Undergraduate ALFALFA team

A Brief Introduction to TOPCAT

Link to TOPCAT

Getting ready for TOPCAT

TOPCAT is a JAVA utility developed under the auspices of the international "Virtual Observatory" concept which enables the manipulation, display and analysis of datasets, specifically astronomical ones. Please refer to the above link for detailed information and downloading instructions. Note that TOPCAT can be installed on Windows, MacOS and Linux platoforms that are also Java-enabled.

Here, I assume that you have already installed TOPCAT successfully.

Getting datasets ready for TOPCAT

To make things easy, we generate files in "CSV" format --- "Comma Separated Variables" --- because that format is simple, well-defined and platform-independent. It is definitely the preferred format. However, it seems that Internet Explorer, which some of you may use as your browser, corrupts the pristine format of these files when it downloads them (totally defeating the whole purpose of having machine-independent files). So, unfortunately, there are different instructions depending on the browser you use.

Firefox (and other users):
Please chose the "CSV" file to download.
- Click on the "CSV" file you want to download
- After it loads, click on "File" (upper left) and then "Save Page as"
- Make sure the file is to be saved in the proper directory; I suggest you leave the name as I have set it. Note that the file type (lower right) should read "plain text document"
- Click "save".
- Check that the file exists in the right directory. If it's there, you are ready to load it into TOPCAT.
Internet explorer users:
Because of the issues with Internet Explorer, you have to select the "ASCII" file version, not the CSV. And then, we have to fool Microsoft a bit....
- Click on the "ASCII" file you want to download
- After it loads, click on "File" and then "Save Page as". Save it as a "plain text document" and be sure to specify that its name ends in ".txt".
- Make sure the file is to be saved in the proper directory, and that it is a "text document".
- Open the file with "WordPad". To do this, you may need to point at the file and right click to that a menu appears; selected "Open with" and then to the right "WordPad".
- Once the file loads, then click on the menu at the top left, then on "Save as" and "Plain text document". Be sure the "Save as type" is set to "Text Document".
- Click "save".
- Check that the file exists in the right directory. If it's there, (we hope that) you are ready to load it into TOPCAT.

A simple example of using TOPCAT

Below are links to two files containing the different versions (CSV and ASVII) of a catalog of 38,000 stars with measured apparent magnitudes at both B and V band, parallaxes and radial velocities from the Hipparcos satellite catalog which we downloaded from Eric Mamajek's page at URochester.

CSV Version

ASCII Version

Download the file following the instructions above. Be sure you know in what directory it is located. Now, let's make the plot shown on the right.

Start TOPCAT. On Windows machines, that means clicking on the file "topcat-full" in the directory where you have downloaded the executable jar file of that name. The TOPCAT window will appear.

Click on "File" (upper left) and then "Load Table". A new "Load New Table" window will appear. Choose the appropriate "Format", either "CSV" or "ASCII"..

Click on "System browser". Find the star data file you download. Click on it so that its name appears under "File name" at the bottom of the "Load Table" menu. On Windows machines, be sure that the bottom file type says "All Files". Click on "Open" and the file should load. It might take some seconds. The file name should appear in the "Table List"..

Left click on "Views" and then "Column Info". A new window will open which lists the Names of each column in the table. Notice what they are.

Back in the main menu, left click on "Graphics" and then on "Plot". A new window will appear. By default, it has plotted column 1 ("StarID") on the X axis and column 2 ("Hip") on the Y axis. What we want however is to plot "BminusV" on the X axis and "AbsMag" on the Y axis. Left click on the downward arrow next to "StarID" and select "BminusV"; then do the same for "AbsMag". This plot should appear.

Notice that it bears some resemblance to the plot we wanted to make (shown above on the right), but (a) the data points appear are denoted by red symbols not black ones, (b) it seems to have the Y axis scale flipped and (c) the range of X and Y values is not the same. We need to fix those things.

Astronomers measure the brightnesses of objects using a system of "magnitudes" that is inverse, that is a larger magnitude means a fainter object. So for our plot, we want to flip the Y axis of the plot. Simple click on the small box next to "Flip" on the row for the Y axis. That looks better!

Next, let's change the color of the data point symbols. On the right, under "Row subsets", there is a small box with a red dot in its center. Click on the red dot. A new "Plot Style Editor" window appears. Left click on the down arrow to the right of the red "Colour" bar. Scroll down and select the black bar. The color of the points will change! You can dismiss this window by clicking on "ok".

To finish the job, we need to reset the range of the X and Y values. At the top of the "Scatter Plot" window, left click on "Plot" and then on "Configure Axes and Title". A new "Axis Configuration" window will appear. You can now give the plot a Title (for example, "Hipparcos Color-Magnitude Diagram") and set the ranges. In this case, set X range from -0.5 to 2.5 and the Y range to -6 to 16 and then click "Apply"; the plot will rescale.

Notice that some of the points disappear because they lie outside the specified ranges. We'll talk about that later....

As one final step in this example, let's save the plot by exporting a copy to your machine's disk. At the top of the "Scatter Plot" window, left click on "Export" and then "Export as gif" (or other format if you want). A window will open which allows you to specify the file name and directory where it will be saved. When you have specified them, click on "Write gif" and you should now have a copy of the plot you have made. When you open the file, select your browser (or other image display utility) when asked for what program to open it with.

TOPCAT has many more features, so explore its capabilities further! Lots of astronomers use TOPCAT, so you are now in good company!

Last modified: Fri Sep 20 15:57:35 EDT 2013 by martha