Limn User Manual
Software overview:
Limn is a software focuses on tools for interacting with visual rendering of large, multidimensional data. It reads the user selected source data, generate index files, and then
display the distribution of the source data via scatterplot matrix and movie. Users can
change the value of some important variables to get the different view effects.
Furthermore, by subset view and contour view, users can highlight and observe a specific
region of data.
User manual:
Running prerequisite:
 Already installed java sdk, version 1.4.1_02 (the other version may not work well
with our tomcat) in your computer;

Already have all the following folders in desired directory (AAA/):
o AAA/limn
o AAA/soapServer
o AAA/serverDataIndex
o AAA/subserverDataIndex

Already make correct changes to the following files:
o AAA/limn/ServerProp
o AAA/limn/SubserverProp
o for Linux machine: AAA/limn/indexGenerate.sh
AAA/limn/matrixView.sh
o for Window machine: AAA/limn/startTomcat.cmd
AAA/limn/indexGenerate.cmd
AAA/limn/matrixView.cmd

Successfully tested Tomcat server
If you already finish above steps, you are ready to run LIMN. Otherwise, please go to
installation guide to finish those steps first.
1. Start Tomcat server:
1.1. If you are using a Linux machine, you can skip this step.
1.2. If you are using a Window machine, run AAA/limn/startTomcat.cmd to start
Tomcat server. You should be able to see a Tomcat server command window
running on your computer.
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2. LIMN index generator:
2.1. Execute the script file “AAA/limn/indexGenerate.sh” for Linux machine; or
“AAA/limn/indexGenerate.cmd” for Window machine.
2.2. The script file will bring out the following window, which lists all the
subservers’ names; the name, size and dimension of source data files located in
the subserver.
If you want to add more source data files, put them in the subserverDataIndex/data/
folder, then next time you run the indexGenerate script file, your new source data
files will show in the list.
2.3. Select source data by clicking its name.
2.4. Fill in the matrix index file name, matrix width and height;
2.4.1. The movie index file name field will be changed to “matrix index file
name” plus “-Movie” automatically;
2.4.2. Movie width and height are fixed to 200, 200 respectively (you can
changed it in ServerProp file, then run the indexGenerate.sh or
indexGenerate.bat again).
2.5. Click the button, “create index files”, to generate the index files for matrix and
movie.
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2.5.1. Subservers generate index files: Subservers read the source data located on
it, and then generate index files. You can see the output in the Tomcat server
window to check the jobs have been done.
2.5.2. Server merge index files: After all the subservers finish generating the
index files, server begins to merge those index files from all subservers back
to server. You can check the output in the server-end.
2.5.3. Suppose you choose the source data “pollen”, and name matrix index file
“pollenOne”. As we mentioned before the movie index file will be named
“pollenOne-Movie” automatically. Then after merging, you should be able
to see the following new files:
2.5.3.1. In subserver-end:
 AAA/subserverDataIndex/data/pollen.minmax which records the
min max values for each variable in source data.
(note: minmax file name is same as the source data file name, not
same as the index file name. So if you use the same source data to
generate several index files, you only can see one minmax file for
the source data)

AAA/subserverDataIndex/data/pollenOne.prop (details see
“LIMN file structure overview” document)

AAA/subserverDataIndex/index/pollenOne (this folder contains
matrix index files for the source data located on subserver)

AAA/subserverDataIndex/index/pollenOne-Movie (this folder
contains movie index files for the source data located on
subserver)
2.5.3.2. In server-end:
 AAA/serverDataIndex/data/pollenOne.prop (details see “LIMN
file structure overview” document)

AAA/serverDataIndex/data/pollenOne-Movie.prop (details see
“LIMN file structure overview” document)

AAA/serverDataIndex/index/pollenOne (this folder contains
matrix index files merged from all subservers)

AAA/serverDataIndex/index/pollenOne-Movie (this folder
contains movie index files merge from all subservers)

AAA/serverDataIndex/basis/pollenOne-Movie.currentbasis
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
AAA/serverDataIndex/basis/pollenOne-Movie.targetbasis
2.6. Now LIMN index generate part for the selected source data is finished, you can
select another source data to generate a new set of index file, or close the window
to terminate the program.
3. LIMN matrix and movie viewer:
3.1. Execute the script file “AAA/limn/limnView.sh” for Linux machine; or
“AAA/limn/limnView.cmd” for Window machine.
3.2. The script file will bring you the file chooser window (below), which lists the
entire existing matrix index files name, source data dimension, matrix canvas
size, movie tour length and source data location.
Note: tour length is an important property, please make sure the tour length in
“AAA/limn/ServerProp” has the same value as the tour length of selected index file.
If not, please change the tour length in ServerProp before click “view matrix and
movie” button.
3.3. Select an index file by clicking its name.
3.4. Click the button, “view matrix and movie”, to view matrix and movie. The file
chooser window will disappear, and then you should be able to see the following
windows. The scatterplot matrix and the frame window will come out by default.
You can mark the check boxes in the “window” menu to awake the other
windows.
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3.5. Scatterplot matrix viewer:
3.5.1. The matrix viewer will contains N*(N-1)/2 canvases, where N is the
variable number (dimension) of the source data. Laying out scatterplots of
any 2 dimensions in a matrix helps to reveal the relationships between the
variable pairs.
3.5.2. The window menu let you enable or disable any other frames from it. The
matrix viewer is the main window of LIMN view part. Close it will
terminate the whole program.
3.6. Gray frame:
3.6.1. Power and intercept: The gray frame provide controls on the points’
grayscale:
grayscale = intercept × (
overplotting count
maximal overplotting count
) power.
(2)
By default, power = 0.2, intercept = 255.
By adjust the 2 transformational parameters, power and intercept, you can
get their ideal contrast between high and low-density region of the plots.
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3.6.2. The histogram below the transformation curve reveals the distribution of a
plot’s overplotting counts; while the transformed density distribution is
displayed by the histogram along the gradient bar.
3.6.3. Mark the “Set Range” checks will bring out the contour view, which
allows you to focus on a certain overplotting level. You can pick a single
density value or a density value range by setting the choosing bar(s) across
the transformation curve. Those points whose density values fall in the
chosen range are then highlighted (in light blue) to form density contour.
3.6.4. Changing the value of “transparency” will change the transparency of the
light blue region of contour view.
3.6.5. Mark the “Apply to All” check will make the changes affect all the matrix
canvases, while unmark it only affect the focused canvas.
3.6.6. The “Invert Color” button will make the point with high-density from light
gray (default) to dark gray, make the points with low-density from dark gray
(default) to light gray. Or the other way around.
3.6.7. The “Reset” button will ignore all the changes; reset everything to the
default value.
3.7. Movie viewer:
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3.7.1. Mark the movie window check box in the “window” menu in matrix
viewer will bring out the movie window.
3.7.2. The axis view in the right upper corner shows the different basis for each
variable in current frame.
3.7.3. Control bar: buttons from left to right are:
Backward, forward, stop, step forward and step backward.
3.7.4. Speed bar allows you to control the movie speed of forward or backward.
3.7.5. Any changed made in the gray frame and subset frame will affect the
movie view. So the movie has the continuity with the matrix.
3.8. Zoom window for matrix canvas:
Zoom window give you the option of zooming in or zooming out on an individual
plot in the matrix.
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3.9. Subset window:
3.9.1. You can enclose their region of interest on a plot in a rectangle. The
resulting selected subset tuples are then retrieved from the data set and
plotted over all other plots in the matrix. The subset window provides the
subset’s information and controls over the subset’s view mode.
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3.9.2. The count table in the middle part of the subset frame shows size of “full
subset” and “sample subset” in subservers. Those number will change, when
you change the sample size or the sample view mode.
3.9.3. Sample size and mode:
Define the smallest plotting unit in a scatterplot as a plotting bin.
Suppose you input M for sample size, the following mode means:
3.9.3.1.
points/pixel: M is the fixed sample size for each bin. No matter
how many data records are over plotted at these bins, a random sample
with the uniform sample size is independently applied to each bin.
3.9.3.2.
%points/pixel: M% samples will be taken from the over plotted
data records for each bin.
3.9.3.3.
total points by density biased sample: M will be the fixed total
sample size for the whole subset. Then the percentage of sample points
in each bin will be computed by the density biased formula:
pi =
M
e
(ni) × ∑ kj=0 (nj)
1-e
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Where ni is the overplotting counts for bin i, and e is fixed to 0.5.
3.9.4. Allocation mode: the “equal” means the sizes of the sample subset are
equally distributed among subservers.
3.9.5. View mode:
3.9.5.1.
Shape view focuses on the overall distribution of the subset data.
All subset points are displayed in the same color regardless of their
density differences. However, by adjusting the transparency level of the
subset color, you can see through the subset and still be aware of the
density distribution of the entire data set.
3.9.5.2.
Density view displays the density distribution of a subset. The
high-density subset points are darker than low-density points.
3.9.6. Once you brushes a new subset, a new subset panel will be added in the
subset frame.
3.9.6.1.
The check box gives you option to view this subset or not;
3.9.6.2.
The color button will bring a color chooser to change the color of
the subset;
3.9.6.3.
The slider bar is designed for setting a subset’s color and
transparency level.
3.10. You can terminate the program by closing the Scatterplot matrix view
window.
4. Terminate Tomcat server:
4.1. For Linux machine:
The Tomcat server will be terminated while you terminate the program.
4.2. For Window machine:
You can terminate the Tomcat server by close the Tomcat command window.
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