Updated Introduction_to_ISIS (markdown)

-----

  - [Introduction to ISIS](#Introduction-to-ISIS-)

      - [What is ISIS3?](#What-is-ISIS3-)

      - [Getting Started](#Getting-Started-)

      - [Setup for Linux/Unix](#Setup-for-LinuxUnix-)

          - [C Shell](#C-Shell-)

          - [Bourne Shell](#Bourne-Shell-)

      - [Getting Help](#Getting-Help-)

      - [User Interface for ISIS3](#User-Interface-for-ISIS3-)

      - [What is ISIS?](#What-is-ISIS-)

      - [User Interface for ISIS](#User-Interface-for-ISIS-)

      - [Reserved Command Line

        Arguments](#Reserved-Command-Line-Arguments-)

      - [Parameter Command Line

        Arguments](#Parameter-Command-Line-Arguments-)

      - [Application Running Modes](#Application-Running-Modes-)

      - [ISIS3 Graphical Mode](#ISIS3-Graphical-Mode-)

      - [ISIS3 Text Mode](#ISIS3-Text-Mode-)

      - [ISIS Graphical Mode](#ISIS-Graphical-Mode-)

      - [ISIS Text Mode](#ISIS-Text-Mode-)

      - [Using qview to View Cubes](#Using-qview-to-View-Cubes-)

          - [Load and Display a Multi-Band

            Cube](#Load-and-Display-a-Multi-Band-Cube-)

                Composite](#Display-a-Red-Green-Blue-Color-Composite-)

      - [Bonus](#Bonus-)

<span id="What-is-ISIS3"></span>

<span id="What-is-ISIS"></span>

## What is ISIS3? [¶](#What-is-ISIS3-)

## What is ISIS? [¶](#What-is-ISIS-)

-----

ISIS3 is an image processing software package. The focus of the software

ISIS is an image processing software package. The focus of the software

is to manipulate imagery collected by current and past NASA planetary

missions sent to Mars, Jupiter, Saturn, and other solar system bodies.

If you're familiar with commercial image processing packages (for

example: Adobe Photoshop, PaintShop Pro, Envi, or ERDAS Imagine) you'll

recognize many of the standard image processing operations ISIS3 is

recognize many of the standard image processing operations ISIS is

capable of, such as contrast stretch, image algebra, filters, and

statistical analysis.

However, the real power of ISIS3 is its unique capabilities for

However, the real power of ISIS is its unique capabilities for

processing data from NASA spacecraft missions such as Voyager, Viking,

Galileo, Mars Global Surveyor, and Mars Odyssey. ISIS3 is able to import

Galileo, Mars Global Surveyor, and Mars Odyssey. ISIS is able to import

raw mission data into a usable geospatial image product, and has tools

for digital mosaicking of adjacent images, photometric modeling and

normalization, removal of systematic noise patterns, overlaying

functions.

The following are just a few examples of how the USGS Astrogeology

Research Program has used ISIS3 in our work (links open in a new

Research Program has used ISIS in our work (links open in a new

window):

  - **Global mosaics** : mosaicking hundreds or thousands of images

![Mars Hemisphere Mosaic](attachments/download/1092/Mars_hemi.gif)

> This famous mosaic of the Valles Marineris hemisphere of Mars was

> created using ISIS3. The mosaic is composed of 102 Viking Orbiter

> created using ISIS. The mosaic is composed of 102 Viking Orbiter

> images of Mars, and is projected into point perspective, a view

> similar to that which one would see from a spacecraft at a distance of

> 2500 kilometers from the surface of the planet.

    Program](http://astrogeology.usgs.gov/Projects/PlanetaryMapping/)

    for more information about this work.

  - **Scientific Research** : Using ISIS3 to mosaic images of a region

  - **Scientific Research** : Using ISIS to mosaic images of a region

    of interest to create a scientifically accurate image product, and

    analyzing the imagery based on spectral, textural, or other

    attributes. See the following Science Magazine abstract for examples

    of images from the Mars Exploration Rover Mission Microscopic Image

    that were processed and analyzed using ISIS3 as part of the

    that were processed and analyzed using ISIS as part of the

    scientific research resulting from the mission: Textures of the

    [Soils and Rocks at Gusev Crater from Spirit's Microscopic

    Imager](http://astrogeology.usgs.gov/search/details/Mars/MER/ImagerFindings/ScienceMI824/pdf)

    .

<span id="Getting-Started"></span>

<span id="User-Interface-for-ISIS"></span>

## Getting Started [¶](#Getting-Started-)

## User Interface for ISIS [¶](#User-Interface-for-ISIS-)

-----

To run ISIS3 applications, two things must happen. First, the ISIS3

software has to be installed. The installation procedure will change

from time to time so please see the ISIS Download and Installation Guide

for the most recent instructions. Second, your environment must be setup

so you can execute ISIS3 applications. To set your environment up

correctly you should first find out where ISIS3 has been installed. The

default location is */usgs/pkgs/isis3/isis* .

The setup process will modify your environment:

  - The environment variables PATH and LD\_LIBRARY\_PATH will be

    modified to include the ISIS3 directories

  - If not already defined, the environment variable ISISROOT will be

    set to its default value

The setup for ISIS3 on a "Unix" type system depends on which shell you

work under. Follow the instructions below for your shell.

<span id="Setup-for-LinuxUnix"></span>

## Setup for Linux/Unix [¶](#Setup-for-LinuxUnix-)

-----

<span id="C-Shell"></span>

### C Shell [¶](#C-Shell-)

If you are using C Shell (i.e. csh) or some variant (such as tcsh):

**Step 1** : If ISIS3 is installed in the default location

(/usgs/pkgs/isis3/isis) go to step 2.  

If ISIS3 is not installed in the default location you need to set the

environment variable ISISROOT.  

On the command line use setenv to set the ISISROOT variable to the

proper location  

(replace the x's and y's with the complete path to where ISIS3 is

installed):

    setenv ISISROOT /xxxxx/yyyyy/isis

**Step 2** : Use the source command to execute the ISIS3 startup script:

    source /xxxxx/yyyyy/isis/scripts/isis3Startup.csh

If you want ISIS3 to be initialized when you login, place the above

commands in your .cshrc file.

<span id="Bourne-Shell"></span>

### Bourne Shell [¶](#Bourne-Shell-)

If you are using the Bourne shell (i.e. sh) or one of its variants

(bash, ksh):

**Step 1** : If ISIS3 is installed in the default location

(/usgs/pkgs/isis3/isis) go to step 2.  

If ISIS3 is not installed in the default location you need to set the

environment variable ISISROOT.  

On the command line set ISISROOT to the proper location and export the

variable using:

    ISISROOT=/xxxxx/yyyyy/isis

    export ISISROOT

**Step 2** : Use the .(dot) command to execute the ISIS3 startup script:

    . /xxxxx/yyyyy/isis/scripts/isis3Startup.sh isis3

If you want ISIS3 to be initialized when you login, place the above

commands in your .profile file.

For those of you who need to work in both version 2 and 3 of ISIS, we

suggest you keep them separate by having different terminal windows for

each instance. For example, have one xterm with the environment set for

version 2 and another set for version 3.

<span id="Getting-Help"></span>

## Getting Help [¶](#Getting-Help-)

-----

The [ISIS Support

Center](https://github.com/USGS-Astrogeology/ISIS3/issues) is our online

knowledge base, bug tracking, announcements, and user support center. If

you need help, want to get the latest news, find out about the status of

a bug (i.e. software glitch), or just want to learn more and interact

with other ISIS3 users, the [ISIS Support

Center](https://github.com/USGS-Astrogeology/ISIS3/issues) is the place to

go\! The ISIS Support Center provides access to help on ISIS3.

[![IsisSupport.png](attachments/thumbnail/1091/300.png)](attachments/download/1091/IsisSupport.png "IsisSupport.png")

Here, you can search for questions, tickets and bug reports from other

ISIS3 users and the ISIS Support Team -- a post about your subject may

already have been answered. If you can't find what you are looking for,

you can register for a user name and then submit your question as a

Question issue. Please read the [Guidelines](Guidelines) page before

registering.

To participate in discussions or post issues, it is important that you

follow the [Guidelines for Reporting

Issues](Guidelines_for_Reporting_Issues) .

<span id="User-Interface-for-ISIS3"></span>

## User Interface for ISIS3 [¶](#User-Interface-for-ISIS3-)

-----

ISIS3 programs fall into two main groups: interactive and

ISIS programs fall into two main groups: interactive and

non-interactive. Interactive programs allow you to observe the results

of actions you take almost immediately. The main interactive program is

[**qview**](http://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/qview/qview.html)

, the image display program for ISIS3. However, most programs in ISIS3

, the image display program for ISIS. However, most programs in ISIS

fall into the non-interactive group. These programs process the data you

supply, usually one or more image files, and write the results to a new

file. Some examples are

[![QviewTwoCubes.png](attachments/thumbnail/1090/300.png)](attachments/download/1090/QviewTwoCubes.png "QviewTwoCubes.png")

> **qview** , ISIS3's image display application, is an interactive

> **qview** , ISIS's image display application, is an interactive

> application\]\]

All ISIS3 programs are launched via the command line. The command line

All ISIS programs are launched via the command line. The command line

refers to the text typed at the prompt of a terminal window such as

xterm, console, or putty, or in a script like cshell, or perl. ISIS3

xterm, console, or putty, or in a script like cshell, or perl. ISIS

programs are started by typing the name of the program followed by any

arguments. All arguments must be separated from each other by at least

one space.

case (i.e., -help is the same as -HElp). A list of basic reserved

arguments includes:

  - **-webhelp** Launch a web browser showing the ISIS3 help page for

  - **-webhelp** Launch a web browser showing the ISIS help page for

    that program. All other arguments will be ignored.

  - **-help** Display a list of the program's parameters showing their

    default values. For example:

different types of parameters:

  - Cube file names - A cube file name is the location on disk of an

    ISIS3 cube. It can be either the input to this program or where to

    ISIS cube. It can be either the input to this program or where to

    place the output. Input cubes, must be the output from some other

    ISIS3 program. Most programs can process cubes from ISIS2, but some

    ISIS program. Most programs can process cubes from ISIS2, but some

    information may be interpreted differently. Output cubes, will

    always be the location to place processed results from the

    application. When entering the filename of a cube it is not

    to= f431a62

  - Data file names - A data file name is the location on disk of a file

    which is not an ISIS3 cube. This includes input files from missions

    which is not an ISIS cube. This includes input files from missions

    such as Mars Global Surveyor or Viking, and output files such as

    that produced by the program **stats** or **isis2std** .

    lines=1024

  - Boolean - Boolean parameters are used as flags to indicate true or

    false. The ISIS3 user interface allows true values to be represented

    false. The ISIS user interface allows true values to be represented

    by True, T, Yes or Y. False values can be False, F, No or N. Any

    mixture of upper and lower case letters is allowed. The name of the

    parameter for boolean's is usually a question such as USEDEM. This

arguments are present on the command line, the program will run in text

mode unless explicitly overridden using the reserved argument -gui.

<span id="ISIS3-Graphical-Mode"></span>

<span id="ISIS-Graphical-Mode"></span>

## ISIS3 Graphical Mode [¶](#ISIS3-Graphical-Mode-)

## ISIS Graphical Mode [¶](#ISIS-Graphical-Mode-)

-----

To run an ISIS3 program in graphical mode, simply type the name of the

To run an ISIS program in graphical mode, simply type the name of the

program followed by the Enter key. The program will display a window

that allows you to set parameters for the program, start/stop running

the algorithm on the data, observe the current status of the program,

argument caused the program to run in graphical mode instead of in text

mode.

<span id="ISIS3-Text-Mode"></span>

<span id="ISIS-Text-Mode"></span>

## ISIS3 Text Mode [¶](#ISIS3-Text-Mode-)

## ISIS Text Mode [¶](#ISIS-Text-Mode-)

-----

For text mode, ISIS3 programs get all their parameters from you via the

For text mode, ISIS programs get all their parameters from you via the

command line arguments, process the data, and then exit. Programs may or

may not show a status message and results on the terminal window. While

running, an application that encounters an error will show the error

Naturally, one of the first things anyone wants to do when they get

their hands on image data is look at it\! The **qview** application is

the image viewer for ISIS3. **qview** has a number of tools to let you

the image viewer for ISIS. **qview** has a number of tools to let you

zoom in and out, change the contrast, choose color combinations,

compare, and otherwise interact with and look at your images. We'll talk

about some of these tools in detail later. For now, let's just learn how

    viewer application window will open.

2.  Select Open... from the File menu. A dialog box labeled "Open" will

    appear. Images in the native ISIS3 format are called ISIS3 cubes or

    appear. Images in the native ISIS format are called ISIS cubes or

    simply cubes.

      - Find the directory containing your ISIS3 cubes

      - Find the directory containing your ISIS cubes

      - Select one or more to open

      - Click the Open button

-----

Now that you know how to run ISIS3 programs go experiment with some of

Now that you know how to run ISIS programs go experiment with some of

the basic ones like **stats** , **hist** or **mirror** .

Download the ISIS3 cube

Download the ISIS cube

[Intro2isis.cub.gz](attachments/download/1084/Intro2isis.cub.gz) - the

cube is compressed in a GZIP archive file. Use gunzip to uncompress the

cube. The filename of the cube is Intro2isis.cub.