Lab01 Exercises (20 pts)#

UW Geospatial Data Analysis
CEE467/CEWA567
David Shean

modified by Eric Gagliano

Introduction#

Let’s play around with some text files to explore the power of the command line and bash shell.

For the following instructions/questions, please document the command you ran, and the resulting output on the terminal. You can copy and paste everything in a text file, or use whatever method is most efficient. Maybe you want to practice markdown formatting, or if you would prefer to wrap everything into a single shell script, and submit that, go for it.

You will almost certainly need to search for tips on how to answer some of these questions. Please use these external resources, but if you find an explicit solution, don’t just copy and paste the code, review it and try to understand what is actually happening. Note that Stack Overflow and other forums will have excellent information (and probably a lot of advanced information that is over your head) - typically the answer you’re looking for has the most “upvotes” (number to the left of the answer) or some kind of indication as the “accepted answer.”

OK, let’s get started!

Part 1: Look it up in the dictionary (1pt each)#

On your Unix/Linux filesystem, you typically have a dictionary of words (https://en.wikipedia.org/wiki/Words_(Unix)). On OS X, this file is located in /usr/share/dict/words. This file is missing from our barebones JupyterHub Linux distribution, so I added one to the assignment git repo (2.4 MB).

Unzip words#

Fortunately for you, the basic linux operating system we’ve provided includes command-line utilities to unzip files. Navigate to the directory containing the data:

unzip gda_2024_data.zip

This should create a new data subdirectory, with three new files. Check them out with ls -l data

Inspect words#

  1. The words file has no extension. What type of file is this?

    • Hint: check out the file command.

  2. Inspect the file more words. How do you exit the more command?

  3. How many words are in this file?

  4. How many characters?

  5. How big is the file size in bytes?

  6. How many bytes are required to store each character?

    • Hopefully this provides some new insight into file size on your computer.

  7. Print the first 3 words. Print the last 3 words (do this with a command, don’t just view or open in text editor and copy/paste).

  8. Does words include the nickname for the UW mascot (if unfamiliar, ask your neighbor)? If so, what line number?

  9. How many characters are in the longest word?

    • Hint: should be simple one-liner, you don’t need awk for this.

  10. How many words end in “ology”?

Part 2: Inspect and manipulate tabular data (1pt each)#

The text file GLAH14_tllz_conus_lulcfilt_demfilt.csv contains processed/filtered records from ICESat satellite laser altimetry measurements over the Western U.S. between 2003 and 2009.

Don’t worry about details for now, we will explore in the coming weeks. For now, pretend your advisor/boss just sent you this random file (with no metadata) and asked you to inspect and clean up for their old-school analysis tools.

  1. Inspect the file on the command line. Use tab-completion after typing the first few letters of the filename. The extension suggests that this is comma-separated value (.csv) text file - is this true?

  2. Fortunately, there is a header on the first line containing strings for each field (column) name. Some of these should sound familiar.

    • How many fields are there?

    • How many rows contain data (excluding the header)?

  3. How many records are from 2005?

    • Utilities like grep and sed offer powerful functionality with “regular expressions” - one could spend weeks learning these.

    • For now, I’ll give you a hint, if you preceed your grep search string with a carat ^ e.g., ^stringtofind, it will only return records that begin with stringtofind, excluding any records with stringtofind elsewhere in the string.

    • You’ll want to use a pipe | here to pass the output of grep to another command that can count the number of lines.

  4. Create a new file named GLAH14_tllz_conus_lulcfilt_demfilt_latlon.txt with only the lat and lon fields, separated by a space, and sorted in ascending order by lat value.

    • This should be possible without any loops, just need to redirect the stream using pipes | and >. Let’s break the problem down.

      • First, isolate the lat and lon fields - several ways to do this

      • Pipe that output to a command that will replace the , with a on all lines

      • Pipe that output to a command that will sort the numeric lat values

      • Redirect that output to a new file

      • Run a quick head and tail on the output file to verify

  5. Try to plot this new file using the command line gnuplot tool.

    • Run the following commands:

      • gnuplot to leave the shell and enter the gnuplot tool

      • set terminal png

      • set output 'latlon_plot.png'

      • set datafile separator ' '

      • plot 'GLAH14_tllz_conus_lulcfilt_demfilt_latlon.txt' using 2:1 with dots

      • quit to exit the gnuplot and get back to the shell

    • Try guessing what you think each command did.

    • Open the new latlon_plot.png file which should be in your data folder. Remember, this data should be over the Western US. Just by inspection, can you guess the approximate latitude and longitude bounds of Washington?

Part 3: Filter and clean tabular data (1pt each)#

Uh oh! Let’s pretend we’ve made some mistakes. We’ve taken the GLAH14_tllz_conus_lulcfilt_demfilt.csv and inserted some incorrect rows to create unfiltered_GLAH14_tllz_conus_lulcfilt_demfilt.csv.

This csv contains additional rows with missing longitudes, rows with impossible latitude values, and rows with lulc values we are not interested in. The following problems are a bit tougher, but can be pretty helpful in practice.

  1. How many records are missing the longitude field?

    • Try awk -F, '$4 == "" {missing_count++} END {print "Rows with missing longitude:", missing_count}' unfiltered_GLAH14_tllz_conus_lulcfilt_demfilt.csv.

    • If you use this suggested code, briefly explain what each part of the command represents.

  2. Display the records that have impossible latitude values.

    • Valid latitude values should be between -90 and 90.

    • If you’re not sure where to start, try modifying the command suggestion from problem 1.

      • Instead of printing a count, you’ll want to print the row.

      • Try {print $0} to print the entire row.

    • Remember, you can express a logical or as ||.

  3. How many records have lulc values of 11?

    • Can also modify the command sugestion from problem 1.

  4. Combined, how many errors have I introduced? You can just add together your answer from 1, the number of records from 2, and add your answer from 3.

    • Can check your answer: the number of rows in unfiltered_GLAH14_tllz_conus_lulcfilt_demfilt.csv minus the number of errors introduced should equal the number of rows in LAH14_tllz_conus_lulcfilt_demfilt.csv :)

  5. Create a new file filtered_GLAH14_tllz_conus_lulcfilt_demfilt.csv that either removes records with missing longitude fields, removes records with impossible latitude values, or removes records with lulc values of 11.

Extra credit (+1 pt)#

Create a new file fully_filtered_GLAH14_tllz_conus_lulcfilt_demfilt.csv that removes all 3 types of errors (removes records with missing longitude fields, removes records with impossible latitude values, and removes records with lulc values of 11).

Extra Credit: Shell script (+2 pts)#

Create and run a script to answer the following question:

How many words begin with each letter of the alphabet (case-insensitive)?

Useful references for review#

Requirements:#

  • Ignore case, so “A” and “a” are considered the same word

  • Your script should accept the words text file as an input argument (assign to a variable named fn)

  • Your script should create a new output file called words_lettercount.txt

    • Pro tip: You can use variable parameter substitution to append strings to the input filename: out_fn=${fn%.*}_lettercount.txt

    • The ${fn} construct is a less ambiguous variable reference. Need this if you wanted to do something like print your filename and add extra characters echo ${fn}:moretext (try echo $fn:moretext for comparison)

    • The %.* can be used to get the first part of the filename string before any . extension (see SO answer)

  • The output file should include a letter and total count on each line (“a 17096”)

Instructions:#

  1. Create a new shell script in your preferred text editor (nano, vim, emacs or Jupyterlab text editor): nano myawesomescript.sh

  2. Write some code.

  3. Save the script.

  4. Make it executable: chmod +x myawesomescript.sh

  5. Run it! ./myawesomescript.sh words

  6. Review the output more words_lettercount.txt

Submission#

We will review this process during Friday lab

  1. Use git add to stage each new file containing your answers/scripts

    • I recommend you start by adding files one at a time: git add myawesomescript.sh

    • For now, resist the temptation to git add . or git commit -a, as you will inevitably include files that don’t belong in a git repo.

  2. Use git commit -m "Message" to commit these changes, replacing “Message” with an appropriate commit message.

  3. Use git push to push your local changes to your remote repo origin on Github.

  4. Check Github to make sure all of your files have been added to the remote repository.