVis
ElVis can display data
that is formatted for gnuplot. See
Python API to ElVis
Python programs can send data to ElVis
for display. See these instructions.
ElVis Data Monitoring Applications
Grid TRANSP Monitor
is the only service that
runs ElVis as an
applet. Run ElVis as a
Java application program via
the launcher for all other
Display a sample
Links to ElVis programming interfaces
available to application programs.
Description of graphs.
Elfresco - The
Wave Reflectometer Simulation Code is an application that uses
ElVis for displaying graphs.