The DUSP GIS Environment

Setting up your DUSP ArcGIS Environment

Working on the computers in the labs around campus is a bit different than working on your own personal machine. All of the MIT-owned (lab) computers are networked on a network called “Athena”. Each member of the community is provided an account on Athena that will travel with you from computer to computer. The network allows access to on-campus computers, authenticates campus wide licenses and applications, and provides each user with a small amount of storage space in something called a ‘locker’. Lockers can store documents and files that you can access wherever you log in.

Figure 1. MIT computer ecosystem

The benefits of Athena are many. For starters, you can create a profile that will configure your computing environment to start up in a consistent manner no matter what computer you sign on to, and you can save documents to the network that you can then open on any computer. However, the network is limited, and not very friendly for users of computationally heavy software, such as ArcGIS, the main software we will be learning GIS on. You have very limited space in your ‘locker’, and your locker is stored remotely. Because working with GIS uses large files, you do not want to keep these on the network. It can make your computer run very slowly, and you will run out of space quickly.

Get an external hard drive! The solution to this is to make sure the datasets you are using are not stored on the network, but instead on a local drive or a thumb/external hard drive. We recommend a drive with atleast of storage.

Pre-Objective - Installing Certificates on your CRON account

Certificates are key to using secure web services at MIT, such as Atlas, WebSIS,and Stellar. They are a safe way for MIT’s web applications to identify you without you needing to type in a username and password. You should have already installed MIT certificates on your personal computer. The following steps will help you install a certificate on your CRON account. This certificate will work whenever you log into any of the CRON computers.

  1. Go to https://ca.mit.edu/ca/ and fill out the identifying information. Click “Next”.
  2. On the next screen, use the default settings to finish the certificate process. Click “Next”
  3. Close your internet browser.

Working with GIS files and setting up your Computing Environment

GIS software, specifically ArcGIS, is a technical tool that requires knowledge and awareness of the computing environment you are working in. In this course, we will be using a software package called ArcGIS. In order to get ArcGIS running optimally, we need to setup your computing environment. In this simple workflow, you will setup a lab computer to optimally run ArcGIS in the MIT Athena environment, and then set up your personal computer to run ArcGIS.

Working with GIS Files

There are two major categories of files you will work with, map documents and data files. Map documents allow you to compose data, overlay layers, and create a map. Data files exist separatly from the Map document, and contain geographic (spatial) data. The map document ‘views’ the data files.

Map Document (MXD) File - One of the key ways ArcMap differs from a regular software program is that an ArcMap map file, or “MXD,” does not contain data, only links to data stored elsewhere. It also contains a limited set of information about layout, symbology, and display settings for the data. Therefore you cannot share a map document by sending an MXD – you must also send the data shown on the map. For these reason most maps are shared by exporting a PDF document. Designers familiar with Adobe InDesign will notice this is similar to how that program works.

Data Files – Spatial data exists in a number of different formats, we will discuss these over the course of the semester. The most common format is called a ‘shapefile’. Shapefiles are actually a collection of files that contain geometry, attributes, and projection information. The standard shapefile can consist of up to seven different files with different extensions. For GIS software to read a shapefile, you need all of these files in the same directory. If any are missing, you will not be able to open it. To move shapefiles, make sure all of the necessary files are in your folder, and then zip or move the entire folder. ArcCatalog is a utility within ArcMap that will assist in moving shapefiles.

Components of a Shapefile

Types of mandatory files:

  • .shp — shape format; the feature geometry itself
  • .shx — shape index format; a positional index of the feature geometry
  • .dbf — attribute format; attributes for each shape, in dBase IV format

Types of optional files:

  • .prj — projection format; the coordinate system and projection information
  • .sbn and .sbx — a spatial index of the features
  • .fbn and .fbx — a spatial index of the features for shapefiles that are read-only
  • .ain and .aih — an attribute index of the active fields in a table
  • .ixs — a geocoding index for read-write shapefiles
  • .mxs — a geocoding index for read-write shapefiles (ODB format)
  • .atx — an attribute index for the .dbf file in the form of shapefile.columnname.atx (ArcGIS 8 and later)
  • .shp.xml — geospatial metadata in XML format
  • .cpg — used to specify the code page (only for .dbf) for identifying the character encoding to be used
Figure 2. Components of a Shapefile

Using Windows Explorer, and not ArcCatalog, will reveal all files associated with a specific shapefile and necessary to open and view that particular shapefile.


A distinctly different type of data file is called a geodatabase. A geodatabase is another way to store geographic data and keeps spatial data in what are called ‘feature classes’, instead of shapefiles. A geodatabase can be thought of as a bin where you can put geographic data into these ‘feature classes’ and then manipulate the data by acting within the geodatabase. ArcGIS uses a ‘default’ geodatabase to store files produced by various analysis tools, and will store files here unless you tell it to do differently.

Default Geodatabase – While working on a map, ArcMap uses a “Default Geodatabase” that serves as a scratch space to store files. By default, this scratch space is set to your Athena locker. Because your Athena locker is on the network, we need to move this scratch space to a local drive. Following are instructions for how change the scratch space from your Athena locker to your C:\temp folder on your local machine.

Figure 3. GIS Computing Environment

1. Set your Home Folder to C:\temp

Your home folder is the location where your Map Document will be stored and is used by default to save results, store new datasets, and access information. Make sure this is not on the network, and set it to your local drive. On the lab machines, we will use C:/temp, on your laptop, create a GIS folder and use that.

  1. Launch ArcMap from Start Menu>All Programs>ArcGIS>ArcMap 10.4.1
  2. From the “New Document” dialog box, select the template for Blank Map and click “OK.”
  3. Click on Windows -> Catalog
  4. Click on the “Options” Button shown in the diagram to the right
  5. Select the “Home Folder” tab. Set your home folder path to C:\temp. (Computer -=> WinAthena (C:) > temp) Set this as your Home Folder and click OK.
  6. Close your map document. This setting should be saved to your profile and stay the same on any CRON PC when you open up ArcMap.
Figure 4. Set Home Folder

We strongly recommend using C:\temp or the root directory of an external hard drive, since many ArcMap tools will not run if the Scratch space path contains spaces.

2. Create and Set a Default Geodatabase

Create a workspace within your Home folder that will be the location of your MXD and will serve as the working directory for your map project, meaning that all your files will by default save to this location.

1. Using Windows Explorer, navigate to C:\temp. (Computer > WinAthena (C:) > temp) This will be our main GIS working directory where files will save by default.

Figure 5. Create a Workspace

2. Open ArcMap. At the default opening screen, you will see the following. Here we set our default geodatabase. A geodatabase is a storage location for files from ArcGIS. In the dialog, set this to C:\temp.

Figure 6. Set your Default Geodatabase

Here, if you browse to C:\temp, you’ll see the following. Select the default.gdb geodatabase. ArcGIS has created this automatically when we told the software we want to use C:\temp as our home folder. Important takeway: C:\temp is NOT ON THE NETWORK, but right there on your machine.

Figure 7. Set your Default Geodatabase
3. Click OK to open up ArcMap.

If you have been working on a map document using a Default Geodatabase that is stored elsewhere, and you have data in it you want to use, you can copy and paste data from your other location into your new Default Geodatabase using ArcCatalog. When completed with your work or you need to move to a different computer, copy and paste this Default Geodatabase scratch space on your external hard drive or thumbdrive.

3. Set Relative Pathnames

A ‘file path’ is the route you take in Windows Explorer to get to the location in which your map document and data files are stored. It is good practice to save all of your files in the same root directory, putting data in a ‘data’ folder and your MXD either on the root or in a ‘projects’ folder. When you move between computers, each computer has different drives and settings, so this path will change. Often, this will ‘break’ the link between the map document and your data files, and your data will not show up within your MXD. ArcGIS allows us to store relative path names, and when stored, it will attempt to fix these broken links. If we set ArcMap to store relative path names, it will store pathnames based on your root directory, and modify them for you if you are working from an external drive and move from one computer to another.

  1. After starting a new blank map go to File>Map Document Properties
  2. Check the box that says “Store relative filenames to data sources”
  3. Click OK and save your file.

4. Clean up Folder Connections

ArcGIS is unique that in order to add data to a map document, or see and modify folders in Catalog, you must ‘Connect’ your map document to the directory in which your data is stored. Unlike other programs, you cannot just use Windows Explorer to locate and find files. Instructions to connect to a folder are as follows:

a. Connect to a Folder
  1. In Catalog, select ‘Connect to Folder’.
  2. Navigate to your working directory, click OK.
Figure 8. Connect to Folder

By default ArcMap will save the locations of folders you have opened to retrieve or view data once you connect to them. Although intended to be a convenience to the user, these connections can slow down the program, especially if they are located on networked or unavailable drives (such as portable hard drives). Therefore it is a good practice to keep these folder connections to a minimum. In addition, if you are an advanced user and connect to remote Database Servers, this same principle applies. We want to remove all folder connections we are not using to prevent ArcGIS from looking for something that is not there.

b. Disconnect from a Folder

If you need to disconnect from a folder, you can do that easily.

  1. In the “Catalog” window find the section labeled “Folder Connections”
  2. Right click on all folders, except for C:\ and C:\temp, and click “Disconnect Folder” (remember these are only shortcuts).

5. Protip! Keep your Workspace Organized and Efficient

Working in GIS for any length of time can very easily create an overwhelming cacophony of files, resulting in wasted time and difficulty tracing your steps. We strongly recommend creating well-organized workspaces and Map Documents. Organize your data files and map documents into folders that will help you keep track of where files and documents are. You should also keep your map documents organized. Organize your ArcMap Table of Contents by right clicking on “Layers” and creating “Group Layers,” as shown below. You don’t need to do anything at this step, just keep your stuff organized!

Figure 9. Organized Workspaces

You can close ArcMap.

6. Set Hidden Files to be visible and Show File Extensions

One last important item to get setup your Windows environment is to change the File Explorer Options in Windows so you can view hidden files and folders and see file extensions. Windows, by default, will hide items from you. They do this to simplify the experience for the average user, but unfortunately, it hides some files that are needed by ArcGIS. Changing your settings is easy, follow the following steps.

  1. In the Start menu, type File Explorer Options. Select File Explorer Options from the list of programs that appears. The File Explorer Options dialog will open.
  2. Click on the View tab, this is where we can make two changes to how Windows displays our files.
Figure 10. Customize File Explorer options
  1. In Advanced Settings, find and check Show hidden files, folders, and drives, and then find and uncheck Hide extensions for known file types
  2. Click OK. You are ready to go!

Before you Start a Map Project - Checklist

Use this checklist every time you start a new GIS project.

  1. The ArcMap (MXD) file, Default Geodatabase, and data files should be located in the same directory. They can be stored within different subfolders within this directory for organization purposes.
  2. The project folder should be copied to the location C:\temp
  3. The MXD file should have “relative filenames” (File>Map Document Properties)
  4. The MXD file should be set to use the Default Geodatabase within the project folder (File>Map Document Properties)

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