NCSA DataBridge and EasyViz Tutorial

Visualization of Macrozooplankton Biomass
CalCOFI Cruise Data, 1990-2004

Introduction | Background | Goals | Lesson 1 | Lesson 2 | Links

Lesson 1: Creating a Three Dimensional Surface To Represent Two Dimensional Data

In this lesson, we will create a 2-dimensional visualization of plankton biomass during the month of March, 1990.

About the Data

The first step is to use NCSA DataBridge to convert an ASCII text file into an EasyViz format file.The CalCOFI web site has made their data readily available to the public. You can view an example of the data in the table format provided by the CalCOFI project, in this case data of Macrozooplankton Biomass measured at dozens of points off the coast of southern California between 1990 and 2004.

Let's consider this data for a moment. In any web browser, you may save this file as an html file and open it in a number of applications including Microsoft Word and Excel. Let's look at the first five rows of data, and keep the map handy for reference.


CalCOFI Cruise Stations Map

Line
Station
Lat N
Long W
Date
Mo/Day
Time(PST)
Water Volume
Stained(m 3 )
Max. Tow
Depth(m)
Volume per
1000m 3 Strained
Start
End
Total (cm3)
Small (cm3)
77
49
35
05.3N
120
46.6W
3/19
0913
0919
107
50
476
308
77
51
35
01.3N
120
55.1W
3/19
0638
0700
427
214
134
134
77
55
34
53.1N
121
11.9W
3/19
0245
0307
439
208
221
221
77
60
34
43.3N
121
33.0W
3/18
2212
2234
416
209
192
192
77
70
34
23.3N
122
14.8W
3/18
1614
1636
447
212
67
67

Based on the direction of travel (look for the arrows along the path), the first data station is just north of San Diego at SIO ("First Station", easternmost station on map). Each line that lies in roughly an east/west direction has a line number associated with it (77, 80, 83, 87, 90, 93). The stations along a specific line have a station number. Therefore, each station may be identified by a combination of its line number and station number. The data above consists of one data point for each station along the route. The data above are sorted first by line number, then by station number, in ascending numeric order.

NOTE: To visualize this data in NCSA EasyViz, we are going to simplify our data by using only the data in a simple rectangular array, leaving out data from all stations below 60 and stations 110 for lines 83, 87, 90, 93, and stations 120 for lines 90 and 93. We will include only those data from stations 60 thru 100 for each line, and zero will be used where there is no data recorded (infrequent).

Data Limits

We would like to visualize our data organized to visually correspond with the geographic distribution of the data stations. This would be the following format:

North
West
Line 77/Sta. 100
Line 77/Sta. 90
Line 77/Sta. 80
Line 77/Sta. 70
Line 77/Sta. 60
East
Line 80/Sta. 100
Line 80/Sta. 90
Line 80/Sta. 80
Line 80/Sta. 70
Line 80/Sta. 60

Line 83/Sta. 100
Line 83/Sta. 90
Line 83/Sta. 80
Line 83/Sta. 70
Line 83/Sta. 60

Line 87/Sta. 100
Line 87/Sta. 90
Line 87/Sta. 80
Line 87/Sta. 70
Line 87/Sta. 60

Line 90/Sta. 100
Line 90/Sta. 90
Line 90/Sta. 80
Line 90/Sta. 70
Line 90/Sta. 60

Line 93/Sta. 100
Line 93/Sta. 90
Line 93/Sta. 80
Line 93/Sta. 70
Line 93/Sta. 60

South

Which in the case of March, 1990, is:

North
West
0
110
67
67
192
East
0
89
75
114
228
38
37
42
18
60
26
45
109
55
61
28
87
98
72
78
38
75
216
90
74

South

Note that this data has six rows and five columns. However, in order to visualize the data properly using NCSA EasyViz, the matrix must be 'flipped' so that row 1 becomes row 6, resulting in the following type of single column format:

1,1,38
1,2,75
1,3,216
1,4,90
1,5,74
2,1,28
2,2,87
2,3,98
2,4,72
2,5,78

... and so on.

The first value of the first row, '1', represents column 1. the second value, '1', represents row 1 (rows are numbered in reverse order to be visualized properly). The third value, '38', represents the data value for row 6, column 1. This process repeats accordingly.

Download the Data File

To generate this single column file we could either do it manually which would be tedious or we could write a program to automate this conversion for all CalCOFI datasets. We have chosen the latter option and have created the necessary file for you. Right-click and choose "Save As..." to save it to your local computer. Remember where you save this file because you will need to open it with NCSA DataBridge in the following step.

Next we will use NCSA DataBridge to convert this file to a .vtk format viewable with EasyViz. If you have not already downloaded and installed NCSA DataBridge and EasyViz, do so now.

Download and Install NCSA DataBridge and EasyViz

Download DataBridge version 2

Download EasyViz version 3

Run the downloaded files to install the applications.

Open Your Data File Using DataBridge and Convert Your Data to EasyViz Format

Launch NCSA DataBridge. When you see the DataBridge Welcome splash screen, click 'Next'.

File Information

You will first be asked to open your data file. Click 'Browse' in the 'Source File' box to locate the text file you saved from the previous step. DataBridge will automatically give the output file a name, but you may rename it by clicking the 'Rename' button in the 'Destination File' box.

Click 'Next' to continue.

Data Organization

The next screen, Data Organization, allows the user to specify how your data is organized. Our data uses comma separation, so we would select the 'Other' radio button and type a comma (,) into the adjacent text box.

Our data does not have a header line, so we would select 'No'.

Our data is in block format, so we would select 'Yes'.

Click 'Next' to continue.

Column Setup

The next screen allows the user to specify the data's column format. The X Value should be set to 'Column 1', Y Value to 'Column 2', and Z Value will be left at 'None', and we will specify the Data Value to be 'Column 3'. Select 'Column 3' from the drop-down menu below Data Value. We will also accept the default Null Value of 0.000000 set by DataBridge.

Click 'Next' to continue.

Data Type

The next screen allows you to specify whether our data is Scatter Data or Uniform Data. Our data is 2-D Uniform data with a value of 5 for Num. X and 6 for Num. Y. The Step X and Step Y values may be left at 1.

Num X: 5 (The X-dimension is west-to-east for 5 stations 100, 90, 80, 70, and 60)
Num Y: 6 (The Y-dimension is north-to-south for 6 lines 77, 80, 83, 87, 90, and 93)

Click 'Next' to continue.

Advanced Settings

Our data does not require us to set any Advanced settings.

Click 'Next' to continue.

Confirm Settings

Confirm your final settings and click 'Next' to continue. You will hopefully see a screen that says 'DataBridge was successful!'. You may now quit DataBridge.

If you have any difficulties with this step and would simply like to skip it and go on to visualize the data in EasyViz, right-click and choose 'Save As ...' to download the file in EasyViz format.

Visualize Your Data With EasyViz

Next, launch NCSA EasyViz.

Select 'Open Existing File' and click 'OK'. Navigate to the location of your output file from DataBridge and open the file into EasyViz. You will hopefully seem something similar to the image below.

There are instructions on how to manipulate your visualization on the left. You may click and drag with the left mouse button in the image area to rotate the data. Right-click and drag to zoom in or out. Select 'Warp' from the 'Settings' menu. If your data disappears momentarily, press the F1 function key a few times until it appears. This adds some elevation to your data visualization. Your visualization should now look something like the image below:

Both the elevation and the color correspond to the data values from your data file.

This is a relatively simple dataset to visualize in this manner, but you have now learned to procedure for visualizing two-dimensional data of virtually any degree of complexity. Compare the above image with the image below which was created using the Excel 3D Chart option:

Excel 3D Chart

The main difference is that the color-coding of the Excel Chart is not based on the data values themselves, but rather on rows or columns. The important feature of both visualizations is the 'topology' of the resulting graphical representation.

Click 'Next' below to continue on to Lesson 2, Advanced Visualization with EasyViz.

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