🗻 Diorama Drama

Python: Geospatial Environment Setup (Part 1)

Here’s a quick run down of what you’re supposed to do to prepare yourself to use Python for data analysis.

Install Python ☑

Install Miniconda ☑

Install the basic Python libraries ☑

Create new environment for your workspace

Install geospatial Python libraries

🐍 Installing Python

Let’s cut to the chase. It’s December 14th, 2021. Python 3 is currently at 3.10.1 version. It’s a great milestone for Python 3 but there were heresay of issues concerning 3.10 when it comes to using it with conda. Since we’re using conda for our Python libraries and environment management, we stay safe by installing Python 3.9.5.

Download 👉🏻 Python 3.10.1 if you want to give a hand at some adventurous troubleshooting

Or download 👉🏻 Python 3.9.5 for something quite fuss-free

📌 During installation, don’t forget to ✔ the option Add Python 3.x to PATH. This enables you to access your Python from the command prompt.

Installing Miniconda

As a beginner, you’ll be informed that Anaconda is the easiest Python library manager GUI to implement conda and where it contains all the core and scientific libraries you ever need for your data analysis upon installation. So far, I believe it’s unnecessarily heavy, the GUI isn’t too friendly and I don’t use most of the pre-installed libraries. So after a few years in the darkness about it, I resorted to jump-ship and use the skimped version of conda; Miniconda.

Yes, it does come with the warning that you should have some sort of experience with Python to know what core libraries you need. And that’s the beauty of it. We’ll get to installing those libraries in the next section.

◾ If you’re skeptical about installing libraries from scratch, you can download 👉🏻 Anaconda Individual Edition directly and install it without issues; it takes some time to download due to the big file and a tad bit longer to install.

◾ Download 👉🏻 Miniconda if you’re up to the challenge.

📌 After you’ve installed Miniconda, you will find that it is installed under the Anaconda folder at your Windows Start. By this time, you will already have Python 3 and Anaconda ready in your computer. Next we’ll jump into installing the basic Python libraries necessary for core data analysis and create an environment to house the geospatial libraries.

📚 Installing core Python libraries

Core libraries for data analysis in Python are the followings:

🔺 numpy: a Python library that enables scientific computing by handling multidimensional array objects, or masked objects including matrices and all the mathematical processes involved.

🔺 pandas: enables the handling of ‘relational’ or 'labeled’ data structure in a flexible and intuitive manner. Basically enables the handling of data in a tabular structure similar to what we see in Excel.

🔺matplotlib: a robust library that helps with the visualization of data; static, animated or interactive. It’s a fun library to explore.

🔺 seaborn: another visualization library that is built based on matplotlib which is more high-level and produces more crowd-appealing visualization. Subject to preference though.

🔺 jupyter lab: a web-based user interface for Project Jupyter where you can work with documents, text editors, terminals and or Jupyter Notebooks. We are installing this library to tap into the notebook package that is available with this library installation

To start installing:

1️⃣ At Start, access the Anaconda folder > Select Anaconda Prompt (miniconda3)

2️⃣ An Anaconda Prompt window similar to Windows command prompt will open > Navigate to the folder you would like to keep your analytics workspace using the following common command prompt codes:

◽ To backtrack folder location 👇🏻

◽ Change the current drive, to x drive 👇🏻

◽ Navigate to certain folders of interest e.g deeper from Lea folder i.e Lea\folder_x\folder_y 👇🏻

3️⃣ Once navigated to the folder of choice, you can start installing all of the libraries in a single command as follows:

The command above will enable the simultaneous installation of all the essential Python libraries needed by any data scientists.

💀 Should there be any issues during the installation such as uncharacteristically long installation time; 1 hour is stretching it, press Ctrl + c to cancel any pending processes and proceed to retry by installing the library one by one i.e

Once you manage to go through the installation of the basic Python libraries above, you are half way there! With these packages, you are already set to actually make some pretty serious data analysis. The numpy, pandas and matplotlib libraries are the triple threat for exploratory data analysis (EDA) processes and the jupyter lab library provides the documentation sans coding notebook that is shareable and editable among team mates or colleagues.

Since we’re the folks who like to make ourselves miserable with the spatial details of our data, we will climb up another 2 hurdles to creating a geospatial workspace using conda and installing the libraries needed for geospatial EDA.

If you're issues following the steps here, check out the real-time demonstration of the installations at this link 👇🏻

See you guys in part 2 soon!

🌱 Google Earth Engine 101

Uploading a shapefile as an asset in GEE and making use of it

🟢 Beginner-friendly.

🆓 Free with no hidden monetary cost.

🤚🏻 Requires registration so sign-up 👉🏻https://signup.earthengine.google.com/, access via browser and Internet connection

🖥️ Available for Windows, Mac and Linux.

Google Earth Engine or lovingly called GEE is another free and open platform provided by Google to provide a very vast and comprehensive collection of earth observation data. Since Sentinel-2 is no longer available for download at USGS Earth Explorer, I find the alternative too challenging for me so GEE seems like the easiest way to go. If you're looking for a one-stop platform to access satellite imagery for free, GEE is a great place to start. You don't have to learn JavaScript explicitly to start using this tool.

Malaysia Bid Round 2023 (MBR 2023)

Tool: ArcGIS Pro 2.6.3 Technique: Symbolization, labeling and SQL expression

MBR 2023 is a peak event that culminates all the effort of data collection and stock take of hydrocarbon resource in the Malaysia. It is an annual event that put together all the exploration blocks, discoverable hydrocarbon fields and late life assets for upstream sectors to evaluate and invest in.

Leading up to the event, the Malaysia Petroleum Management (MPM) updates, re-evaluate and produces maps; static and digital, to cater to the need for the most update stock-take of information that can be gained from various source of exploration output; seismic, full tensor gradiometry, assets; cables, pipelines, platforms, as well as discoverable resources. This year's them aims to include various prospects and initiative to align the industry itself with lower carbon emission and to explore the option for carbon capture storage (CCS) attempts in the popular basins such as the Malay and Penyu Basin. This is a big follow-up with the closing of MBR 2022 with the PSC signing for 9 blocks a few days earlier.

Credit: Sh Shahira Wafa Syed Khairulmunir Wafa

Over ~70 maps for unique blocks have been produced during the finalization stage, ~210 maps during data evaluation and additional 20 for the event. And this excludes the standardized maps to formalize information requested by prospective bidders as well as clients who are facing prospects of extending their contract.

The standardization of the map requires the optimization of workflow and standard templates to cater to rapid changes and exporting to rapid output.

For more information on the event, please access the following resources:

PETRONAS: Malaysia Bid Round

PETRONAS myPROdata

The Malaysian Reserve: Petronas offers 10 exploration blocks in MBR 2023

take care

Studying is hard enough when you are fighting the onset of hormonal hurricane of emotions while you're a teenager. Then you have you formative 5 to 6 years of collegiate years where you learn that your idealistic notions of the world is just plain snobbish and that you're one of the many that finds satisfaction in pushing your ideas into other people's head. Doing all that while studying, it was hard too.

Then comes the job hunting, climbing ladders to nowhere from one workplace to another...just drifting. That was the vacation off from studying and just wanting to find stability.

Then one day, you broke your heart at the same time you get an opportunity to a decent work somewhere. You ran. Then it was about understanding this whole new dimension of knowledge that you've fallen in love with. It was like your first love came back to find you and tell you he's back and that he won't leave you alone anymore. So, back to the books you fall into.

So yeah...studying is a rollercoaster of emotions. Learning is a lifelong journey. You're never too old to learn something new. And then phrase where you can't teach old dogs new tricks is just plain inaccurate. You can teach them new tricks and they can do it if they want to. It's the matter of either they want to do it or if their body can still keep up with them.

If you're an older student, I feel you. You feel left behind at times and frustrated because you feel like you can't catch up with things. If you're someone who's starting to work on research studies, it may be a harder state of mind. Because you're almost always on your own lamenting on you're comprehension of theories and questioning if you get whatever you absorbed right. So...it is hard. How do you know that you're alright and that you're not spinning down the road of doomed isolation? You don't. These are some of the glaring things I think are the universal problems among people who, with the courage of a lion, answered the call of hermitage and subject themselves to an occupation so feared that it is deemed over once high school ends; student:

Wardrobe reduction to daily uniform of hoodies/sweaters and jog-pants/sweatpants

It's totally ok. If you're wearing the same one everyday for the rest of the week, you still win. It's practical, it's easy and for hijabsters, the hoodie helps with instant full head cover while you run to receive those stuff you endlessly ordered online. There's nothing to be ashamed off.

💡I say: Shower 🚿. Every. Day. Twice a day is most ideal. Stay fresh and hygienic. If you're not going anywhere nor are you working out in those attire, then you're good. At least for a week. When you shower, you're giving your body a break from the exhausting task of slouching, the heat of your brain going overdrive and your own face breaking out from the stress. So yeah...shower. Wash your face. Brush your teeth. You're gonna be at risk of letting yourself go when you're left alone too comfortable in your own company. If you're an introvert, it feels like heaven but it doesn't mean you should be at the risk of losing out on the joys of prepping yourself to look good once in a while. Regularly make the effort to find decent clothes you'll use to go out on a Saturday window shopping and kick back to relax. On the rare occasion you get a break from your endless paper chasing, Zoom calls and writing, you can use your wardrobe clearing day to match few clothing and have a runway at home yourself or for a date with yourself to the Netflix movie you're gonna watch on your laptop. Who says you can't dress up to do online shopping? That's the only way you'll know that you do not need that new shade of Forencos lipstick you saw the other day. Duh.

Sudden weight gain/loss

I can't say that is unexpected especially if you're the kind who can go long without exercises and the type who munch while you work (which is a bad habit by the way). But sometimes you can't help if especially if you live on your own or have your own living space. Being on your own makes it kind of easy to get off-track about the norm of things; how much have you eaten today...is that your 5th coffee...should you be finishing that leftovers...etc. It is harder if you don't have your own kitchen and rely on packed food or processed ones.

💡I say: I can assure you, it is NOT unusual. This happens often. Each one of us have different eating habits. There isn't a flexible advise to cater this problem. But it helps to think that when you're setting up a study environment, you're setting up a living environment that enable you to be inspired enough for productivity. I make it a point to have food available but at a good distance and exercise attire/equipment nearby. Better yet, wear them. To curb that crazy cravings, I try my best to have my meal on-time; breakfast at 8 am, lunch at 12 pm or 1 pm etc. Eat what you love, but in moderation. Hydrate regularly. It's hard, I know. All the chips🍟 and chocolate chip cookies🍪 and sweetened 3-in-1 lattes☕...I just...well, just remember...in moderation and you're a human. Don't beat yourself up if you eat them anyway.

Back pain, knee pain, frozen shoulder...everything hurts

I have a hard time tearing away from what I am doing for the 20-minutes-work-5-minutes-rest rule but I try my best to maintain good posture. The bad habit of crouching and slouching at desk jobs is a universal problem. At the onset of the pandemic, for the first time in my life, my back felt strained. I panicked and started to seriously stretch myself and found that not only I am killing my back, I was not breathing properly when I am doing my work due to my posture.

💡I say: Don't break the bank trying to buy new furniture or tools because from experience, you end up not actually using them for the purpose you bought them in the first place. Eg. treadmill...you're more likely to hang your clothes or towels there...or super expensive yoga mats. Carpet works just fine too.

Standing desk is deemed to have little to no effects on spinal/muscle health by some studies but I went on ahead and made a make-shift standing desk. I found that I'm more alert when I work standing and breathe better. There was no contest...standing desk is a choice made. My standing table is an old dining table that I turned into my bed where I put my portable laptop desk. So, it also works as a barre that I used to stretch my legs for that mid-splits I've been working on.

These are some of the stuff that plague me daily and how I cope. How about you guys? How do you take care of yourself as someone who willingly serve yourself on a platter to tertiary educational torture to console your ever-thirsty curious mind?

📚 Nature in the Heart of Borneo (2020)

Tool: ArcGIS Pro 2.6.1

Technique: Annotation, Labeling and Symbology

A series of maps were created for the book published by WWF-Malaysia and FORMADAT (Forum Masyarakat Adat Dataran Tinggi Borneo) back in 2020 called Nature in the Heart of Borneo.

This book was meant as a guide to some of the natural attractions at Northern parts of Sarawak. If it was clear, Northern Sarawak is where the we have our very own highlanders which consist of primarily the Lundayeh/Lun Bawang, Sa'ban and Kelabit people. Some of the beautiful settlements up in the north that should not be missed are Ba'kelalan and Long Semadoh. They have beautiful homestays and even more beautiful landscapes with trekking activities lined up for tourists. And this is the culmination of ardent passion by my two absolutely wonderful colleagues, Alicia Ng and Cynthia Chin.

Most part of the maps were made using readily available basemap provided by Esri in their Living Atlas. But in entirety, many of the features and details are drawn manually within ArcGIS Pro. Like many other mapmakers out there, the labeling feature is horrendously temperamental and I either end up using annotations instead.

In summary, technically, there are 2 lessons learned here:

1️⃣ Establish concept or pick an idea before you start drawing

A concept of the map and palette should be established at the earliest stage possible. And don't just throw the task of making maps and split them evenly between cartographers. They won't have similar ideas or similar interpretations of the concept. It'll only give you double the pain of creating the maps again from scratch.

2️⃣ Omit borders

If you're making maps for books, don't border trying to make borders and fully utilize the whole layout. In the end, you'll need to export out your maps and they will resize it anyway and it'll compromise the maps you created. As if it wasn't graining enough in the first place, it'll look absolutely microscopic by the time they're done.

mapshaper

Ok. 

I wanna know why have I never heard of this online tool before. Like, what the hell is wrong with the social media? Is something wrong with Twitter or Instagram or something that they never caught on mapshaper? Or was it just me and my hazardous ignorance, yet again?

Have you tried this free nifty online tool that literally simplify crazy complicated shapefile polygons like it’s no one’s business?!

It started with some last minute inspiration on how to collate data from 3 different regions; developed from remote sensing techniques which vary from one another. The common output here is to turn all of them into a vector file; namely shapefile, and start working on the attribute to ease merging of the different shapefile layers.

Once merged, this shapefile is to be published as a hosted feature layer into the ArcGIS Online platform and incorporated into a webmap that serves as a reference data to configure/design a dashboard. What is a dashboard? It's basically an app template in ArcGIS Online that summarizes all the important information in your spatial data. It's a fun app to create, no coding skills required. Check out the gallery here for reference:

Operations Dashboard for ArcGIS Gallery

There are two common ways to publish hosted feature layer into ArcGIS Online platform.

Method 1: Zip up the shapefile and upload it as your content. This will trigger the command inquiring if you would like to publish it as a hosted feature layer. You click 'Yes' and give it a name and et voila! You have successfully publish a hosted feature layer.

Method 2: From an ArcGIS Desktop or ArcGIS Pro, you publish them as feature service (as ArcMap calls them) or web layer (as the its sister ArcGIS Pro calls them). Fill up the details and enabling the function then hit 'Publish' and it will be in the platform should there be no error or conflicting issues.

So, what was the deal with me and mapshaper? 

🛑 A fair warning here and please read these bullet points very carefully:

I need you to remember...I absolve any responsibility of what happens to your data should you misinterpreted the steps I shared. 

Please always  👏🏻  BACK 👏🏻 UP  👏🏻  YOUR 👏🏻 DATA. Don’t even try attempting any tools or procedure that I am sharing without doing so. Please. Cause I am an analyst too and hearing someone else forget to save their data or create a backup is enough to make me die a little inside. 

For this tool, please export out the attribute table of your shapefile because this tool will CHANGE YOUR SHAPEFILE ATTRIBUTES. 

When I was publishing the vector I have cleaned and feature-engineered via ArcGIS Pro...it took so long that I was literally dying inside. I'm not talking about 20 minutes or an hour. It took more than 12 hours and it did not conjure the 'Successfully published' notification as I would've expected from it.

So at around 5.30 am, I randomly type 'simplify shapefily online free'. Lo and behold, there was mapshaper.

All I did was, zip up my polygon, drag it to the homepage and it will bring you to the option of choosing the actions that will be executed while the data is being imported into mapshaper:

detect line intersections

snap vertices

This option will help you to detect the intersections of lines within your vector/shapefile. This can help identify topological error.

The option to snap vertices will snap together points of similar or almost identical coordinate system. But it does not work with TopoJSON formats.

There is something interesting about this options too; you can enter other types of customized options provided by the tool from its command line interface! But hold your horses peeps. I did not explore that because here, we want to fix an issue and we'll focus on that first. I checked both options and import them in.

This will bring the to a page where there you can start configuring options and method to simplify your vector.

To simplify your shapefile, you can have both options to prevent the shape of the polygon being compromised; prevent shape removal, and to utilize the planar Cartesian geometry instead of the usual geoid longitude and latitude; use planar geometry. The implication of the second option is not obvious to me yet since all I wanted was to get the data simplified for easy upload and clean topology, thus, I chose both options to maintain the shape and visibility of all my features despite the highest degree of simplification.

Alike to the options of methodology for simplication in the mainstream software, I can see familiar names:

Douglas-Peuker

Visvalingam / effective area

Visvalingam / weighted area

First and foremost, I had no slightest idea of what these were. Like for real. I used to just go first for the default to understand what sort of output it will bring me. But here, the default; Visvalingam / weighted area, seemed like the best option. What are these methodologies of simplification? There are just algorithms used to help simplify your vectors:

🎯 Douglas-Peucker algorithm decimates a curve composed of line segments to a similar curve with fewer points (Ramer-Douglas-Peucker algorithm, Wikipedia; 2021).

🎯 Visvalingam algorithm is a line simplication operator that works eliminating any less significant points of the line based on effective area concept. That basically means that the triangle formed by each of the line points with two of its immediate neighboring points (Visvalingam Algorithm | aplitop).

🎯 Visvalingam algorithm with weight area is another version of Visvalingam algorithm of subsequent development where an alternative metrics is used and weighted to take into account the shape (Visvalingam & Whelan, 2016).

For reasons I can't even explain, I configured my methodology to utilize the third option and now that I have the time to google it, Thank God I did.

Then, see and play with the magic at the 'Settings' slider where you can adjust and view the simplification made onto the vector! I adjusted it to 5%. The shape retained beautifully. And please bear in mind, this vector was converted from a raster. So, what I really wanted is the simplified version of the cleaned data and to have them uploaded.

Now that you've simplified it, export it into a zipped folder of shapefile and you can use it like any other shapefile after you extracted it.

Remember when I say you have got to export your table of attributes out before you use this tool? Yea...that's the thing. The attribute table will shock you cause it'll be empty. Literally. With only the OBJECTID left. Now, with that attribute table you've backed up, use the 'Join Table' tool in ArcGIS Pro or ArcMap and join the attribute table in without any issues.

Phewh!!

I know that it has alot more functions than this but hey, I'm just getting started. Have you ever done anything more rocket science than I did like 2 days ago, please share it with the rest of us. Cause I gotta say, this thing is cray!! Love it so much.

mapshaper developer, if you're seeing this, I 🤟🏻 you!

UPDATE

I have been asked about the confidentiality of the data. I think this is where you understand the reason behind the fact that they will work even with using just the ‘.shp’ file of the shapefile since _that_ is the vector portion of the shapefile. 

Shapefile is a spatial data format that is actually made up of 4 files; minimum. Each of these files share the same name with different extensions; .prj, .shx, .shp and .dbf. Although I am not familiar with what .shx actually accounts for, the rest of them are pretty straightforward:

.prj: stores the projection information

.dbf: stores the tabulated attributes of each features in the vector file

.shp: stores the shape/vector information of the shapefile. 

So, as the tool indicate, it actually helps with the vector aspect of your data which is crucial in cartography. 

Story Map for Noobs: Cascade | WWF Network

Story Map is a web application template product that has been popularized in ArcGIS Online for a user-friendly and comprehensive narrative of maps. The ‘Cascade’ template has become the seamless interface of choice due to it’s ribbon transitions and availability of content streaming from external sources. 

Please refer to the following link for resources used in this webinar:

Story Map for Noobs: Cascade web application

📌 Availability: Retracted in 2021

train on water

survey123 offline

Survey123 for ArcGIS is perhaps, one of those applications that superficial nerds like me would like; it's easy to configure, kiddie-level degree of customization with 'coding' (for that fragile ego-stroke) and user-friendly template to use. 

No app development/coding experience is required to publish a survey form and believe it or not, you can, personalize your survey to not look so meh. 

It took me some time to stumble through the procedures of enabling this feature before I understand the 'ArcGIS Online' ecosystem to which this app is chained to. 

So how do we do it? And why doesn't it work pronto?

This issue may be due to the fact that when we first start creating our forms, we go through the generic step-by-step procedures that leave little to imagination what was happening. Most of the time, we're too eager to find out how it really work. 

When we publish a Survey123 form; be it from the Survey123 website portal or the Survey123 Connect for ArcGIS software, we are actually creating and publishing a folder that contains a hosted feature layer and a form. It is on that hosted feature layer that we add, delete, update or edit data it. From ArcGIS Online, it looks like any feature service that we publish out of ArcGIS Desktop or ArcGIS Pro, save for the special folder it is placed in with a 'Form' file. 

To enable any offline function in any hosted feature layer in ArcGIS Online, you will need to enable the 'Sync' feature. So far, in many technical articles that I have gone through to learn how to enable this offline feature always goes back to 'Prepare basemaps for offline use'. It is a tad bit frustrating. But my experience when deal with 'Collector for ArcGIS' gave me the sense of epiphany when it comes to Survey123. So when you have prepared your Survey123 form for offline usage and it still doesn't work...do not be alarmed and let's see how to rectify the issue. 

1. Locate your survey's hosted feature layer

At your ArcGIS Online home page, click 'Content' at the main tab. We're going to go directly to your hosted feature layer that was generated for your survey when you published. 

Locate your survey folder. Click it open 

In the survey folder, navigate to the survey's hosted feature layer and click 'Options' button; the triple ellipses icon

At at the dropdown, click 'View item details'. Please refer to the screenshot below: 

2. Change the hosted feature layer settings

At the item details page, navigate to the 'Settings' button at the main header and click it. This will prompt open the settings page for the feature layer. Refer to the screenshot below:

At the 'Settings' page, there are two tabs at the subheader; 'General' and 'Feature layer (hosted)'. Click 'Feature layer (hosted)' to configure its settings.

At the 'Feature layer (hosted)' option, locate the 'Editing' section. Here, check the 'Enable sync' option. This is the option that will enable offline data editing. Please refer to the following screenshot: 

Don't forget to click 'Save'

With this, your hosted feature layer which serves as the data model is enabled for synchronization. Synchronization helps to sync back any changes you've made when you're out on the field collecting data; editing, adding, deleting or update...depending on what feature editing you've configured. 

It's pretty easy once you get the hang of it and just bear in mind that the data hierarchy in the ArcGIS Online universe are as follows:

Feature layer (hosted) > Web map > Web application

Once you get that out of the way, go crazy with your data collection without any worries!