Using JS9 with Astrolabe Atmosphere

Starting an existing instance takes 10-15 minutes

  • Login to Cyverse: https://cyverse.org
  • Select Atmosphere
  • Go to the Astrolabe project
  • Select the instance Astrolabe Ubuntu 16_04 GUI XFCE Base
  • You will be using this VM instance mostly as a gateway to other computers so it need not be large. Accept the default “Tiny” size with one CPU or add more.

Atmosphere Screenshot 1

  • After it is launched and active, click on the link called “Astrolabe V2.0”. Starting a new image is very much like booting a computer but can sometimes be slow depending on other users of the systems. It may take a long time (15 minutes) depending on system usage and the amount of resources that you have requested. The status bar will tell you where you are in the process.
  • REMEMBER to delete the session when you are done or it will keep burning CPU time in your allocation.
  • You will see a screen showing options and status. You will see something like this:

Atmosphere Screenshot 2

    • Select “OpenWeb Shell” on the bottom right.
    • Use “FUSE” to link your personal Cyverse DataStore to this VM Operating System. Fuse and iCommands is preinstalled in the Astrolabe Atmosphere instance. This method is relatively easy to use since once it is set up, it works like your desktop file system but it is low throughput, meaning it works best for small files no larger than a few tens of megabytes each.
    • (You can use other methods, as well, as documented at: https://wiki.cyverse.org/wiki/display/atmman/Managing+Your+Atmosphere+Data)
      • Initialize iRODS and login:
        • bash-3.2$ iinit
        • Enter your current iRODS password
      • Connect (mount) your personal Cyverse DataStore space to a local directory:
        • bash-3.2$ irodsMountMyDataStore
      • If you type ‘ls $HOME/data_store’ you should see the contents of your DataStore Home directory.
    • Select “Open Web Desktop” on the bottom right.
    • You will see something like below. Select the default configuration.

Atmosphere Screenshot 3

  • Open the Web Browser by clicking the icon at the bottom of the screen. An Instance of Firefox will open.
  • Enter the URL: http:astrolabe.arizona.edu
  • On the top tab of that website select prototype services. This will launch JS9 a software package for manipulating FITS files images. It will look something like this:

Atmosphere Screenshot 4

  • You can now load files from Cyverse into JS9 using “File/Open Local File” and going to the DataStore directory that you just made ($HOME/data_store). Here, we have opened the directory /heidorn/data_store/testfits:

Atmosphere Screenshot 5

  • This will load the image below:

Atmosphere Screenshot 6

  • Any of the JS9/DS9 functions are available. Below is an example of applying a log transform:

Atmosphere Screenshot 7

  • This image can be saved permanently to your Cyverse DataStore and shared with the Astrolabe project by selecting:

Atmosphere Screenshot 8

  • By default this file will be saved in the Firefox download directory. This file is on the Atmosphere instance so would be deleted when the VM is shut down when you are done. That is why we made the link to the DataStore using FUSE. In this case We used Firefox instances to change the default download directory. You could also allow it to save to the Download directory and then copy the file from terminal emulator or using the Astrolabe Atmosphere native GUI.
  • You can see any files in your atmosphere VM by clicking on the “folder” icon at the bottom of the screen:

Atmosphere Screenshot 9

  • Since we linked the astrolabe directory to the data store using FUSE to the DataStore you can see data store files there:

Atmosphere Screenshot 10