Approaching a Scripting Task

ENV 859 - Geospatial Data Analytics   |   Fall 2024   |   Instructor: John Fay  

Introduction: The Challenge

Your research team just caught wind that you know Python. They have some ARGOS tracking data - a text file in a marginally human readable format and with a lot of “noise” - and they want you to build a tool that will parse this data into a format whereby a user can enter a date and retrieve the location at which the turtle was found.

With some trepidation, we accept this challenge. It’s a great opportunity for us to apply the concepts we learned in the last section, namely Python syntax, variables & objects, properties & methods, data structures, etc. It’s also a great opportunity to learn how these elements are assembled into a coherent and effective workflow, i.e., writing a Python script.

In this first session, we examine how to approach a scripting task. Writing code is somewhat like translating human ideas into computer logic, and some simple techniques will make that process easier.

Learning Objectives

On completion of this lesson, you should be able to:

  • Articulate an example task where Python is helpful
  • Develop pseudocode for an example task
  • Dissect your pseudocode into a coding workplan
  • Prepare a coding workspace

Background - The Overall Task

SeaTurtle.org posts tracking data for various individual turtles. These data are in a somewhat raw format derived from ARGOS satellite tracking systems. I have downloaded data for an adult loggerhead turtle, Sara, and our task is to develop code that can interpret Sara’s raw tracking data. Specifically, we want to allow a user to specify a date and have our code report where Sara was seen on that date.

Tackling this task requires some understanding of the raw ARGOS data, both its format and the data reported. We will discuss this in class and later in this lab. However, you can see in the figure above, that all the information needed to do this task is in the Sara.txt file; we just need to develop code to extract exactly the data we want and report it.

Resources

  • Tracking data for Sara the turtle: sara.txt (Right-click and save the file…)
  • A page listing the raw code for specific tasks in this exercise is here.
  • A link to a finished Git repository for this project is here: https://github.com/ENV859/TurtleTest

Step 1. Generating pseudocode

The context of this exercise is as follows: We have obtained data in a standard format, in this case ARGOS tracking data. We want to write a script that can read any ARGOS tracking data set, extract records matching a date specified by the user, and report the location of any observations made at that date. Reported observations must also meet quality criteria using tags included in the ARGOS dataset.

Such a script requires many steps, and to take on all the steps at once is a daunting task. Therefore, we first consider the pseudocode of the exercise, that is, the logical steps involved in meeting our objective given our inputs. In generating pseudocode, we don’t have to know the exact Python commands we’ll implement; we just want to identify the key steps. It’s quite possible we’ll revise some of our pseudocode when actually implementing it, but sketching things out is nonetheless a useful first step in writing a script of any complexity.

Generating pseudocode can be more art than science and gets easier the more you understand particular coding environment. (Think about how much better you are at putting together geoprocessing models now than when you first started learning ArcGIS…) In other words, it may not come naturally at first, but with practice you’ll get better. I’ve listed the pseudocode for this exercise below:

» Task 1.1: Develop pseudocode for your project

  1. Open the ARGOS data file

  2. Read and parse each line

    a. Skip comment lines

    b. Skip records below a quality threshold (qc <> 1, 2, or 3)

    c. Add observation date to a date dictionary, keyed by the observation UID

    d. Add observation lat./long. to a location dictionary, keyed by the observation UID

  3. Allow user to specify date

    a. Inform if date is invalid

  4. Identify keys in date dictionary matching user supplied date

  5. Identify values in location dictionary with keys found above

  6. Print information to screen

Step 2. Devising a plan of attack…

The pseudocode we developed in Step 1 is a blueprint, but not a construction plan.

The next step, therefore, is to map out a sequence - going from simple to more involved - of putting the necessary steps together. The idea here is to isolate the tasks involved in the script into discrete steps such that each step can be built, and debugged in sequence. If we do too much at once and it doesn’t work, we’ll spend more time figuring out where it went wrong. However, if we start simple and something goes awry, our debugging is more confined.

Determining an appropriate sequence for tackling a project is a bit of an art form, one that you improve with more experience and comfort with the coding language. The general idea, however, is start with a very simple task and add complexity. For example, if you are going to iterate through a chunk of sub-code, first get the chunk of sub-code working, and then add the iteration.

A more relevant example for us is the fact that we need to read text in from a file, and for each line of text in this file, split it into a list of values, and then work with each value. That in itself seems like a tall order, but if we start with just a line of text copied from the data file and pasted into our code - by us, not via Python command - we can tackle the simpler task of parsing that string into a list.

With that in mind, the sequence I suggest we take is as follows:

Sequence Task
1. Parse a single line of tracking data into variables
2. Read a single line of tracking data from the file into Python (and then parse into variables)
3. Read in all lines of tracking data from a file into Python (and then parse into variables)
4. While reading in all lines of tracking data, add variables into dictionaries of values
5. Add conditional statements so only valid values are added to the dictionaries.
6. From our dictionaries, extract data for a selected date.
7. All the user to specify the date used to select data from our dictionary
8. Add code to handle if the user enters an improper date

There are certainly other ways of going about this, but I’m hopeful you’ll at least see and appreciate the utility of breaking a scripting objective down into sub tasks can really help in writing complex scripts. We will also, almost certainly, deviate from this sequence as we encounter unexpected glitches or possibly improved pathways to our goal. Still, it’s always useful to start with a plan, one that goes from simple to complex.

I should also add that we will encounter plenty of tasks that we have not covered so far (e.g. reading data from a file?!?). But this provides a great way to learn Python - by doing!

Next up, we will embark on writing code to get this done. But first, we are going to explore a technology that is going to greatly assist us as we bumble through lots and lots of mistakes in getting there, namely Git and GitHub.

Step 3. Preparing your coding workspace

[Prior to actually doing this we may pause and learn Git/GitHub as it will be useful from here on…]

Much like when we approach a task in ArcGIS Pro, we’ll want to create a project workspace that keeps data, code, and output organized and easy to navigate among. Here we’ll create a project folder, and within that a data folder and a docs folder as well as a ReadMe.txt file. Additionally, we’ll create a raw and a processed folder within the data folder.

Once set, we’ll add raw data to our project as well as a metadata file to go with these data.

» Task 3.1: Create your project workspace and add the data

  1. Create a new project folder in your V: drive.
    • As with ArcGIS Pro, you should avoid spaces and odd characters in the folder name or anywhere in its path. We’ll call ours TurtleTrackerProject.
  2. Within the project folder, create a data folder to hold our data files.
    • Within this data folder create a raw data folder to hold raw, original data files, i.e., data not modified by us. This is an important notion in the concept of building a reproducible data pipeline in that any changes we make to the original data should be documented and begin with the data in a format that others can obtain as well.
    • Also within this data folder, create a processed data subfolder. This will keep any data we create with out scripts.
  3. Within the project folder, create a ReadMe.txt file.
    • This file will hold a brief summary of your projects purpose, the date is was created, and info on its author(s).
  4. Add a copy of the sara.txt file to your data/raw folder.
    • You can create a new text file and copy and paste the contents of the online version into that file.
  5. Add a metadata file to go along with your copy of the sara.txt file.
    • As the data we obtained does not have any associated metadata file already, we’ll create our own. This can include the link from which you obtained the data, the date downloaded, and any other useful information we can provide to allow the user to obtain the same data. Name this file something that obviously links this with the original file, e.g., README_sara.txt.
  6. Lastly, open your project workspace in VSCode.
    • Open VS Code.
    • From the File menu, select Open Folder and open your project folder.
    • Trust the folder.

Step 4. Building (and debugging) your code

From here, we incrementally build, run, debug our coding tasks, often finding obstacles we need to work around and sometimes finding ways to improve our workflow. This will be the topic for upcoming lessons…