EOVSA Data Analysis Tutorial

From EOVSA Wiki
Revision as of 16:07, 5 May 2019 by Sjyu (Talk | contribs)

Jump to: navigation, search

Software

We have developed two packages for EOVSA data processing and analysis:

  • SunCASA A wrapper around CASA for imaging and visualizing spectral imaging data of the Sun. More information about CASA can be found on NRAO's CASA website . Note, (Sun)CASA is ONLY AVAILABLE on UNIX-BASED PLATFORMS (sorry Windows users).
  • GSFIT: A IDL-widget(GUI)-based spectral fitting package called gsfit, which provides a user-friendly display of EOVSA image cubes and an interface to fast fitting codes (via platform-dependent shared-object libraries).

There are two approaches in accessing our software packages. One is through our Amazon AWS server (recommended for participants of the EOVSA tutorial at the RHESSI 18 Workshop). Another is to install them on your own machine. We discuss the first approach in Section 1.1, and the second in Section 1.2.1 (SunCASA) and 1.2.2 (GSFIT).

Connecting to AWS server

We use an Amazon AWS Lightsail server for testing purposes. The server has 2 CPUs, 8 GB RAM, and 160 GB SSD storage. It runs CentOS 7 (1901-01) Linux. Please limit your usage to LIGHTWEIGHT DATA PROCESSING ONLY.

NOTE: THE ACCOUNT IS ONLY INTENDED FOR THE EOVSA TUTORIAL, BUT *NOT* FOR CARRYING OUT ACTUAL DATA REDUCTION

  • Obtain SSH Key from Bin Chen
  • Put it under a secure location on your own machine.
  • Follow remaining directions depending on your client machine.

Linux / Mac

Recommend to use "~/.ssh" (create if it does not exist by "mkdir ~/.ssh").

  • Edit the permission of ~/.ssh and the key (here I use ~/.ssh as the directory to place your key)
chmod 700 ~/.ssh
chmod 400 ~/.ssh/guest-virgo.pem
  • Log on to test AWS server (password-less)
ssh -X -i ~/.ssh/guest-virgo.pem guest@virgo.arcs.az.njit.edu

Windows (MobaXterm)

Recommend to use "Documents\MobaXterm\home\.ssh", which should exist if you have already installed the free MobaXterm[1].

  • Create new session, click SSH, enter virgo.arcs.az.njit.edu for Remote host, guest for username.
  • On advanced SSH settings tab, click Use private key, navigate to and select file guest_key.pem
  • Close setup window and click the new sessions icon, which will log you in.

Once the connection is setup, you will have access to SunCASA and GSFIT (included in the sswIDL installation): Enter SunCASA

[guest@ip-172-26-5-203 ~]$ suncasa

Enter sswIDL

[guest@ip-172-26-5-203 ~]$ sswidl

Installation on Your Own Machine

SunCASA

MacOS

We have packed a standard disk image (dmg) for installation on MacOS. It has been tested to work under Mojave (macOS v10.14). YMMV for earlier versions of macOS. Installation steps below:

  • Download SunCASA disk image (SunCASA-0.7.4_Pre-release.OSX.dmg).
  • If you do not have Java SE Development Kit (JDK) installed on your Mac, please download from the official site and install it before SunCASA installation. The latest version (JDK 12) was tested to work properly. Earlier versions may also work but YMMV.
  • Open the disk image file (if your browser does not do so automatically).
  • Drag the SunCASA application to the Applications folder of your hard disk.
  • Eject the SunCASA disk image.
  • Double-click the SunCASA application to run it for the first time. If the OS does not allow you to install apps from non-Apple sources, please Change the settings in "System Preferences-> Security & Privacy -> General" and "Allow applications downloaded from: Mac App store and identified developers". If the OS still reports that the app is damaged, please turn off the OS Gatekeeper for now by running command sudo spctl --master-disable in Terminal. Then double-click the SunCASA application again.
  • Initialize SunCASA. To do so, run !install_suncasa from a SunCASA prompt. This step also allow you to create symbolic links to the SunCASA version and its executables (Administrator privileges are required), which will allow you to run suncasa, casaviewer, casaplotms, etc. from any terminal command line.
  • Important: Make sure to turn the OS Gatekeeper back on after the installation by running sudo spctl --master-enable in Terminal.
  • Optional: To update the data repository, run !update-data from the SunCASA prompt.
  • Restart SunCASA by exiting the current SunCASA prompt, and run suncasa in Terminal or double-click the SunCASA application icon.
  • Now SunCASA has been up and running on your Mac.

Linux

  • To install SunCASA for Linux, we have packaged up a binary distribution of SunCASA which is available as a downloadable tar file. We have tested the package under Scientific Linux 6 (derived from RHEL 6) and CentOS 7 (equivalent to RHEL 7). They may work under some other Linux distributions (e.g. Ubuntu), but YMMV.
  • If the following library packaages are not on your machine, please install them before installing SunCASA.
    • xauth
    • libXft
    • libXi
    • libXrandr
    • libXfixes
    • libXcursor
    • libXinerama
    • libGL
    • libXpm


tar -xzvf SunCASA-release-##version##.tar.gz

You do not have to have root or sudo permission to install or run SunCASA. The package is self-contained in the (untarred) directory "SunCASA-release-##version##". You can move/delete the SunCASA directory as you wish. But to use the executables, do the following:

  • All executables, including suncasa are in the SunCASA-release-##version##/bin directory. Include these executables to your path (examples below are in bash)
cd SunCASA-release-##version##/bin
PATH=`pwd`:$PATH 
  • Then you can initialize SunCASA with the command in bash
install_suncasa
  • Optional: To update the data repository, run !update-data from the SunCASA prompt.
  • Now SunCASA has been successfully installed on your machine. Open a new Terminal and run suncasa.

GSFIT

We have developed a IDL-widget(GUI)-based spectral fitting package called gsfit, which provides a user-friendly display of EOVSA image cubes and an interface to fast fitting codes (via platform-dependent shared-object libraries). Fits to individual spectra can be done quickly for manual investigation, while parallel/multi-core batch processing of selected blocks of data can also be performed. A helper routine called gsfitview allows further display and investigation of the fitting results.

Spectral Imaging with SunCASA

Spectral Fitting with GSFIT